guppy_basecaller: env/lib/python3.7/site-packages/planemo/shed2tap/base.py annotate

annotate env/lib/python3.7/site-packages/planemo/shed2tap/base.py @ 4:79f47841a781 draft

"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"

author	shellac
date	Thu, 14 May 2020 16:47:39 -0400
parents	26e78fe6e8c4
children

rev	line source
0 26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1 from __future__ import print_function
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	3 import os
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	4 import subprocess
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	5 import sys
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	6 import tarfile
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	7 import zipfile
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	8 from ftplib import all_errors as FTPErrors # tuple of exceptions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	9 from xml.etree import ElementTree
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	10
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	11 from galaxy.util import unicodify
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	12 from six import iteritems
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	13 from six import string_types
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	14 from six.moves import map as imap
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	15 from six.moves.urllib.error import URLError
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	16 from six.moves.urllib.request import urlretrieve
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	17
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	18
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	19 TOOLSHED_MAP = {
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	20 "toolshed": "https://toolshed.g2.bx.psu.edu",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	21 "testtoolshed": "https://testtoolshed.g2.bx.psu.edu",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	22 }
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	23
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	24
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	25 class Dependencies(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	26 """ Base class for parsing Tool Shed dependency files.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	27 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	28
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	29 def __init__(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	30 self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	31 dependencies_file,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	32 repo=None,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	33 package_factory=None,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	34 ):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	35 if package_factory is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	36 package_factory = BasePackage
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	37 self.repo = repo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	38 self.root = ElementTree.parse(dependencies_file).getroot()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	39 packages = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	40 dependencies = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	41 package_els = self.root.findall("package")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	42 assert package_els is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	43 for package_el in package_els:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	44 install_els = package_el.findall("install")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	45 readme_els = package_el.findall("readme")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	46 if len(readme_els) > 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	47 readme = readme_els[0].text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	48 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	49 readme = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	50 assert len(install_els) in (0, 1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	51 if len(install_els) == 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	52 install_el = install_els[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	53 package = package_factory(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	54 self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	55 package_el,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	56 install_el,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	57 readme=readme
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	58 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	59 packages.append(package)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	60 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	61 repository_el = package_el.find("repository")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	62 if repository_el is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	63 message = "no repository in package el for %s" % repo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	64 raise AssertionError(message)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	65 dependency = Dependency(self, package_el, repository_el)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	66 dependencies.append(dependency)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	67
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	68 self.packages = packages
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	69 self.dependencies = dependencies
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	70
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	71 def single_package(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	72 return len(self.packages) == 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	73
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	74 def __repr__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	75 return "Dependencies[for_repo=%s]" % self.repo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	76
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	77
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	78 class Repo(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	79
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	80 def __init__(self, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	81 for key, value in iteritems(kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	82 setattr(self, key, value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	83
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	84 def recipe_base_name(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	85 owner = self.owner.replace("-", "")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	86 name = self.name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	87 name = name.replace("_", "").replace("-", "")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	88 base = "%s_%s" % (owner, name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	89 return base
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	90
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	91 @staticmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	92 def from_xml(elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	93 tool_shed_url = elem.attrib.get("toolshed", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	94 if tool_shed_url and ("testtoolshed" in tool_shed_url):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	95 prefix = "testtoolshed"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	96 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	97 prefix = "toolshed"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	98 prior = elem.attrib.get("prior_installation_required", False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	99 return Repo(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	100 prefix=prefix,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	101 name=elem.attrib["name"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	102 owner=elem.attrib["owner"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	103 tool_shed_url=tool_shed_url,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	104 changeset_revision=elem.attrib.get("changeset_revision", None),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	105 prior_installation_required=prior,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	106 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	107
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	108 @staticmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	109 def from_api(prefix, repo_json):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	110 return Repo(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	111 prefix=prefix,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	112 name=repo_json["name"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	113 owner=repo_json["owner"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	114 tool_shed_url=TOOLSHED_MAP[prefix],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	115 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	116
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	117 def get_file(self, path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	118 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	119 url_template = "%s/repos/%s/%s/raw-file/tip/%s"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	120 url = url_template % (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	121 self.tool_shed_url,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	122 self.owner,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	123 self.name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	124 path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	125 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	126 path, headers = urlretrieve(url)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	127 return path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	128 except Exception as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	129 print(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	130 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	131
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	132 def __repr__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	133 return "Repository[name=%s,owner=%s]" % (self.name, self.owner)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	134
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	135
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	136 class Dependency(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	137
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	138 def __init__(self, dependencies, package_el, repository_el):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	139 self.dependencies = dependencies
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	140 self.package_el = package_el
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	141 self.repository_el = repository_el
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	142 self.repo = Repo.from_xml(repository_el)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	143
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	144 def __repr__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	145 temp = "Dependency[package_name=%s,version=%s,dependent_package=%s]"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	146 return temp % (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	147 self.package_el.attrib["name"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	148 self.package_el.attrib["version"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	149 self.repository_el.attrib["name"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	150 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	151
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	152
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	153 class BasePackage(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	154
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	155 def __init__(self, dependencies, package_el, install_el, readme):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	156 self.dependencies = dependencies
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	157 self.package_el = package_el
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	158 self.install_el = install_el
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	159 self.readme = readme
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	160 self.all_actions = self.get_all_actions()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	161 self.no_arch_option = self.has_no_achitecture_install()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	162
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	163 def get_all_actions(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	164 action_or_group = self.install_el[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	165 parsed_actions = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	166 if action_or_group.tag == "actions":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	167 parsed_actions.append(self.parse_actions(action_or_group))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	168 elif action_or_group.tag == "actions_group":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	169 actions_els = action_or_group.findall("actions")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	170 assert actions_els is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	171 for actions in actions_els:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	172 parsed_actions.append(self.parse_actions(actions))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	173 action_els = action_or_group.findall("action")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	174 assert action_els is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	175 for action in action_els:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	176 for parsed_a in parsed_actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	177 parsed_a.actions.append(self.parse_action(action))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	178 return parsed_actions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	179
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	180 def has_no_achitecture_install(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	181 all_actions = self.all_actions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	182 if len(all_actions) < 2:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	183 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	184 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	185 last_action = all_actions[-1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	186 return (not last_action.architecture) and (not last_action.os)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	187
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	188 def has_explicit_set_environments(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	189 all_actions = self.all_actions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	190 for actions in all_actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	191 for action in actions.actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	192 if action.explicit_variables:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	193 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	194 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	195
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	196 def has_multiple_set_environments(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	197 all_actions = self.all_actions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	198 for actions in all_actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	199 count = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	200 for action in actions.actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	201 if action.explicit_variables:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	202 count += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	203 if count > 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	204 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	205 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	206
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	207 def parse_actions(self, actions):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	208 os = actions.attrib.get("os", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	209 architecture = actions.get("architecture", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	210 action_els = actions.findall("action")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	211 assert action_els is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	212 parsed_actions = list(imap(self.parse_action, action_els))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	213 action_packages = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	214 for package in actions.findall("package"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	215 action_packages.append(self.parse_action_package(package))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	216 return Actions(parsed_actions, os, architecture, action_packages)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	217
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	218 def parse_action_package(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	219 name = elem.attrib["name"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	220 version = elem.attrib["version"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	221 repo = Repo.from_xml(elem.find("repository"))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	222 return ActionPackage(name, version, repo)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	223
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	224 def parse_action(self, action):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	225 return BaseAction.from_elem(action, package=self)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	226
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	227 def __repr__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	228 actions = self.all_actions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	229 parts = (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	230 self.package_el.attrib["name"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	231 self.package_el.attrib["version"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	232 self.dependencies,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	233 actions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	234 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	235 template = "Install[name=%s,version=%s,dependencies=%s,actions=%s]"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	236 return template % parts
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	237
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	238
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	239 class Actions(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	240
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	241 def __init__(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	242 self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	243 actions,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	244 os=None,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	245 architecture=None,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	246 action_packages=[]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	247 ):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	248 self.os = os
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	249 self.architecture = architecture
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	250 self.actions = actions or []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	251 self.action_packages = action_packages
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	252
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	253 def first_download(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	254 for action in self.actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	255 if action.action_type in ["download_by_url", "download_file"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	256 return action
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	257 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	258
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	259 def downloads(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	260 actions = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	261 for action in self.actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	262 if action.action_type in ["download_by_url", "download_file"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	263 actions.append(action)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	264 return actions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	265
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	266 def __repr__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	267 platform = ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	268 if self.os or self.architecture:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	269 platform = "os=%s,arch=%s," % (self.os, self.architecture)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	270 return "Actions[%s%s]" % (platform, map(str, self.actions))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	271
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	272 def _indent_extend(self, target, new_entries, indent=" "):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	273 for line in new_entries:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	274 target.append(indent + line)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	275
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	276 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	277 # Use self.os.title() to match "Linux" or "Darwin" in bash where case matters:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	278 if self.os and self.architecture:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	279 condition = '("%s" == `uname`) && ("%s" == `arch`)' % (self.os.title(), self.architecture)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	280 elif self.os:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	281 condition = '"%s" == `uname`' % self.os.title()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	282 elif self.architecture:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	283 condition = '"%s" == `arch`' % self.architecture
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	284 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	285 condition = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	286
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	287 install_cmds = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	288 env_cmds = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	289
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	290 if condition:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	291 # Conditional actions block
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	292 install_cmds = [
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	293 '#' + '-' * 60,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	294 'if [[ $specifc_action_done == 0 && %s ]]' % condition,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	295 'then',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	296 ' echo "Platform-specific action for os=%s, arch=%s"' % (self.os, self.architecture)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	297 env_cmds = install_cmds[:]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	298 # TODO - Refactor block indentation?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	299 for action in self.actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	300 i_cmds, e_cmds = action.to_bash()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	301 self._indent_extend(install_cmds, i_cmds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	302 self._indent_extend(env_cmds, e_cmds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	303 # If we run the action, do not want to run any later actions!
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	304 install_cmds.extend([' specifc_action_done=1', 'fi'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	305 env_cmds.extend([' specifc_action_done=1', 'fi'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	306 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	307 # Non-specific default action...
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	308 install_cmds = [
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	309 '#' + '-' * 60,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	310 'if [[ $specifc_action_done == 0 ]]',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	311 'then',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	312 ' echo "Non-platform-specific actions"']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	313 env_cmds = install_cmds[:]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	314 for action in self.actions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	315 i_cmds, e_cmds = action.to_bash()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	316 self._indent_extend(install_cmds, i_cmds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	317 self._indent_extend(env_cmds, e_cmds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	318 install_cmds.append('fi')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	319 env_cmds.append('fi')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	320 return install_cmds, env_cmds
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	321
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	322
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	323 class ActionPackage(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	324
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	325 def __init__(self, name, version, repo):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	326 self.name = name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	327 self.version = version
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	328 self.repo = repo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	329
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	330
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	331 class BaseAction(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	332
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	333 def __repr__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	334 return "Action[type=%s]" % self.action_type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	335
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	336 def same_as(self, other):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	337 if self._keys != other._keys:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	338 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	339 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	340 for key in self._keys:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	341 if getattr(self, key) != getattr(other, key):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	342 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	343
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	344 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	345
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	346 def parse_action_repo(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	347 repo_elem = elem.find("repository")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	348 repo = Repo.from_xml(repo_elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	349 self.repo = repo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	350
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	351 def parse_package_elems(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	352 package_els = elem.findall("package")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	353 packages = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	354 assert package_els is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	355 for package_el in package_els:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	356 packages.append(package_el.text)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	357 self.packages = packages
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	358
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	359 @classmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	360 def from_elem(cls, elem, package):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	361 type = elem.attrib["type"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	362 action_class = actions_by_type[type]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	363 return action_class(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	364
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	365 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	366 """Return lists of bash shell commands to execute this action.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	367
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	368 This method is be implemented by each sub-class, and will
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	369 return two list of strings (for ``dep_install.sh`` and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	370 ``env.sh`` respectively).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	371 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	372 raise NotImplementedError("No to_bash defined for %r" % self)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	373
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	374
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	375 def _tar_folders(filename):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	376 with tarfile.open(filename, "r", errorlevel=0) as archive:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	377 folders = set()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	378 for i in archive.getmembers():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	379 if i.isdir():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	380 folders.add(i.name.rstrip("/"))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	381 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	382 folders.add(os.path.split(i.name)[0])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	383 return list(folders)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	384
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	385
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	386 def _zip_folders(filename):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	387 archive = zipfile.ZipFile(filename, "r")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	388 return list(set(i.filename.rstrip("/") for i in archive.infolist() if i.filename.endswith("/")))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	389
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	390
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	391 def _common_prefix(folders):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	392 common_prefix = ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	393 if len(folders) == 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	394 common_prefix = list(folders)[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	395 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	396 common_prefix = os.path.commonprefix(folders)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	397 assert not os.path.isabs(common_prefix), folders
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	398 return common_prefix
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	399
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	400
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	401 def _cache_download(url, filename, sha256sum=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	402 """Returns local path to cached copy of URL using given filename."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	403 cache = os.environ.get("DOWNLOAD_CACHE", "./download_cache/")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	404 # TODO - expose this as a command line option
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	405
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	406 if not os.path.isdir(cache):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	407 os.mkdir(cache)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	408
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	409 local = os.path.join(cache, filename)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	410
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	411 if not os.path.isfile(local):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	412 # Must download it...
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	413 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	414 # TODO - log this nicely...
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	415 sys.stderr.write("Downloading %s to %r\n" % (url, local))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	416 urlretrieve(url, local)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	417 except URLError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	418 # Most likely server is down, could be bad URL in XML action:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	419 raise RuntimeError("Unable to download %s" % url)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	420 except FTPErrors:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	421 # Most likely server is down, could be bad URL in XML action:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	422 raise RuntimeError("Unable to download %s" % url)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	423
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	424 # Verifying the checksum is slow, only do this on a fresh
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	425 # download. Assume locally cached files are already OK.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	426 if sha256sum:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	427 # TODO - log this nicely...
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	428 sys.stderr.write("Verifying checksum for %s\n" % filename)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	429 filehash = subprocess.check_output(['shasum', '-a', '256', local])[0:64].strip()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	430 filehash = unicodify(filehash)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	431 if filehash != sha256sum:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	432 raise RuntimeError("Checksum failure for %s, got %r but wanted %r" % (local, filehash, sha256sum))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	433
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	434 return local
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	435
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	436
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	437 def _determine_compressed_file_folder(url, downloaded_filename, target_filename=None, sha256sum=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	438 """Determine how to decompress the file & its directory structure.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	439
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	440 Returns a list of shell commands. Consider this example where the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	441 folder to change to cannot be guessed from the tar-ball filename:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	442
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	443 $ curl -o "ncbi-blast-2.2.30+-ia32-linux.tar.gz" \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	444 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-ia32-linux.tar.gz"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	445 $ tar -zxvf ncbi-blast-2.2.30+-ia32-linux.tar.gz
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	446 $ cd ncbi-blast-2.2.30+
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	447
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	448 Here it would return:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	449
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	450 ['tar -zxvf ncbi-blast-2.2.30+-ia32-linux.tar.gz', 'cd ncbi-blast-2.2.30+']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	451
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	452 If not cached, this function will download the file to the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	453 $DOWNLOAD_CACHE folder, and then open it / decompress it in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	454 order to find common folder prefix used. This will also verify
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	455 how to decompress the file, and the checksum if given.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	456 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	457 answer = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	458
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	459 local = _cache_download(url, downloaded_filename, sha256sum)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	460
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	461 if not target_filename:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	462 target_filename = downloaded_filename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	463
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	464 if tarfile.is_tarfile(local):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	465 folders = _tar_folders(local)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	466 if target_filename.endswith((".tar.gz", ".tgz")):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	467 answer.append('tar -zxvf %s' % target_filename)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	468 elif target_filename.endswith(".tar.bz2"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	469 answer.append('tar -jxvf %s' % target_filename)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	470 elif target_filename.endswith(".tar"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	471 answer.extend('tar -xvf %s' % target_filename)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	472 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	473 # Quite possibly this file doesn't need decompressing,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	474 # but until we've tested lots of real world tool_dependencies.xml
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	475 # files I'd like to check these cases to confirm this.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	476 raise NotImplementedError("How to decompress tar file %s?" % target_filename)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	477 elif zipfile.is_zipfile(local):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	478 if target_filename.endswith(".jar"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	479 # Do not decompress!
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	480 return answer
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	481 folders = _zip_folders(local)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	482 answer.append('unzip %s' % target_filename)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	483 elif target_filename.endswith(".dmg"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	484 # Do not decompress!
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	485 return answer
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	486 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	487 # No compression? Leave as it is?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	488 raise NotImplementedError("What kind of compression is %s using?" % local)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	489
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	490 common_prefix = _common_prefix(folders)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	491 if common_prefix:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	492 answer.append('cd "%s"' % common_prefix)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	493
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	494 return answer
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	495
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	496
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	497 def _commands_and_downloaded_file(url, target_filename=None, sha256sum=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	498 # We preserve the filename from the URL in the cache.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	499 # i.e. We do NOT use the target_filename in the cache.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	500 # This because some Galaxy recipes normalise platform specific downloads
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	501 # to use a single target filename, which would therefore break checksums etc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	502 # e.g. tests/data/repos/package_1/tool_dependencies.xml
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	503 downloaded_filename = os.path.split(url)[-1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	504 if "?" in downloaded_filename:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	505 downloaded_filename = downloaded_filename[:downloaded_filename.index("?")]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	506 if "#" in downloaded_filename:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	507 downloaded_filename = downloaded_filename[:downloaded_filename.index("#")]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	508
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	509 if not target_filename:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	510 target_filename = downloaded_filename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	511
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	512 # Curl is present on Mac OS X, can we assume it will be on Linux?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	513 # Cannot assume that wget will be on Mac OS X.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	514 answer = [
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	515 'if [[ -f "%s" ]]' % target_filename,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	516 'then',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	517 ' echo "Reusing existing %s"' % target_filename,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	518 'elif [[ -f "$DOWNLOAD_CACHE/%s" ]]' % downloaded_filename,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	519 'then',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	520 ' echo "Reusing cached %s"' % downloaded_filename,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	521 ' cp "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, target_filename),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	522 'else',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	523 ' echo "Downloading %s"' % downloaded_filename,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	524 ' curl -L -o "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, url),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	525 ' cp "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, target_filename),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	526 ]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	527 if sha256sum:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	528 # This is inserted into the if-else for a fresh download only.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	529 # Note double space between checksum and filename:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	530 answer.append(' echo "%s %s" \| shasum -a 256 -c -' % (sha256sum, target_filename))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	531 answer.append('fi')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	532
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	533 return answer, downloaded_filename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	534
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	535
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	536 def _commands_to_download_and_extract(url, target_filename=None, sha256sum=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	537 answer, downloaded_filename = _commands_and_downloaded_file(url, target_filename, sha256sum)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	538 # Now should we unpack the tar-ball etc?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	539 answer.extend(_determine_compressed_file_folder(url, downloaded_filename, target_filename, sha256sum))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	540 return answer, []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	541
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	542
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	543 class DownloadByUrlAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	544 action_type = "download_by_url"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	545 _keys = ["url"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	546
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	547 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	548 self.url = elem.text.strip()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	549 assert self.url
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	550 self.sha256sum = elem.attrib.get("sha256sum", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	551 self.target_filename = elem.attrib.get("target_filename", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	552
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	553 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	554 # See class DownloadByUrl in Galaxy,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	555 # lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	556 return _commands_to_download_and_extract(self.url, self.target_filename, self.sha256sum)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	557
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	558
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	559 class DownloadFileAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	560 action_type = "download_file"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	561 _keys = ["url", "extract"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	562
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	563 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	564 self.url = elem.text.strip()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	565 self.extract = asbool(elem.attrib.get("extract", False))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	566 self.sha256sum = elem.attrib.get("sha256sum", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	567 self.target_filename = elem.attrib.get("target_filename", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	568
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	569 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	570 if self.extract:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	571 return _commands_to_download_and_extract(self.url, self.target_filename, self.sha256sum)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	572 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	573 commands, downloaded_file = _commands_and_downloaded_file(self.url, self.target_filename, self.sha256sum)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	574 return commands, []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	575
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	576
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	577 class DownloadBinary(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	578 action_type = "download_binary"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	579 _keys = ["url_template", "target_directory"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	580
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	581 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	582 self.url_template = elem.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	583 assert self.url_template
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	584 self.target_directory = elem.get('target_directory', None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	585
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	586
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	587 class ShellCommandAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	588 action_type = "shell_command"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	589 _keys = ["command"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	590
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	591 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	592 self.command = elem.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	593
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	594 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	595 # Galaxy would run each action from the same temp
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	596 # working directory - possible that tool_dependencies.xml
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	597 # shell_command could change $PWD so reset this:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	598 return ["pushd . > /dev/null", self.command, "popd > /dev/null"], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	599
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	600
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	601 class TemplateShellCommandAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	602 action_type = "template_command"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	603 _keys = ["language", "command"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	604
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	605 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	606 self.command = elem.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	607 self.language = elem.get('language', 'cheetah').lower()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	608 assert self.command
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	609 assert self.language == "cheetah"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	610
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	611
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	612 class MoveFileAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	613 action_type = "move_file"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	614 _keys = ["move_file"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	615
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	616 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	617 self.source = elem.find("source").text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	618 self.destination = elem.find("destination").text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	619
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	620 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	621 return ["mv %s %s" % (self.source, self.destination)], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	622
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	623
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	624 class MoveDirectoryFilesAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	625 action_type = "move_directory_files"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	626 _keys = ["source_directory", "destination_directory"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	627
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	628 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	629 source_directory = elem.find("source_directory").text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	630 destination_directory = elem.find("destination_directory").text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	631 self.source_directory = source_directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	632 self.destination_directory = destination_directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	633
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	634 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	635 return ["mv %s/* %s/" % (self.source_directory, self.destination_directory)], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	636
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	637
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	638 class SetEnvironmentAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	639 action_type = "set_environment"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	640 _keys = ["variables"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	641
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	642 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	643 variables = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	644 var_els = elem.findall("environment_variable")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	645 assert var_els is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	646 for ev_elem in var_els:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	647 var = SetVariable(ev_elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	648 variables.append(var)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	649 self.variables = variables
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	650 assert self.variables
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	651
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	652 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	653 answer = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	654 for var in self.variables:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	655 # Expand $INSTALL_DIR here?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	656 if var.action == "set_to":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	657 answer.append('export %s=%s' % (var.name, var.raw_value))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	658 elif var.action == "prepend_to":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	659 answer.append('export %s=%s:$%s' % (var.name, var.raw_value, var.name))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	660 elif var.action == "append_to":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	661 answer.append('export %s=$%s:%s' % (var.name, var.name, var.raw_value))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	662 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	663 raise ValueError("Undefined environment variable action %r" % var.action)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	664 return answer, answer # Actions needed in env.sh here!
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	665
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	666
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	667 class ChmodAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	668 action_type = "chmod"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	669 _keys = ["mods"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	670
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	671 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	672 mods = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	673 file_els = elem.findall("file")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	674 assert file_els is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	675 for mod_elem in file_els:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	676 mod = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	677 mod["mode"] = mod_elem.attrib["mode"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	678 mod["target"] = mod_elem.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	679 mods.append(mod)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	680 self.mods = mods
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	681 assert self.mods
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	682
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	683 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	684 return ["chmod %s %s" % (m["mode"], m["target"]) for m in self.mods], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	685
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	686
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	687 class MakeInstallAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	688 action_type = "make_install"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	689 _keys = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	690
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	691 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	692 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	693
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	694 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	695 return ["make install"], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	696
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	697
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	698 class AutoconfAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	699 action_type = "autoconf"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	700 _keys = ["options"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	701
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	702 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	703 self.options = elem.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	704
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	705 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	706 if self.options:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	707 raise NotImplementedError("Options with action autoconf not implemented yet.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	708 return ['./configure', 'make', 'make install'], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	709
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	710
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	711 class ChangeDirectoryAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	712 action_type = "change_directory"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	713 _keys = ["directory"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	714
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	715 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	716 self.directory = elem.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	717 assert self.directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	718
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	719 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	720 return ["cd %s" % self.directory], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	721
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	722
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	723 class MakeDirectoryAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	724 action_type = "make_directory"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	725 _keys = ["directory"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	726
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	727 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	728 self.directory = elem.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	729
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	730 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	731 return ["mkdir -p %s" % self.directory], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	732
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	733
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	734 class SetupPerlEnvironmentAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	735 action_type = "setup_perl_environment"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	736 _keys = ["repo", "packages"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	737
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	738 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	739 self.parse_action_repo(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	740 self.parse_package_elems(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	741
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	742
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	743 class SetupRubyEnvironmentAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	744 action_type = "setup_ruby_environment"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	745 _keys = ["repo", "packages"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	746
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	747 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	748 self.parse_action_repo(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	749 self.parse_package_elems(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	750
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	751
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	752 class SetupPythonEnvironmentAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	753 action_type = "setup_python_environment"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	754 _keys = ["repo", "packages"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	755
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	756 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	757 self.parse_action_repo(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	758 self.parse_package_elems(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	759
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	760
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	761 class SetupVirtualenvAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	762 action_type = "setup_virtualenv"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	763 _keys = ["use_requirements_file", "python", "requirements"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	764
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	765 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	766 use_reqs = elem.attrib.get("use_requirements_file", "True")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	767 self.use_requirements_file = asbool(use_reqs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	768 self.python = elem.get('python', 'python')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	769 self.requirements = elem.text or 'requirements.txt'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	770
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	771
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	772 class SetupREnvironmentAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	773 action_type = "setup_r_environment"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	774 _keys = ["repo", "packages"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	775
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	776 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	777 self.parse_action_repo(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	778 self.parse_package_elems(elem)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	779
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	780
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	781 class SetEnvironmentForInstallAction(BaseAction):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	782 action_type = "set_environment_for_install"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	783
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	784 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	785 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	786
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	787 def to_bash(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	788 # TODO - How could we resolve/check the dependencies?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	789 return ['echo "WARNING: Assuming packages already installed!"'], []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	790
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	791
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	792 class SetVariable(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	793
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	794 def __init__(self, elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	795 self.action = elem.attrib["action"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	796 self.name = elem.attrib["name"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	797 self.raw_value = elem.text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	798
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	799
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	800 truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	801 falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	802
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	803
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	804 def asbool(obj):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	805 if isinstance(obj, string_types):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	806 obj = obj.strip().lower()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	807 if obj in truthy:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	808 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	809 elif obj in falsy:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	810 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	811 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	812 raise ValueError("String is not true/false: %r" % obj)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	813 return bool(obj)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	814
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	815
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	816 action_classes = [
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	817 DownloadByUrlAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	818 DownloadFileAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	819 DownloadBinary,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	820 ShellCommandAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	821 TemplateShellCommandAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	822 MoveFileAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	823 MoveDirectoryFilesAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	824 SetEnvironmentAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	825 ChmodAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	826 MakeInstallAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	827 AutoconfAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	828 ChangeDirectoryAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	829 MakeDirectoryAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	830 SetupPerlEnvironmentAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	831 SetupRubyEnvironmentAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	832 SetupPythonEnvironmentAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	833 SetupVirtualenvAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	834 SetupREnvironmentAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	835 SetEnvironmentForInstallAction,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	836 ]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	837
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	838 actions_by_type = dict(map(lambda c: (c.action_type, c), action_classes))

Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/shed2tap/base.py @ 4:79f47841a781 draft