toolfactory_gtn: toolfactory/rgToolFactory2.py annotate

author	fubar
date	Sat, 17 Apr 2021 23:43:33 +0000
parents
children	2fc9b11bbdba

rev	line source
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	1 # replace with shebang for biocontainer
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	2 # see https://github.com/fubar2/toolfactory
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	3 #
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	5 #
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	6 # all rights reserved
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	7 # Licensed under the LGPL
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	8 # suggestions for improvement and bug fixes welcome at
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	9 # https://github.com/fubar2/toolfactory
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	10 #
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	12 # Decided to
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	13 # 1. Fix the toolfactory so it works - done for simplest case
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	14 # 2. Fix planemo so the toolfactory function works
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	16
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	17 import argparse
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	18 import copy
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	19 import json
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	20 import logging
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	21 import os
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	22 import re
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	23 import shlex
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	24 import shutil
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	25 import subprocess
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	26 import sys
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	27 import tarfile
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	28 import tempfile
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	29 import time
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	30
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	31 from bioblend import ConnectionError
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	32 from bioblend import toolshed
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	33
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	34 import galaxyxml.tool as gxt
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	35 import galaxyxml.tool.parameters as gxtp
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	36
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	37 import lxml
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	38
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	39 import yaml
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	40
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	41 myversion = "V2.2 February 2021"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	42 verbose = True
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	43 debug = True
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	44 toolFactoryURL = "https://github.com/fubar2/toolfactory"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	45 foo = len(lxml.__version__)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	46 FAKEEXE = "~~~REMOVE~~~ME~~~"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	47 # need this until a PR/version bump to fix galaxyxml prepending the exe even
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	48 # with override.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	49
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	50
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	51 def timenow():
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	52 """return current time as a string"""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	53 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	54
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	55
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	56 cheetah_escape_table = {"$": "\\$", "#": "\\#"}
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	57
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	58
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	59 def cheetah_escape(text):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	60 """Produce entities within text."""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	61 return "".join([cheetah_escape_table.get(c, c) for c in text])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	62
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	63
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	64 def parse_citations(citations_text):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	65 """"""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	66 citations = [c for c in citations_text.split("ENTRY") if c.strip()]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	67 citation_tuples = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	68 for citation in citations:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	69 if citation.startswith("doi"):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	70 citation_tuples.append(("doi", citation[len("doi") :].strip()))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	71 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	72 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	73 return citation_tuples
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	74
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	75
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	76 class ScriptRunner:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	77 """Wrapper for an arbitrary script
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	78 uses galaxyxml
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	79
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	80 """
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	81
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	82 def __init__(self, args=None): # noqa
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	83 """
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	84 prepare command line cl for running the tool here
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	85 and prepare elements needed for galaxyxml tool generation
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	86 """
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	87 self.ourcwd = os.getcwd()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	88 self.collections = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	89 if len(args.collection) > 0:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	90 try:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	91 self.collections = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	92 json.loads(x) for x in args.collection if len(x.strip()) > 1
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	93 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	94 except Exception:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	95 print(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	96 f"--collections parameter {str(args.collection)} is malformed - should be a dictionary"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	97 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	98 try:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	99 self.infiles = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	100 json.loads(x) for x in args.input_files if len(x.strip()) > 1
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	101 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	102 except Exception:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	103 print(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	104 f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	105 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	106 try:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	107 self.outfiles = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	108 json.loads(x) for x in args.output_files if len(x.strip()) > 1
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	109 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	110 except Exception:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	111 print(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	112 f"--output_files parameter {args.output_files} is malformed - should be a dictionary"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	113 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	114 try:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	115 self.addpar = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	116 json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	117 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	118 except Exception:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	119 print(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	120 f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	121 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	122 try:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	123 self.selpar = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	124 json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	125 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	126 except Exception:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	127 print(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	128 f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	129 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	130 self.args = args
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	131 self.cleanuppar()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	132 self.lastclredirect = None
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	133 self.lastxclredirect = None
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	134 self.cl = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	135 self.xmlcl = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	136 self.is_positional = self.args.parampass == "positional"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	137 if self.args.sysexe:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	138 if ' ' in self.args.sysexe:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	139 self.executeme = self.args.sysexe.split(' ')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	140 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	141 self.executeme = [self.args.sysexe, ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	142 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	143 if self.args.packages:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	144 self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	145 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	146 self.executeme = None
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	147 aCL = self.cl.append
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	148 aXCL = self.xmlcl.append
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	149 assert args.parampass in [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	150 "0",
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	151 "argparse",
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	152 "positional",
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	153 ], 'args.parampass must be "0","positional" or "argparse"'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	154 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	155 self.tool_id = self.tool_name
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	156 self.newtool = gxt.Tool(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	157 self.tool_name,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	158 self.tool_id,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	159 self.args.tool_version,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	160 self.args.tool_desc,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	161 FAKEEXE,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	162 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	163 self.newtarpath = "%s_toolshed.gz" % self.tool_name
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	164 self.tooloutdir = "./tfout"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	165 self.repdir = "./TF_run_report_tempdir"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	166 self.testdir = os.path.join(self.tooloutdir, "test-data")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	167 if not os.path.exists(self.tooloutdir):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	168 os.mkdir(self.tooloutdir)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	169 if not os.path.exists(self.testdir):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	170 os.mkdir(self.testdir)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	171 if not os.path.exists(self.repdir):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	172 os.mkdir(self.repdir)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	173 self.tinputs = gxtp.Inputs()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	174 self.toutputs = gxtp.Outputs()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	175 self.testparam = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	176 if self.args.script_path:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	177 self.prepScript()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	178 if self.args.command_override:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	179 scos = open(self.args.command_override, "r").readlines()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	180 self.command_override = [x.rstrip() for x in scos]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	181 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	182 self.command_override = None
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	183 if self.args.test_override:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	184 stos = open(self.args.test_override, "r").readlines()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	185 self.test_override = [x.rstrip() for x in stos]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	186 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	187 self.test_override = None
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	188 if self.args.script_path:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	189 for ex in self.executeme:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	190 aCL(ex)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	191 aXCL(ex)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	192 aCL(self.sfile)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	193 aXCL("$runme")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	194 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	195 for ex in self.executeme:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	196 aCL(ex)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	197 aXCL(ex)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	198
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	199 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	200 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	201 if self.args.parampass == "0":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	202 self.clsimple()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	203 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	204 if self.args.parampass == "positional":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	205 self.prepclpos()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	206 self.clpositional()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	207 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	208 self.prepargp()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	209 self.clargparse()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	210 if self.args.cl_suffix: # DIY CL end
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	211 clp = shlex.split(self.args.cl_suffix)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	212 for c in clp:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	213 aCL(c)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	214 aXCL(c)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	215
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	216 def clsimple(self):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	217 """no parameters or repeats - uses < and > for i/o"""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	218 aCL = self.cl.append
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	219 aXCL = self.xmlcl.append
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	220 if len(self.infiles) > 0:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	221 aCL("<")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	222 aCL(self.infiles[0]["infilename"])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	223 aXCL("<")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	224 aXCL("$%s" % self.infiles[0]["infilename"])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	225 if len(self.outfiles) > 0:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	226 aCL(">")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	227 aCL(self.outfiles[0]["name"])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	228 aXCL(">")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	229 aXCL("$%s" % self.outfiles[0]["name"])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	230
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	231 def prepargp(self):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	232 clsuffix = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	233 xclsuffix = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	234 for i, p in enumerate(self.infiles):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	235 nam = p["infilename"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	236 if p["origCL"].strip().upper() == "STDIN":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	237 appendme = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	238 nam,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	239 nam,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	240 "< %s" % nam,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	241 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	242 xappendme = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	243 nam,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	244 nam,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	245 "< $%s" % nam,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	246 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	247 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	248 rep = p["repeat"] == "1"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	249 over = ""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	250 if rep:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	251 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	252 appendme = [p["CL"], p["CL"], ""]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	253 xappendme = [p["CL"], "$%s" % p["CL"], over]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	254 clsuffix.append(appendme)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	255 xclsuffix.append(xappendme)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	256 for i, p in enumerate(self.outfiles):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	257 if p["origCL"].strip().upper() == "STDOUT":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	258 self.lastclredirect = [">", p["name"]]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	259 self.lastxclredirect = [">", "$%s" % p["name"]]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	260 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	261 clsuffix.append([p["name"], p["name"], ""])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	262 xclsuffix.append([p["name"], "$%s" % p["name"], ""])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	263 for p in self.addpar:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	264 nam = p["name"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	265 rep = p["repeat"] == "1"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	266 if rep:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	267 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	268 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	269 over = p["override"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	270 clsuffix.append([p["CL"], nam, over])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	271 xclsuffix.append([p["CL"], nam, over])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	272 for p in self.selpar:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	273 clsuffix.append([p["CL"], p["name"], p["override"]])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	274 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	275 self.xclsuffix = xclsuffix
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	276 self.clsuffix = clsuffix
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	277
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	278 def prepclpos(self):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	279 clsuffix = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	280 xclsuffix = []
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	281 for i, p in enumerate(self.infiles):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	282 if p["origCL"].strip().upper() == "STDIN":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	283 appendme = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	284 "999",
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	285 p["infilename"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	286 "< $%s" % p["infilename"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	287 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	288 xappendme = [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	289 "999",
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	290 p["infilename"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	291 "< $%s" % p["infilename"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	292 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	293 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	294 appendme = [p["CL"], p["infilename"], ""]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	295 xappendme = [p["CL"], "$%s" % p["infilename"], ""]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	296 clsuffix.append(appendme)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	297 xclsuffix.append(xappendme)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	298 for i, p in enumerate(self.outfiles):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	299 if p["origCL"].strip().upper() == "STDOUT":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	300 self.lastclredirect = [">", p["name"]]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	301 self.lastxclredirect = [">", "$%s" % p["name"]]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	302 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	303 clsuffix.append([p["CL"], p["name"], ""])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	304 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	305 for p in self.addpar:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	306 nam = p["name"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	307 rep = p["repeat"] == "1" # repeats make NO sense
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	308 if rep:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	309 print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	310 over = p["override"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	311 clsuffix.append([p["CL"], nam, over])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	312 xclsuffix.append([p["CL"], '"$%s"' % nam, over])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	313 for p in self.selpar:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	314 clsuffix.append([p["CL"], p["name"], p["override"]])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	315 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	316 clsuffix.sort()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	317 xclsuffix.sort()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	318 self.xclsuffix = xclsuffix
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	319 self.clsuffix = clsuffix
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	320
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	321 def prepScript(self):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	322 rx = open(self.args.script_path, "r").readlines()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	323 rx = [x.rstrip() for x in rx]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	324 rxcheck = [x.strip() for x in rx if x.strip() > ""]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	325 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	326 self.script = "\n".join(rx)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	327 fhandle, self.sfile = tempfile.mkstemp(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	328 prefix=self.tool_name, suffix="_%s" % (self.executeme[0])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	329 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	330 tscript = open(self.sfile, "w")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	331 tscript.write(self.script)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	332 tscript.close()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	333 self.escapedScript = [cheetah_escape(x) for x in rx]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	334 self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	335 art = "%s.%s" % (self.tool_name, self.executeme[0])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	336 artifact = open(art, "wb")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	337 artifact.write(bytes("\n".join(self.escapedScript), "utf8"))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	338 artifact.close()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	339
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	340 def cleanuppar(self):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	341 """ positional parameters are complicated by their numeric ordinal"""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	342 if self.args.parampass == "positional":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	343 for i, p in enumerate(self.infiles):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	344 assert (
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	345 p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	346 ), "Positional parameters must be ordinal integers - got %s for %s" % (
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	347 p["CL"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	348 p["label"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	349 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	350 for i, p in enumerate(self.outfiles):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	351 assert (
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	352 p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	353 ), "Positional parameters must be ordinal integers - got %s for %s" % (
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	354 p["CL"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	355 p["name"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	356 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	357 for i, p in enumerate(self.addpar):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	358 assert p[
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	359 "CL"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	360 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	361 p["CL"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	362 p["name"],
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	363 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	364 for i, p in enumerate(self.infiles):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	365 infp = copy.copy(p)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	366 infp["origCL"] = infp["CL"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	367 if self.args.parampass in ["positional", "0"]:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	368 infp["infilename"] = infp["label"].replace(" ", "_")
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	369 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	370 infp["infilename"] = infp["CL"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	371 self.infiles[i] = infp
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	372 for i, p in enumerate(self.outfiles):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	373 p["origCL"] = p["CL"] # keep copy
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	374 self.outfiles[i] = p
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	375 for i, p in enumerate(self.addpar):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	376 p["origCL"] = p["CL"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	377 self.addpar[i] = p
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	378
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	379 def clpositional(self):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	380 # inputs in order then params
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	381 aCL = self.cl.append
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	382 for (k, v, koverride) in self.clsuffix:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	383 if " " in v:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	384 aCL("%s" % v)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	385 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	386 aCL(v)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	387 aXCL = self.xmlcl.append
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	388 for (k, v, koverride) in self.xclsuffix:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	389 aXCL(v)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	390 if self.lastxclredirect:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	391 aXCL(self.lastxclredirect[0])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	392 aXCL(self.lastxclredirect[1])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	393
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	394 def clargparse(self):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	395 """argparse style"""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	396 aCL = self.cl.append
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	397 aXCL = self.xmlcl.append
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	398 # inputs then params in argparse named form
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	399
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	400 for (k, v, koverride) in self.xclsuffix:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	401 if koverride > "":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	402 k = koverride
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	403 aXCL(k)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	404 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	405 if len(k.strip()) == 1:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	406 k = "-%s" % k
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	407 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	408 k = "--%s" % k
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	409 aXCL(k)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	410 aXCL(v)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	411 for (k, v, koverride) in self.clsuffix:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	412 if koverride > "":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	413 k = koverride
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	414 elif len(k.strip()) == 1:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	415 k = "-%s" % k
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	416 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	417 k = "--%s" % k
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	418 aCL(k)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	419 aCL(v)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	420 if self.lastxclredirect:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	421 aXCL(self.lastxclredirect[0])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	422 aXCL(self.lastxclredirect[1])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	423
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	424 def getNdash(self, newname):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	425 if self.is_positional:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	426 ndash = 0
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	427 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	428 ndash = 2
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	429 if len(newname) < 2:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	430 ndash = 1
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	431 return ndash
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	432
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	433 def doXMLparam(self):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	434 """Add all needed elements to tool""" # noqa
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	435 for p in self.outfiles:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	436 newname = p["name"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	437 newfmt = p["format"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	438 newcl = p["CL"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	439 test = p["test"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	440 oldcl = p["origCL"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	441 test = test.strip()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	442 ndash = self.getNdash(newcl)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	443 aparm = gxtp.OutputData(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	444 name=newname, format=newfmt, num_dashes=ndash, label=newname
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	445 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	446 aparm.positional = self.is_positional
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	447 if self.is_positional:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	448 if oldcl.upper() == "STDOUT":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	449 aparm.positional = 9999999
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	450 aparm.command_line_override = "> $%s" % newname
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	451 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	452 aparm.positional = int(oldcl)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	453 aparm.command_line_override = "$%s" % newname
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	454 self.toutputs.append(aparm)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	455 ld = None
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	456 if test.strip() > "":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	457 if test.startswith("diff"):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	458 c = "diff"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	459 ld = 0
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	460 if test.split(":")[1].isdigit:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	461 ld = int(test.split(":")[1])
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	462 tp = gxtp.TestOutput(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	463 name=newname,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	464 value="%s_sample" % newname,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	465 compare=c,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	466 lines_diff=ld,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	467 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	468 elif test.startswith("sim_size"):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	469 c = "sim_size"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	470 tn = test.split(":")[1].strip()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	471 if tn > "":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	472 if "." in tn:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	473 delta = None
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	474 delta_frac = min(1.0, float(tn))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	475 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	476 delta = int(tn)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	477 delta_frac = None
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	478 tp = gxtp.TestOutput(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	479 name=newname,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	480 value="%s_sample" % newname,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	481 compare=c,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	482 delta=delta,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	483 delta_frac=delta_frac,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	484 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	485 else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	486 c = test
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	487 tp = gxtp.TestOutput(
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	488 name=newname,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	489 value="%s_sample" % newname,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	490 compare=c,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	491 )
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	492 self.testparam.append(tp)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	493 for p in self.infiles:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	494 newname = p["infilename"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	495 newfmt = p["format"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	496 ndash = self.getNdash(newname)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	497 reps = p.get("repeat", "0") == "1"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	498 if not len(p["label"]) > 0:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	499 alab = p["CL"]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	500 else:

0

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1 # replace with shebang for biocontainer

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

2 # see https://github.com/fubar2/toolfactory

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

3 #

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

5 #

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

7 # Licensed under the LGPL

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

8 # suggestions for improvement and bug fixes welcome at

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

9 # https://github.com/fubar2/toolfactory

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

10 #

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

12 # Decided to

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

13 # 1. Fix the toolfactory so it works - done for simplest case

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

14 # 2. Fix planemo so the toolfactory function works

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

16

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

17 import argparse

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

18 import copy

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

19 import json

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

20 import logging

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

21 import os

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

22 import re

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

23 import shlex

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

24 import shutil

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

25 import subprocess

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

26 import sys

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

27 import tarfile

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

28 import tempfile

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

29 import time

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

30

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

31 from bioblend import ConnectionError

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

32 from bioblend import toolshed

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

33

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

34 import galaxyxml.tool as gxt

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

35 import galaxyxml.tool.parameters as gxtp

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

36

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

37 import lxml

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

38

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

39 import yaml

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

40

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

41 myversion = "V2.2 February 2021"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

42 verbose = True

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

43 debug = True

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

44 toolFactoryURL = "https://github.com/fubar2/toolfactory"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

45 foo = len(lxml.__version__)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

46 FAKEEXE = "~~~REMOVE~~~ME~~~"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

47 # need this until a PR/version bump to fix galaxyxml prepending the exe even

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

48 # with override.

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

49

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

50

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

51 def timenow():

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

52 """return current time as a string"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

53 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

54

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

55

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

56 cheetah_escape_table = {"$": "\\$", "#": "\\#"}

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

57

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

58

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

59 def cheetah_escape(text):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

60 """Produce entities within text."""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

61 return "".join([cheetah_escape_table.get(c, c) for c in text])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

62

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

63

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

64 def parse_citations(citations_text):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

65 """"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

66 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

67 citation_tuples = []

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

68 for citation in citations:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

69 if citation.startswith("doi"):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

70 citation_tuples.append(("doi", citation[len("doi") :].strip()))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

71 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

72 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

73 return citation_tuples

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

74

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

75

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

76 class ScriptRunner:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

77 """Wrapper for an arbitrary script

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

78 uses galaxyxml

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

79

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

80 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

81

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

82 def __init__(self, args=None): # noqa

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

83 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

84 prepare command line cl for running the tool here

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

85 and prepare elements needed for galaxyxml tool generation

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

86 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

87 self.ourcwd = os.getcwd()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

88 self.collections = []

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

89 if len(args.collection) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

90 try:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

91 self.collections = [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

92 json.loads(x) for x in args.collection if len(x.strip()) > 1

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

93 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

94 except Exception:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

95 print(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

96 f"--collections parameter {str(args.collection)} is malformed - should be a dictionary"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

97 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

98 try:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

99 self.infiles = [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

100 json.loads(x) for x in args.input_files if len(x.strip()) > 1

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

101 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

102 except Exception:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

103 print(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

104 f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

105 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

106 try:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

107 self.outfiles = [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

108 json.loads(x) for x in args.output_files if len(x.strip()) > 1

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

109 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

110 except Exception:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

111 print(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

112 f"--output_files parameter {args.output_files} is malformed - should be a dictionary"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

113 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

114 try:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

115 self.addpar = [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

116 json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

117 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

118 except Exception:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

119 print(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

120 f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

121 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

122 try:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

123 self.selpar = [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

124 json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

125 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

126 except Exception:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

127 print(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

128 f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

129 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

130 self.args = args

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

131 self.cleanuppar()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

132 self.lastclredirect = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

133 self.lastxclredirect = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

134 self.cl = []

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

135 self.xmlcl = []

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

136 self.is_positional = self.args.parampass == "positional"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

137 if self.args.sysexe:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

138 if ' ' in self.args.sysexe:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

139 self.executeme = self.args.sysexe.split(' ')

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

140 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

141 self.executeme = [self.args.sysexe, ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

142 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

143 if self.args.packages:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

144 self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

145 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

146 self.executeme = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

147 aCL = self.cl.append

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

148 aXCL = self.xmlcl.append

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

149 assert args.parampass in [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

150 "0",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

151 "argparse",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

152 "positional",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

153 ], 'args.parampass must be "0","positional" or "argparse"'

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

154 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

155 self.tool_id = self.tool_name

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

156 self.newtool = gxt.Tool(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

157 self.tool_name,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

158 self.tool_id,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

159 self.args.tool_version,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

160 self.args.tool_desc,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

161 FAKEEXE,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

162 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

163 self.newtarpath = "%s_toolshed.gz" % self.tool_name

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

164 self.tooloutdir = "./tfout"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

165 self.repdir = "./TF_run_report_tempdir"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

166 self.testdir = os.path.join(self.tooloutdir, "test-data")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

167 if not os.path.exists(self.tooloutdir):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

168 os.mkdir(self.tooloutdir)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

169 if not os.path.exists(self.testdir):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

170 os.mkdir(self.testdir)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

171 if not os.path.exists(self.repdir):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

172 os.mkdir(self.repdir)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

173 self.tinputs = gxtp.Inputs()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

174 self.toutputs = gxtp.Outputs()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

175 self.testparam = []

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

176 if self.args.script_path:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

177 self.prepScript()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

178 if self.args.command_override:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

179 scos = open(self.args.command_override, "r").readlines()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

180 self.command_override = [x.rstrip() for x in scos]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

181 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

182 self.command_override = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

183 if self.args.test_override:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

184 stos = open(self.args.test_override, "r").readlines()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

185 self.test_override = [x.rstrip() for x in stos]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

186 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

187 self.test_override = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

188 if self.args.script_path:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

189 for ex in self.executeme:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

190 aCL(ex)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

191 aXCL(ex)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

192 aCL(self.sfile)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

193 aXCL("$runme")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

194 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

195 for ex in self.executeme:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

196 aCL(ex)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

197 aXCL(ex)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

198

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

199 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)

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200 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)

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diff changeset

201 if self.args.parampass == "0":

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202 self.clsimple()

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diff changeset

203 else:

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diff changeset

204 if self.args.parampass == "positional":

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diff changeset

205 self.prepclpos()

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diff changeset

206 self.clpositional()

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diff changeset

207 else:

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fubar

parents:

diff changeset

208 self.prepargp()

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fubar

parents:

diff changeset

209 self.clargparse()

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210 if self.args.cl_suffix: # DIY CL end

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211 clp = shlex.split(self.args.cl_suffix)

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diff changeset

212 for c in clp:

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diff changeset

213 aCL(c)

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diff changeset

214 aXCL(c)

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diff changeset

215

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diff changeset

216 def clsimple(self):

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217 """no parameters or repeats - uses < and > for i/o"""

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218 aCL = self.cl.append

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219 aXCL = self.xmlcl.append

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220 if len(self.infiles) > 0:

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221 aCL("<")

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222 aCL(self.infiles[0]["infilename"])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

223 aXCL("<")

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224 aXCL("$%s" % self.infiles[0]["infilename"])

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diff changeset

225 if len(self.outfiles) > 0:

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226 aCL(">")

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diff changeset

227 aCL(self.outfiles[0]["name"])

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diff changeset

228 aXCL(">")

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229 aXCL("$%s" % self.outfiles[0]["name"])

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diff changeset

230

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231 def prepargp(self):

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232 clsuffix = []

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233 xclsuffix = []

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234 for i, p in enumerate(self.infiles):

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235 nam = p["infilename"]

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diff changeset

236 if p["origCL"].strip().upper() == "STDIN":

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237 appendme = [

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diff changeset

238 nam,

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fubar

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diff changeset

239 nam,

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parents:

diff changeset

240 "< %s" % nam,

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diff changeset

241 ]

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242 xappendme = [

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diff changeset

243 nam,

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fubar

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diff changeset

244 nam,

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fubar

parents:

diff changeset

245 "< $%s" % nam,

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fubar

parents:

diff changeset

246 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

247 else:

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diff changeset

248 rep = p["repeat"] == "1"

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249 over = ""

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250 if rep:

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diff changeset

251 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'

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diff changeset

252 appendme = [p["CL"], p["CL"], ""]

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253 xappendme = [p["CL"], "$%s" % p["CL"], over]

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diff changeset

254 clsuffix.append(appendme)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

255 xclsuffix.append(xappendme)

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parents:

diff changeset

256 for i, p in enumerate(self.outfiles):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

257 if p["origCL"].strip().upper() == "STDOUT":

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diff changeset

258 self.lastclredirect = [">", p["name"]]

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diff changeset

259 self.lastxclredirect = [">", "$%s" % p["name"]]

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diff changeset

260 else:

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diff changeset

261 clsuffix.append([p["name"], p["name"], ""])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

262 xclsuffix.append([p["name"], "$%s" % p["name"], ""])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

263 for p in self.addpar:

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diff changeset

264 nam = p["name"]

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265 rep = p["repeat"] == "1"

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diff changeset

266 if rep:

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diff changeset

267 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'

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268 else:

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269 over = p["override"]

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270 clsuffix.append([p["CL"], nam, over])

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271 xclsuffix.append([p["CL"], nam, over])

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272 for p in self.selpar:

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273 clsuffix.append([p["CL"], p["name"], p["override"]])

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diff changeset

274 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])

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diff changeset

275 self.xclsuffix = xclsuffix

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diff changeset

276 self.clsuffix = clsuffix

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diff changeset

277

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diff changeset

278 def prepclpos(self):

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279 clsuffix = []

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280 xclsuffix = []

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diff changeset

281 for i, p in enumerate(self.infiles):

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parents:

diff changeset

282 if p["origCL"].strip().upper() == "STDIN":

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283 appendme = [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

284 "999",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

285 p["infilename"],

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parents:

diff changeset

286 "< $%s" % p["infilename"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

287 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

288 xappendme = [

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parents:

diff changeset

289 "999",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

290 p["infilename"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

291 "< $%s" % p["infilename"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

292 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

293 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

294 appendme = [p["CL"], p["infilename"], ""]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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295 xappendme = [p["CL"], "$%s" % p["infilename"], ""]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

296 clsuffix.append(appendme)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

297 xclsuffix.append(xappendme)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

298 for i, p in enumerate(self.outfiles):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

299 if p["origCL"].strip().upper() == "STDOUT":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

300 self.lastclredirect = [">", p["name"]]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

301 self.lastxclredirect = [">", "$%s" % p["name"]]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

302 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

303 clsuffix.append([p["CL"], p["name"], ""])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

304 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

305 for p in self.addpar:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

306 nam = p["name"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

307 rep = p["repeat"] == "1" # repeats make NO sense

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

308 if rep:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

309 print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!')

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

310 over = p["override"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

311 clsuffix.append([p["CL"], nam, over])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

312 xclsuffix.append([p["CL"], '"$%s"' % nam, over])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

313 for p in self.selpar:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

314 clsuffix.append([p["CL"], p["name"], p["override"]])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

315 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

316 clsuffix.sort()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

317 xclsuffix.sort()

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diff changeset

318 self.xclsuffix = xclsuffix

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319 self.clsuffix = clsuffix

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diff changeset

320

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

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diff changeset

321 def prepScript(self):

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diff changeset

322 rx = open(self.args.script_path, "r").readlines()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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323 rx = [x.rstrip() for x in rx]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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324 rxcheck = [x.strip() for x in rx if x.strip() > ""]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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325 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

326 self.script = "\n".join(rx)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

327 fhandle, self.sfile = tempfile.mkstemp(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

328 prefix=self.tool_name, suffix="_%s" % (self.executeme[0])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

329 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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330 tscript = open(self.sfile, "w")

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331 tscript.write(self.script)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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diff changeset

332 tscript.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

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333 self.escapedScript = [cheetah_escape(x) for x in rx]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

334 self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

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335 art = "%s.%s" % (self.tool_name, self.executeme[0])

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parents:

diff changeset

336 artifact = open(art, "wb")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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337 artifact.write(bytes("\n".join(self.escapedScript), "utf8"))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

338 artifact.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

339

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

340 def cleanuppar(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

341 """ positional parameters are complicated by their numeric ordinal"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

342 if self.args.parampass == "positional":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

343 for i, p in enumerate(self.infiles):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

344 assert (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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345 p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"

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parents:

diff changeset

346 ), "Positional parameters must be ordinal integers - got %s for %s" % (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

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parents:

diff changeset

347 p["CL"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

348 p["label"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

349 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

350 for i, p in enumerate(self.outfiles):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

351 assert (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

352 p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

353 ), "Positional parameters must be ordinal integers - got %s for %s" % (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

354 p["CL"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

355 p["name"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

356 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

357 for i, p in enumerate(self.addpar):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

358 assert p[

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

359 "CL"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

360 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

361 p["CL"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

362 p["name"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

363 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

364 for i, p in enumerate(self.infiles):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

365 infp = copy.copy(p)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

366 infp["origCL"] = infp["CL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

367 if self.args.parampass in ["positional", "0"]:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

368 infp["infilename"] = infp["label"].replace(" ", "_")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

369 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

370 infp["infilename"] = infp["CL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

371 self.infiles[i] = infp

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

372 for i, p in enumerate(self.outfiles):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

373 p["origCL"] = p["CL"] # keep copy

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

374 self.outfiles[i] = p

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

375 for i, p in enumerate(self.addpar):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

376 p["origCL"] = p["CL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

377 self.addpar[i] = p

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

378

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

379 def clpositional(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

380 # inputs in order then params

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

381 aCL = self.cl.append

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

382 for (k, v, koverride) in self.clsuffix:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

383 if " " in v:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

384 aCL("%s" % v)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

385 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

386 aCL(v)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

387 aXCL = self.xmlcl.append

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

388 for (k, v, koverride) in self.xclsuffix:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

389 aXCL(v)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

390 if self.lastxclredirect:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

391 aXCL(self.lastxclredirect[0])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

392 aXCL(self.lastxclredirect[1])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

393

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

394 def clargparse(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

395 """argparse style"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

396 aCL = self.cl.append

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

397 aXCL = self.xmlcl.append

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

398 # inputs then params in argparse named form

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

399

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

400 for (k, v, koverride) in self.xclsuffix:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

401 if koverride > "":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

402 k = koverride

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

403 aXCL(k)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

404 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

405 if len(k.strip()) == 1:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

406 k = "-%s" % k

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

407 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

408 k = "--%s" % k

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

409 aXCL(k)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

410 aXCL(v)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

411 for (k, v, koverride) in self.clsuffix:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

412 if koverride > "":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

413 k = koverride

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

414 elif len(k.strip()) == 1:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

415 k = "-%s" % k

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

416 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

417 k = "--%s" % k

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

418 aCL(k)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

419 aCL(v)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

420 if self.lastxclredirect:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

421 aXCL(self.lastxclredirect[0])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

422 aXCL(self.lastxclredirect[1])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

423

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

424 def getNdash(self, newname):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

425 if self.is_positional:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

426 ndash = 0

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

427 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

428 ndash = 2

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

429 if len(newname) < 2:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

430 ndash = 1

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

431 return ndash

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

432

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

433 def doXMLparam(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

434 """Add all needed elements to tool""" # noqa

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

435 for p in self.outfiles:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

436 newname = p["name"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

437 newfmt = p["format"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

438 newcl = p["CL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

439 test = p["test"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

440 oldcl = p["origCL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

441 test = test.strip()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

442 ndash = self.getNdash(newcl)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

443 aparm = gxtp.OutputData(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

444 name=newname, format=newfmt, num_dashes=ndash, label=newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

445 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

446 aparm.positional = self.is_positional

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

447 if self.is_positional:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

448 if oldcl.upper() == "STDOUT":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

449 aparm.positional = 9999999

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

450 aparm.command_line_override = "> $%s" % newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

451 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

452 aparm.positional = int(oldcl)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

453 aparm.command_line_override = "$%s" % newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

454 self.toutputs.append(aparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

455 ld = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

456 if test.strip() > "":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

457 if test.startswith("diff"):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

458 c = "diff"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

459 ld = 0

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

460 if test.split(":")[1].isdigit:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

461 ld = int(test.split(":")[1])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

462 tp = gxtp.TestOutput(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

463 name=newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

464 value="%s_sample" % newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

465 compare=c,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

466 lines_diff=ld,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

467 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

468 elif test.startswith("sim_size"):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

469 c = "sim_size"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

470 tn = test.split(":")[1].strip()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

471 if tn > "":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

472 if "." in tn:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

473 delta = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

474 delta_frac = min(1.0, float(tn))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

475 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

476 delta = int(tn)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

477 delta_frac = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

478 tp = gxtp.TestOutput(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

479 name=newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

480 value="%s_sample" % newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

481 compare=c,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

482 delta=delta,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

483 delta_frac=delta_frac,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

484 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

485 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

486 c = test

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

487 tp = gxtp.TestOutput(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

488 name=newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

489 value="%s_sample" % newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

490 compare=c,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

491 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

492 self.testparam.append(tp)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

493 for p in self.infiles:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

494 newname = p["infilename"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

495 newfmt = p["format"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

496 ndash = self.getNdash(newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

497 reps = p.get("repeat", "0") == "1"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

498 if not len(p["label"]) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

499 alab = p["CL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

500 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

501 alab = p["label"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

502 aninput = gxtp.DataParam(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

503 newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

504 optional=False,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

505 label=alab,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

506 help=p["help"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

507 format=newfmt,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

508 multiple=False,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

509 num_dashes=ndash,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

510 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

511 aninput.positional = self.is_positional

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

512 if self.is_positional:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

513 if p["origCL"].upper() == "STDIN":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

514 aninput.positional = 9999998

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

515 aninput.command_line_override = "> $%s" % newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

516 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

517 aninput.positional = int(p["origCL"])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

518 aninput.command_line_override = "$%s" % newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

519 if reps:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

520 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {alab} as needed")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

521 repe.append(aninput)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

522 self.tinputs.append(repe)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

523 tparm = gxtp.TestRepeat(name=f"R_{newname}")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

524 tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

525 tparm.append(tparm2)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

526 self.testparam.append(tparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

527 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

528 self.tinputs.append(aninput)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

529 tparm = gxtp.TestParam(newname, value="%s_sample" % newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

530 self.testparam.append(tparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

531 for p in self.addpar:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

532 newname = p["name"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

533 newval = p["value"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

534 newlabel = p["label"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

535 newhelp = p["help"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

536 newtype = p["type"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

537 newcl = p["CL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

538 oldcl = p["origCL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

539 reps = p["repeat"] == "1"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

540 if not len(newlabel) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

541 newlabel = newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

542 ndash = self.getNdash(newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

543 if newtype == "text":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

544 aparm = gxtp.TextParam(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

545 newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

546 label=newlabel,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

547 help=newhelp,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

548 value=newval,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

549 num_dashes=ndash,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

550 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

551 elif newtype == "integer":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

552 aparm = gxtp.IntegerParam(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

553 newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

554 label=newlabel,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

555 help=newhelp,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

556 value=newval,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

557 num_dashes=ndash,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

558 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

559 elif newtype == "float":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

560 aparm = gxtp.FloatParam(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

561 newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

562 label=newlabel,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

563 help=newhelp,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

564 value=newval,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

565 num_dashes=ndash,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

566 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

567 elif newtype == "boolean":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

568 aparm = gxtp.BooleanParam(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

569 newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

570 label=newlabel,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

571 help=newhelp,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

572 value=newval,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

573 num_dashes=ndash,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

574 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

575 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

576 raise ValueError(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

577 'Unrecognised parameter type "%s" for\

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

578 additional parameter %s in makeXML'

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

579 % (newtype, newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

580 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

581 aparm.positional = self.is_positional

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

582 if self.is_positional:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

583 aparm.positional = int(oldcl)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

584 if reps:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

585 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

586 repe.append(aparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

587 self.tinputs.append(repe)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

588 tparm = gxtp.TestRepeat(name=f"R_{newname}")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

589 tparm2 = gxtp.TestParam(newname, value=newval)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

590 tparm.append(tparm2)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

591 self.testparam.append(tparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

592 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

593 self.tinputs.append(aparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

594 tparm = gxtp.TestParam(newname, value=newval)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

595 self.testparam.append(tparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

596 for p in self.selpar:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

597 newname = p["name"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

598 newval = p["value"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

599 newlabel = p["label"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

600 newhelp = p["help"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

601 newtype = p["type"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

602 newcl = p["CL"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

603 if not len(newlabel) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

604 newlabel = newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

605 ndash = self.getNdash(newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

606 if newtype == "selecttext":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

607 newtext = p["texts"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

608 aparm = gxtp.SelectParam(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

609 newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

610 label=newlabel,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

611 help=newhelp,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

612 num_dashes=ndash,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

613 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

614 for i in range(len(newval)):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

615 anopt = gxtp.SelectOption(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

616 value=newval[i],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

617 text=newtext[i],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

618 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

619 aparm.append(anopt)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

620 aparm.positional = self.is_positional

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

621 if self.is_positional:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

622 aparm.positional = int(newcl)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

623 self.tinputs.append(aparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

624 tparm = gxtp.TestParam(newname, value=newval)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

625 self.testparam.append(tparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

626 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

627 raise ValueError(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

628 'Unrecognised parameter type "%s" for\

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

629 selecttext parameter %s in makeXML'

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

630 % (newtype, newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

631 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

632 for p in self.collections:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

633 newkind = p["kind"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

634 newname = p["name"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

635 newlabel = p["label"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

636 newdisc = p["discover"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

637 collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

638 disc = gxtp.DiscoverDatasets(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

639 pattern=newdisc, directory=f"{newname}", visible="false"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

640 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

641 collect.append(disc)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

642 self.toutputs.append(collect)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

643 try:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

644 tparm = gxtp.TestOutputCollection(newname) # broken until PR merged.

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

645 self.testparam.append(tparm)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

646 except Exception:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

647 print("#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

648

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

649 def doNoXMLparam(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

650 """filter style package - stdin to stdout"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

651 if len(self.infiles) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

652 alab = self.infiles[0]["label"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

653 if len(alab) == 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

654 alab = self.infiles[0]["infilename"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

655 max1s = (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

656 "Maximum one input if parampass is 0 but multiple input files supplied - %s"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

657 % str(self.infiles)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

658 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

659 assert len(self.infiles) == 1, max1s

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

660 newname = self.infiles[0]["infilename"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

661 aninput = gxtp.DataParam(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

662 newname,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

663 optional=False,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

664 label=alab,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

665 help=self.infiles[0]["help"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

666 format=self.infiles[0]["format"],

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

667 multiple=False,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

668 num_dashes=0,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

669 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

670 aninput.command_line_override = "< $%s" % newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

671 aninput.positional = True

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

672 self.tinputs.append(aninput)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

673 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

674 self.testparam.append(tp)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

675 if len(self.outfiles) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

676 newname = self.outfiles[0]["name"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

677 newfmt = self.outfiles[0]["format"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

678 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

679 anout.command_line_override = "> $%s" % newname

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

680 anout.positional = self.is_positional

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

681 self.toutputs.append(anout)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

682 tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

683 self.testparam.append(tp)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

684

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

685 def makeXML(self): # noqa

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

686 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

687 Create a Galaxy xml tool wrapper for the new script

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

688 Uses galaxyhtml

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

689 Hmmm. How to get the command line into correct order...

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

690 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

691 if self.command_override:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

692 self.newtool.command_override = self.command_override # config file

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

693 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

694 self.newtool.command_override = self.xmlcl

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

695 cite = gxtp.Citations()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

696 acite = gxtp.Citation(type="doi", value="10.1093/bioinformatics/bts573")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

697 cite.append(acite)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

698 self.newtool.citations = cite

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

699 safertext = ""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

700 if self.args.help_text:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

701 helptext = open(self.args.help_text, "r").readlines()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

702 safertext = "\n".join([cheetah_escape(x) for x in helptext])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

703 if len(safertext.strip()) == 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

704 safertext = (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

705 "Ask the tool author (%s) to rebuild with help text please\n"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

706 % (self.args.user_email)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

707 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

708 if self.args.script_path:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

709 if len(safertext) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

710 safertext = safertext + "\n\n------\n" # transition allowed!

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

711 scr = [x for x in self.spacedScript if x.strip() > ""]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

712 scr.insert(0, "\n\nScript::\n")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

713 if len(scr) > 300:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

714 scr = (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

715 scr[:100]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

716 + [" >300 lines - stuff deleted", " ......"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

717 + scr[-100:]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

718 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

719 scr.append("\n")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

720 safertext = safertext + "\n".join(scr)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

721 self.newtool.help = safertext

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

722 self.newtool.version_command = f'echo "{self.args.tool_version}"'

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

723 std = gxtp.Stdios()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

724 std1 = gxtp.Stdio()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

725 std.append(std1)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

726 self.newtool.stdios = std

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

727 requirements = gxtp.Requirements()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

728 if self.args.packages:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

729 for d in self.args.packages.split(","):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

730 ver = ""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

731 d = d.replace("==", ":")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

732 d = d.replace("=", ":")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

733 if ":" in d:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

734 packg, ver = d.split(":")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

735 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

736 packg = d

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

737 requirements.append(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

738 gxtp.Requirement("package", packg.strip(), ver.strip())

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

739 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

740 self.newtool.requirements = requirements

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

741 if self.args.parampass == "0":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

742 self.doNoXMLparam()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

743 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

744 self.doXMLparam()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

745 self.newtool.outputs = self.toutputs

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

746 self.newtool.inputs = self.tinputs

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

747 if self.args.script_path:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

748 configfiles = gxtp.Configfiles()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

749 configfiles.append(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

750 gxtp.Configfile(name="runme", text="\n".join(self.escapedScript))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

751 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

752 self.newtool.configfiles = configfiles

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

753 tests = gxtp.Tests()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

754 test_a = gxtp.Test()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

755 for tp in self.testparam:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

756 test_a.append(tp)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

757 tests.append(test_a)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

758 self.newtool.tests = tests

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

759 self.newtool.add_comment(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

760 "Created by %s at %s using the Galaxy Tool Factory."

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

761 % (self.args.user_email, timenow())

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

762 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

763 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

764 exml0 = self.newtool.export()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

765 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

766 if (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

767 self.test_override

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

768 ): # cannot do this inside galaxyxml as it expects lxml objects for tests

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

769 part1 = exml.split("<tests>")[0]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

770 part2 = exml.split("</tests>")[1]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

771 fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

772 exml = fixed

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

773 # exml = exml.replace('range="1:"', 'range="1000:"')

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

774 xf = open("%s.xml" % self.tool_name, "w")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

775 xf.write(exml)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

776 xf.write("\n")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

777 xf.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

778 # ready for the tarball

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

779

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

780 def run(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

781 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

782 generate test outputs by running a command line

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

783 won't work if command or test override in play - planemo is the

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

784 easiest way to generate test outputs for that case so is

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

785 automagically selected

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

786 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

787 scl = " ".join(self.cl)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

788 err = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

789 if self.args.parampass != "0":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

790 if os.path.exists(self.elog):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

791 ste = open(self.elog, "a")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

792 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

793 ste = open(self.elog, "w")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

794 if self.lastclredirect:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

795 sto = open(self.lastclredirect[1], "wb") # is name of an output file

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

796 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

797 if os.path.exists(self.tlog):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

798 sto = open(self.tlog, "a")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

799 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

800 sto = open(self.tlog, "w")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

801 sto.write(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

802 "## Executing Toolfactory generated command line = %s\n" % scl

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

803 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

804 sto.flush()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

805 subp = subprocess.run(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

806 self.cl, shell=False, stdout=sto, stderr=ste

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

807 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

808 sto.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

809 ste.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

810 retval = subp.returncode

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

811 else: # work around special case - stdin and write to stdout

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

812 if len(self.infiles) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

813 sti = open(self.infiles[0]["name"], "rb")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

814 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

815 sti = sys.stdin

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

816 if len(self.outfiles) > 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

817 sto = open(self.outfiles[0]["name"], "wb")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

818 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

819 sto = sys.stdout

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

820 subp = subprocess.run(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

821 self.cl, shell=False, stdout=sto, stdin=sti

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

822 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

823 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

824 retval = subp.returncode

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

825 sto.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

826 sti.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

827 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

828 os.unlink(self.tlog)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

829 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

830 os.unlink(self.elog)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

831 if retval != 0 and err: # problem

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

832 sys.stderr.write(err)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

833 logging.debug("run done")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

834 return retval

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

835

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

836 def shedLoad(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

837 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

838 use bioblend to create new repository

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

839 or update existing

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

840

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

841 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

842 if os.path.exists(self.tlog):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

843 sto = open(self.tlog, "a")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

844 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

845 sto = open(self.tlog, "w")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

846

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

847 ts = toolshed.ToolShedInstance(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

848 url=self.args.toolshed_url,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

849 key=self.args.toolshed_api_key,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

850 verify=False,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

851 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

852 repos = ts.repositories.get_repositories()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

853 rnames = [x.get("name", "?") for x in repos]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

854 rids = [x.get("id", "?") for x in repos]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

855 tfcat = "ToolFactory generated tools"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

856 if self.tool_name not in rnames:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

857 tscat = ts.categories.get_categories()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

858 cnames = [x.get("name", "?").strip() for x in tscat]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

859 cids = [x.get("id", "?") for x in tscat]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

860 catID = None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

861 if tfcat.strip() in cnames:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

862 ci = cnames.index(tfcat)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

863 catID = cids[ci]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

864 res = ts.repositories.create_repository(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

865 name=self.args.tool_name,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

866 synopsis="Synopsis:%s" % self.args.tool_desc,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

867 description=self.args.tool_desc,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

868 type="unrestricted",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

869 remote_repository_url=self.args.toolshed_url,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

870 homepage_url=None,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

871 category_ids=catID,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

872 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

873 tid = res.get("id", None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

874 sto.write(f"#create_repository {self.args.tool_name} tid={tid} res={res}\n")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

875 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

876 i = rnames.index(self.tool_name)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

877 tid = rids[i]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

878 try:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

879 res = ts.repositories.update_repository(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

880 id=tid, tar_ball_path=self.newtarpath, commit_message=None

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

881 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

882 sto.write(f"#update res id {id} ={res}\n")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

883 except ConnectionError:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

884 sto.write(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

885 "####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

886 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

887 sto.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

888

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

889 def eph_galaxy_load(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

890 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

891 use ephemeris to load the new tool from the local toolshed after planemo uploads it

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

892 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

893 if os.path.exists(self.tlog):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

894 tout = open(self.tlog, "a")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

895 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

896 tout = open(self.tlog, "w")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

897 cll = [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

898 "shed-tools",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

899 "install",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

900 "-g",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

901 self.args.galaxy_url,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

902 "--latest",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

903 "-a",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

904 self.args.galaxy_api_key,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

905 "--name",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

906 self.tool_name,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

907 "--owner",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

908 "fubar",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

909 "--toolshed",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

910 self.args.toolshed_url,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

911 "--section_label",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

912 "ToolFactory",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

913 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

914 tout.write("running\n%s\n" % " ".join(cll))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

915 subp = subprocess.run(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

916 cll,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

917 cwd=self.ourcwd,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

918 shell=False,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

919 stderr=tout,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

920 stdout=tout,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

921 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

922 tout.write(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

923 "installed %s - got retcode %d\n" % (self.tool_name, subp.returncode)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

924 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

925 tout.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

926 return subp.returncode

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

927

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

928 def writeShedyml(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

929 """for planemo"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

930 yuser = self.args.user_email.split("@")[0]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

931 yfname = os.path.join(self.tooloutdir, ".shed.yml")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

932 yamlf = open(yfname, "w")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

933 odict = {

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

934 "name": self.tool_name,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

935 "owner": yuser,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

936 "type": "unrestricted",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

937 "description": self.args.tool_desc,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

938 "synopsis": self.args.tool_desc,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

939 "category": "TF Generated Tools",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

940 }

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

941 yaml.dump(odict, yamlf, allow_unicode=True)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

942 yamlf.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

943

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

944 def makeTool(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

945 """write xmls and input samples into place"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

946 if self.args.parampass == 0:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

947 self.doNoXMLparam()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

948 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

949 self.makeXML()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

950 if self.args.script_path:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

951 stname = os.path.join(self.tooloutdir, self.sfile)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

952 if not os.path.exists(stname):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

953 shutil.copyfile(self.sfile, stname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

954 xreal = "%s.xml" % self.tool_name

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

955 xout = os.path.join(self.tooloutdir, xreal)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

956 shutil.copyfile(xreal, xout)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

957 for p in self.infiles:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

958 pth = p["name"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

959 dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

960 shutil.copyfile(pth, dest)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

961 dest = os.path.join(self.repdir, "%s_sample" % p["infilename"])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

962 shutil.copyfile(pth, dest)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

963

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

964 def makeToolTar(self, report_fail=False):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

965 """move outputs into test-data and prepare the tarball"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

966 excludeme = "_planemo_test_report.html"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

967

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

968 def exclude_function(tarinfo):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

969 filename = tarinfo.name

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

970 return None if filename.endswith(excludeme) else tarinfo

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

971

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

972 if os.path.exists(self.tlog):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

973 tout = open(self.tlog, "a")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

974 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

975 tout = open(self.tlog, "w")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

976 for p in self.outfiles:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

977 oname = p["name"]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

978 tdest = os.path.join(self.testdir, "%s_sample" % oname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

979 src = os.path.join(self.testdir, oname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

980 if not os.path.isfile(tdest):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

981 if os.path.isfile(src):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

982 shutil.copyfile(src, tdest)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

983 dest = os.path.join(self.repdir, "%s.sample" % (oname))

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

984 shutil.copyfile(src, dest)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

985 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

986 if report_fail:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

987 tout.write(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

988 "###Tool may have failed - output file %s not found in testdir after planemo run %s."

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

989 % (tdest, self.testdir)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

990 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

991 tf = tarfile.open(self.newtarpath, "w:gz")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

992 tf.add(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

993 name=self.tooloutdir,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

994 arcname=self.tool_name,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

995 filter=exclude_function,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

996 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

997 tf.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

998 shutil.copyfile(self.newtarpath, self.args.new_tool)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

999

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1000 def moveRunOutputs(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1001 """need to move planemo or run outputs into toolfactory collection"""

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1002 with os.scandir(self.tooloutdir) as outs:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1003 for entry in outs:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1004 if not entry.is_file():

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1005 continue

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1006 if "." in entry.name:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1007 _, ext = os.path.splitext(entry.name)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1008 if ext in [".tgz", ".json"]:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1009 continue

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1010 if ext in [".yml", ".xml", ".yaml"]:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1011 newname = f"{entry.name.replace('.','_')}.txt"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1012 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1013 newname = entry.name

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1014 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1015 newname = f"{entry.name}.txt"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1016 dest = os.path.join(self.repdir, newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1017 src = os.path.join(self.tooloutdir, entry.name)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1018 shutil.copyfile(src, dest)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1019 if self.args.include_tests:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1020 with os.scandir(self.testdir) as outs:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1021 for entry in outs:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1022 if (not entry.is_file()) or entry.name.endswith(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1023 "_planemo_test_report.html"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1024 ):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1025 continue

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1026 if "." in entry.name:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1027 _, ext = os.path.splitext(entry.name)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1028 if ext in [".tgz", ".json"]:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1029 continue

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1030 if ext in [".yml", ".xml", ".yaml"]:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1031 newname = f"{entry.name.replace('.','_')}.txt"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1032 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1033 newname = entry.name

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1034 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1035 newname = f"{entry.name}.txt"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1036 dest = os.path.join(self.repdir, newname)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1037 src = os.path.join(self.testdir, entry.name)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1038 shutil.copyfile(src, dest)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1039

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1040 def planemo_test_once(self):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1041 """planemo is a requirement so is available for testing but needs a

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1042 different call if in the biocontainer - see above

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1043 and for generating test outputs if command or test overrides are

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1044 supplied test outputs are sent to repdir for display

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1045 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1046 xreal = "%s.xml" % self.tool_name

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1047 tool_test_path = os.path.join(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1048 self.repdir, f"{self.tool_name}_planemo_test_report.html"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1049 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1050 if os.path.exists(self.tlog):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1051 tout = open(self.tlog, "a")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1052 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1053 tout = open(self.tlog, "w")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1054 cll = [

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1055 "planemo",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1056 "test",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1057 "--galaxy_python_version",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1058 self.args.python_version,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1059 "--conda_auto_init",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1060 "--test_data",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1061 os.path.abspath(self.testdir),

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1062 "--test_output",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1063 os.path.abspath(tool_test_path),

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1064 "--galaxy_root",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1065 self.args.galaxy_root,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1066 "--update_test_data",

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1067 os.path.abspath(xreal),

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1068 ]

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1069 p = subprocess.run(

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1070 cll,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1071 shell=False,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1072 cwd=self.tooloutdir,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1073 stderr=tout,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1074 stdout=tout,

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1075 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1076 tout.close()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1077 return p.returncode

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1078

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1079 def set_planemo_galaxy_root(self, galaxyroot='/galaxy-central', config_path=".planemo.yml"):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1080 # bug in planemo - bogus '--dev-wheels' passed to run_tests.sh as at april 2021 - need a fiddled copy so it is ignored until fixed

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1081 CONFIG_TEMPLATE = """## Planemo Global Configuration File.

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1082 ## Everything in this file is completely optional - these values can all be

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1083 ## configured via command line options for the corresponding commands.

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1084

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1085 ## Specify a default galaxy_root for test and server commands here.

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1086 galaxy_root: %s

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1087 ## Username used with toolshed(s).

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1088 #shed_username: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1089 sheds:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1090 # For each tool shed you wish to target, uncomment key or both email and

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1091 # password.

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1092 toolshed:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1093 #key: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1094 #email: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1095 #password: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1096 testtoolshed:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1097 #key: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1098 #email: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1099 #password: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1100 local:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1101 #key: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1102 #email: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1103 #password: "<TODO>"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1104 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1105 if not os.path.exists(config_path):

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1106 with open(config_path, "w") as f:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1107 f.write(CONFIG_TEMPLATE % galaxyroot)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1108

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1109

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1110 def main():

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1111 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1112 This is a Galaxy wrapper.

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1113 It expects to be called by a special purpose tool.xml

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1114

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1115 """

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1116 parser = argparse.ArgumentParser()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1117 a = parser.add_argument

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1118 a("--script_path", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1119 a("--history_test", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1120 a("--cl_suffix", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1121 a("--sysexe", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1122 a("--packages", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1123 a("--tool_name", default="newtool")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1124 a("--tool_dir", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1125 a("--input_files", default=[], action="append")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1126 a("--output_files", default=[], action="append")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1127 a("--user_email", default="Unknown")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1128 a("--bad_user", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1129 a("--make_Tool", default="runonly")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1130 a("--help_text", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1131 a("--tool_desc", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1132 a("--tool_version", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1133 a("--citations", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1134 a("--command_override", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1135 a("--test_override", default=None)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1136 a("--additional_parameters", action="append", default=[])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1137 a("--selecttext_parameters", action="append", default=[])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1138 a("--edit_additional_parameters", action="store_true", default=False)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1139 a("--parampass", default="positional")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1140 a("--tfout", default="./tfout")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1141 a("--new_tool", default="new_tool")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1142 a("--galaxy_url", default="http://localhost:8080")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1143 a("--toolshed_url", default="http://localhost:9009")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1144 # make sure this is identical to tool_sheds_conf.xml

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1145 # localhost != 127.0.0.1 so validation fails

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1146 a("--toolshed_api_key", default="fakekey")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1147 a("--galaxy_api_key", default="fakekey")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1148 a("--galaxy_root", default="/galaxy-central")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1149 a("--galaxy_venv", default="/galaxy_venv")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1150 a("--collection", action="append", default=[])

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1151 a("--include_tests", default=False, action="store_true")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1152 a("--python_version", default="3.9")

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1153 args = parser.parse_args()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1154 assert not args.bad_user, (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1155 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1156 admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file'

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1157 % (args.bad_user, args.bad_user)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1158 )

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1159 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1160 assert (

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1161 args.sysexe or args.packages

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1162 ), "## Tool Factory wrapper expects an interpreter \

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1163 or an executable package in --sysexe or --packages"

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1164 r = ScriptRunner(args)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1165 r.writeShedyml()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1166 r.makeTool()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1167 if args.make_Tool == "generate":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1168 r.run()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1169 r.moveRunOutputs()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1170 r.makeToolTar()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1171 else:

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1172 r.planemo_test_once()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1173 r.moveRunOutputs()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1174 r.makeToolTar(report_fail=True)

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1175 if args.make_Tool == "gentestinstall":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1176 r.shedLoad()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1177 r.eph_galaxy_load()

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1178

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1179

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1180 if __name__ == "__main__":

43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again

fubar

parents:

diff changeset

1181 main()

Mercurial > repos > fubar > toolfactory_gtn

annotate toolfactory/rgToolFactory2.py @ 0:43edf22e8cbc draft