ms_to_peakforest_it: server.py annotate

annotate server.py @ 1:7e3085fc60c1 draft default tip

master branch Updating

author	lain
date	Wed, 30 Aug 2023 14:21:18 +0000
parents	b58b229c4cbf
children

rev	line source
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1 #!/usr/bin/env python3
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	2
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	3 import atexit
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	4 import csv
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	5 import http.server
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	6 import json
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	7 import logging
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	8 import os
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	9 import re
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	10 import shutil
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	11 import socketserver
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	12 import sys
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	13 import tempfile
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	14 import yaml
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	15
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	16 TAB_LIST_PLACEHOLDER = "TAB_LIST_PLACEHOLDER"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	17 MS_PEAK_VALUES_PLACEHOLDER = "MS_PEAK_VALUES_PLACEHOLDER"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	18 COMPOUND_NAME_PLACEHOLDER = "COMPOUND_NAME_PLACEHOLDER"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	19 TAB_INDEX_PLACEHOLDER = "TAB_INDEX_PLACEHOLDER"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	20 EMBED_JS_PLACEHOLDER = "EMBED_JS"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	21 ACTIVE_TAB_PLACEHOLDER = "ACTIVE_TAB_PLACEHOLDER"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	22 ADD_SPECTRUM_FORM = "ADD_SPECTRUM_FORM"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	23 PRODUCE_JSON_PLACEHOLDER = "PRODUCE_JSON_PLACEHOLDER"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	24
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	25 COMPOUND_REF = "compound-ref"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	26 COMPOUND_MIX = "compound-mix"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	27
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	28 END_MS_PEAK_VALUES_PLACEHOLDER = " ]"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	29 MS_DATA_COLUMN_NUMBER = 9
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	30 DEFAULT_MS_PEAK_VALUES = (
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	31 "[\n"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	32 + (" [" + ','.join([' ""'] * MS_DATA_COLUMN_NUMBER) + "],\n") * 17
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	33 + END_MS_PEAK_VALUES_PLACEHOLDER
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	34 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	35
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	36 FRAGNOT_HEADER = {
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	37 "m/z": "fragment_mz",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	38 "absolute_intensity": "abs_intensity",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	39 "relative_intensity": "rel_intensity",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	40 "theo_mass": "",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	41 "delta_ppm": "ppm",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	42 "rdbequiv": "",
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	43 "composition": "fragment",
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	44 "attribution": "composition",
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	45 }
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	46
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	47 MS_2_SNOOP_HEADER = {
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	48 "name": str,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	49 "inchikey": str,
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	50 # "composition": str,
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	51 "composition": lambda *args:"",
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	52 "fragment": str,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	53 "fragment_mz": str,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	54 "ppm": str,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	55 "fileid": str,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	56 "correlation": str,
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	57 "abs_intensity": lambda x:float(x), # * 100,
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	58 "rel_intensity": lambda x:float(x) * 100 if x != "" else "",
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	59 "valid_corelation": str
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	60 }
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	61
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	62
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	63 class ConfigException(ValueError):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	64 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	65 An exception raised when something went wrong in the config and we
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	66 cannot continue - i.e: when there's no token for peakforest
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	67 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	68
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	69 class YAMLConfig(dict):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	70
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	71 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	72 Dictionary that handles key with dot in them:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	73 test["truc.chose"]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	74 is equivalant to
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	75 test["truc"]["chose"]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	76 Assignation works too.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	77 Add the possibility to use placeholders:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	78 --- yaml
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	79 test: {{ truc.chose }}
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	80 truc:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	81 chose: bidule
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	82 ---
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	83 here, test's value is "bidule"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	84 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	85
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	86 def __init__(self, args, *kwargs):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	87 meta_conf = kwargs.pop("__meta_config__", {})
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	88 self._debug = meta_conf.get("__debug__", False)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	89 self._stream_name = meta_conf.get("__debug_stream__", "stdout")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	90 self._debug_stream = getattr(sys, self._stream_name)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	91 self._only_root_debug = meta_conf.get("__only_root_debug__", False)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	92 if "__root__" in kwargs:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	93 if self._only_root_debug:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	94 self._debug = False
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	95 self._name = kwargs.pop("__name__")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	96 self._debugger("Is not root config.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	97 self._root = kwargs.pop("__root__")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	98 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	99 self._name = "root"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	100 self._debugger("Is root config.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	101 self._root = self
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	102 super().__init__(args, *kwargs)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	103 for key, value in self.copy().items():
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	104 if isinstance(value, dict) and not isinstance(value, YAMLConfig):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	105 self._debugger(f"Parsing sub-config for {key}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	106 self[key] = self._propagate(value, key)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	107 self._replace_placeholders(self)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	108 self._extract_defaults()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	109
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	110 def _propagate(self, sub_dict, name):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	111 if isinstance(sub_dict, dict) and not isinstance(sub_dict, self.__class__):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	112 return YAMLConfig(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	113 **sub_dict,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	114 __name__=name,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	115 __root__=self._root,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	116 __meta_config__={
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	117 "__debug__": self._debug,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	118 "__debug_stream__": self._stream_name,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	119 "__only_root_debug__": self._only_root_debug,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	120 }
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	121 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	122 return sub_dict
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	123
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	124 def _debugger(self, message):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	125 if self._debug:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	126 self._debug_stream.write(f"[{self._name}]: {message}\n")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	127 self._debug_stream.flush()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	128
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	129 def __getattr__(self, attr):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	130 if attr in self:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	131 return self[attr]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	132 if '.' in attr:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	133 attr, sub = attr.split('.', 1)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	134 return getattr(getattr(self, attr), sub)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	135 return super().__getattribute__(attr)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	136
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	137 def _replace_placeholders(self, subpart):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	138 self._debugger("Replacing placeholders...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	139 for sub_key, sub_item in subpart.copy().items():
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	140 if isinstance(sub_item, str):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	141 for placeholder in re.findall("{{ (?P<placeholder>.*?) }}", sub_item):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	142 if placeholder not in self._root:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	143 self._debugger(f"Could not fine replacement for {placeholder}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	144 continue
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	145 replacement = self._root[placeholder]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	146 if isinstance(replacement, str):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	147 self._debugger(f"Found placeholder: {placeholder} -> {replacement}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	148 sub_item = sub_item.replace(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	149 "{{ " + placeholder + " }}",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	150 replacement
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	151 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	152 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	153 self._debugger(f"Found placeholder: {placeholder} -> {replacement.__class__.__name__}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	154 sub_item = self._propagate(replacement, placeholder)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	155 dict.__setitem__(subpart, sub_key, sub_item)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	156 elif isinstance(sub_item, dict):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	157 super().__setitem__(sub_key, self._propagate(sub_item, sub_key))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	158
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	159 def _extract_defaults(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	160 if self._root is not self:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	161 return
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	162 if "defaults" not in self:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	163 self._debugger("No defaults here.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	164 return
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	165 if "arguments" not in self:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	166 self._debugger("Arguments creation...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	167 self["arguments"] = self._propagate({}, "arguments")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	168 self._debugger("Populating arguments with defaults values")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	169 for key, value in self.defaults.items():
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	170 if key not in self:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	171 if isinstance(value, dict):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	172 value = self._propagate(value, key)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	173 self.arguments[key] = value
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	174 self._debugger(f"Default {key} = {value}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	175
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	176 def __setitem__(self, key, value):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	177 if isinstance(value, dict):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	178 value = self._propagate(value, key)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	179 if "." not in key:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	180 return super().__setitem__(key, value)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	181 curent = self
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	182 key, subkey = key.rsplit(".", 1)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	183 self[key][subkey] = value
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	184
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	185 def __getitem__(self, key):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	186 if super().__contains__(key):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	187 return super().__getitem__(key)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	188 if "." not in key:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	189 return super().__getitem__(key)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	190 curent = self
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	191 while "." in key:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	192 key, subkey = key.split(".", 1)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	193 curent = curent[key]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	194 key = subkey
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	195 if subkey not in curent:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	196 curent[subkey] = self._propagate({}, subkey)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	197 result = curent[subkey]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	198 return result
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	199
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	200 def __contains__(self, key):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	201 if "." not in key:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	202 return super().__contains__(key)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	203 key, subkey = key.split(".", 1)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	204 if not super().__contains__(key):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	205 return False
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	206 return subkey in self[key]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	207
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	208 def copy(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	209 return {
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	210 key: (
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	211 value if not isinstance(value, dict)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	212 else value.copy()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	213 ) for key, value in self.items()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	214 }
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	215
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	216 class YAMLParameters(YAMLConfig):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	217
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	218 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	219 Parses parameters from the command line and put them
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	220 in the config.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	221 Uses the config to know which parameter is recognized, or not,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	222 to know the metadata (author, version),
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	223 which command is a flag, is optional, the help strings, etc...
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	224 Assigns default small parameter if not defined in the "shortcut"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	225 section of the config file.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	226 CLI config must be in the root section "parameters":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	227 ---
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	228 parameters:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	229 mandatory:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	230 input: input file path
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	231 flags:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	232 help: Show this help
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	233 optional:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	234 method: "default is {{ defaults.method }}"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	235 meta:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	236 author: Lain Pavot
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	237 version: 1.2.0
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	238 shortcuts:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	239 help: h
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	240 ## will autogenerate -i for input and -m for method
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	241 ---
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	242 default parameters are searched in the "default" root section.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	243 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	244
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	245 def __init__(self, args, *kwargs):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	246 super().__init__(args, *kwargs)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	247 self._errors = list()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	248 if not self.parameters.shortcuts:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	249 self.parameters["shortcuts"] = YAMLConfig()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	250 self._mandatory = self.parameters.mandatory
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	251 self._optional = self.parameters.optional
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	252 self._flags = {
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	253 flag: False
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	254 for flag in self.parameters.flags
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	255 }
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	256 self._all_params = self._optional.copy()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	257 self._all_params.update(self._mandatory)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	258 self._all_params.update(self._flags)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	259 self._small_params = dict()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	260 self._determine_small_params()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	261
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	262 @property
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	263 def in_error(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	264 return bool(self._errors)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	265
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	266 @property
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	267 def sorted_keys(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	268 return sorted(self._all_params.keys())
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	269
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	270 @property
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	271 def sorted_items(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	272 return sorted(self._all_params.items())
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	273
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	274 def _determine_small_params(self, verbose=False):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	275 self._small_params = (self.parameters.shortcuts or {}).copy()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	276 chars = list(map(chr, range(97, 123))) + list(map(chr, range(65, 91)))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	277 all_params = self._all_params.copy()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	278 for long, short in self._small_params.items():
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	279 chars.remove(short)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	280 del all_params[long]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	281 for param in all_params.copy().keys():
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	282 for operation in (
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	283 lambda x:x[0], ## select first char
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	284 lambda x:x.split('-', 1)[-1][0], ## first char after -
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	285 lambda x:x.split('_', 1)[-1][0], ## first char after _
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	286 lambda x:x.split('.', 1)[-1][0], ## first char after .
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	287 lambda x:x[0].upper(), ## select first char
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	288 lambda x:x.split('-', 1)[-1][0].upper(), ## first char after -
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	289 lambda x:x.split('_', 1)[-1][0].upper(), ## first char after _
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	290 lambda x:x.split('.', 1)[-1][0].upper(), ## first char after .
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	291 lambda x: chars[0], ## first letter in the alphabet
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	292 ):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	293 char = operation(param)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	294 if char not in self._small_params.values():
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	295 self._small_params[param] = char
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	296 chars.remove(char)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	297 del all_params[param]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	298 break
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	299
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	300 def _get_parameter_index(self, parameter, original):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	301 if f"--{parameter}" in sys.argv:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	302 return sys.argv.index(f"--{parameter}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	303 parameter = self._small_params[original]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	304 if f"-{parameter}" in sys.argv:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	305 return sys.argv.index(f"-{parameter}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	306 return None
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	307
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	308 def as_parameter(self, string):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	309 return (
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	310 string
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	311 .replace('.', '-')
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	312 .replace('_', '-')
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	313 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	314
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	315 def show_version(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	316 print(self.parameters.meta.version)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	317
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	318 def show_help(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	319 parameters = [
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	320 f"-{self._small_params[arg]}\|--{self.as_parameter(arg)} {arg}"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	321 for arg in self._mandatory
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	322 ] + [
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	323 f"[-{self._small_params[arg]}\|--{self.as_parameter(arg)} {arg}]"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	324 for arg in self._optional
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	325 ] + [
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	326 f"[-{self._small_params[arg]}\|--{self.as_parameter(arg)}]"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	327 for arg in self._flags
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	328 ]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	329 print(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	330 f"Usage: {__file__} " + ' '.join(parameters)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	331 + "\n\n"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	332 + '\n'.join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	333 f" -{self._small_params[args]}\|--{self.as_parameter(args)}: {help_str}"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	334 for args, help_str in self.sorted_items
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	335 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	336 + "\n\n"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	337 + '\n'.join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	338 f"{key}: {value}"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	339 for key, value in self.parameters.meta.items()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	340 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	341 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	342 sys.exit(0)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	343
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	344 def parse_args(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	345 errors = list()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	346 for kind in ("mandatory", "optional", "flags"):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	347 keys = list(sorted(getattr(self, f"_{kind}").keys()))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	348 for original_param, actual_param in zip(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	349 keys,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	350 map(self.as_parameter, keys),
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	351 ):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	352 if original_param in self.defaults:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	353 self.arguments[original_param] = self.defaults[original_param]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	354 elif kind == "flags":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	355 self.arguments[original_param] = False
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	356 parser = getattr(self, f"parse_{kind}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	357 if (error := parser(original_param, actual_param)):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	358 errors.append(error)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	359 self._errors = errors
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	360 return self
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	361
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	362 def parse_mandatory(self, original, actual):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	363 if (index := self._get_parameter_index(actual, original)) is None:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	364 return f"The parameter --{actual} is mandatory."
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	365 if index == len(sys.argv) - 1:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	366 return f"The parameter --{actual} needs a value."
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	367 self.arguments[original] = sys.argv[index + 1]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	368
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	369 def parse_optional(self, original, actual):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	370 if (index := self._get_parameter_index(actual, original)) is None:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	371 return
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	372 if index == len(sys.argv) - 1:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	373 return f"The parameter --{actual} needs a value."
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	374 self.arguments[original] = sys.argv[index + 1]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	375
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	376 def parse_flags(self, original, actual):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	377 if (index := self._get_parameter_index(actual, original)) is None:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	378 return
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	379 self.arguments[original] = True
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	380
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	381 def parse_config(**kwargs):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	382 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	383 opens the config file, extract it using pyyaml's safe loader
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	384 and tries to extract and apply a maximum of informations/directives
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	385 from the config:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	386 - token retrieval
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	387 - workdir management
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	388 - tempfile management
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	389 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	390 root_dir = os.path.dirname(os.path.abspath(__file__))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	391 with open(os.path.join(root_dir, "config.yml")) as config_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	392 config = YAMLConfig(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	393 **yaml.load(config_file.read(), Loader=yaml.SafeLoader),
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	394 **kwargs
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	395 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	396
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	397 if not config.token.value:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	398 if config.token.use_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	399 if (not os.path.exists(path := config.token.file_path)):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	400 raise ConfigException("Missing token value or token file.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	401 with open(path) as token_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	402 config.token["value"] = token_file.read()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	403 elif config.defaults.peakforest.token:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	404 config.token["value"] = config.defaults.peakforest.token
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	405
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	406 if config.workdir.create_tmp:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	407 tmp_dir = tempfile.mkdtemp()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	408 atexit.register(lambda:shutil.rmtree(tmp_dir))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	409 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	410 tmp_dir = tempfile.gettempdir()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	411 config.workdir["tmp_dir"] = tmp_dir
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	412
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	413 config["root_dir"] = root_dir
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	414 config["tab_list"] = []
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	415 config["form_template"] = os.path.join(root_dir, config.templates.form)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	416 config["meta_template"] = os.path.join(root_dir, config.templates.main)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	417 config["js_template"] = os.path.join(root_dir, config.templates.js)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	418 config["tab_list_template"] = os.path.join(root_dir, config.templates.tab_list)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	419 config["placeholders"] = dict()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	420 config.placeholders[MS_PEAK_VALUES_PLACEHOLDER] = DEFAULT_MS_PEAK_VALUES
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	421 config.placeholders[TAB_INDEX_PLACEHOLDER] = "1"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	422 config.placeholders[ACTIVE_TAB_PLACEHOLDER] = "active"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	423 config.placeholders[ADD_SPECTRUM_FORM] = ""
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	424 config.placeholders[EMBED_JS_PLACEHOLDER] = ""
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	425 config.placeholders[TAB_LIST_PLACEHOLDER] = ""
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	426 # config.placeholders["DEFAULT_MIN_MZ"] = "50"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	427 # config.placeholders["DEFAULT_MAX_MZ"] = "500"
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	428 config.placeholders["DEFAULT_RESOLUTION_LOW"] = ""
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	429 config.placeholders["DEFAULT_RESOLUTION_HIGH"] = "selected=\"selected\""
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	430 config.placeholders["DEFAULT_RESOLUTION_UNSET"] = ""
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	431 return config
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	432
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	433 def parse_parameters(config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	434 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	435 parses command line and checks provided values are acceptable/usable.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	436 Raises some error if not.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	437 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	438 parameters = YAMLParameters(**config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	439 parameters.parse_args()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	440
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	441 parameters["json_result"] = []
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	442
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	443 get_logger(parameters)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	444
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	445 arguments = parameters.arguments
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	446 if arguments.help:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	447 parameters.show_help()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	448 sys.exit(0)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	449
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	450 if arguments.version:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	451 parameters.show_version()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	452 sys.exit(0)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	453
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	454 if parameters.in_error:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	455 raise ValueError(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	456 "Some errors occured during parameters extraction: \n"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	457 + '\n'.join(parameters.errors)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	458 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	459
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	460 parameters.placeholders["DEFAULT_MIN_RT"] = str(arguments.rt_min)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	461 parameters.placeholders["DEFAULT_MAX_RT"] = str(arguments.rt_max)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	462
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	463 if arguments.sample_type == COMPOUND_MIX:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	464 parameters["form_template"] = os.path.join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	465 parameters["root_dir"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	466 parameters.templates.form_mix
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	467 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	468 parameters["meta_template"] = os.path.join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	469 parameters["root_dir"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	470 parameters.templates.main_mix
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	471 )
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	472 else: # elif arguments.sample_type == COMPOUND_REF:
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	473 parameters["form_template"] = os.path.join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	474 parameters["root_dir"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	475 parameters.templates.form_ref
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	476 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	477 parameters["meta_template"] = os.path.join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	478 parameters["root_dir"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	479 parameters.templates.main_ref
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	480 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	481
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	482 arguments["produce_json"] = (
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	483 "output_json" in arguments
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	484 and arguments["output_json"] != ""
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	485 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	486 if arguments.produce_json:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	487 parameters.placeholders[PRODUCE_JSON_PLACEHOLDER] = "true"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	488 parameters.json_result = []
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	489 arguments["output_json"] = os.path.abspath(arguments["output_json"])
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	490 atexit.register(save_json, parameters)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	491 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	492 parameters.placeholders[PRODUCE_JSON_PLACEHOLDER] = "false"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	493
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	494 if arguments.run_dry_html:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	495 arguments["do_run_dry"] = True
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	496 parameters.generated["html"] = os.path.abspath(arguments.run_dry_html)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	497
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	498 if arguments.run_dry_js:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	499 arguments["do_run_dry"] = True
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	500 parameters.generated["js"] = os.path.abspath(arguments.run_dry_js)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	501
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	502 if arguments.do_run_dry:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	503 parameters.logger.info("Dry run. Server will ne be run.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	504 if arguments.run_dry_html:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	505 parameters.logger.info(f"HTML file will be put in {arguments.run_dry_html}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	506 if arguments.run_dry_js:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	507 parameters.logger.info(f"JS file will be put in {arguments.run_dry_js}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	508
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	509 if arguments.peakforest.token:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	510 config.token["value"] = arguments.peakforest.token
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	511 if not config.token.value:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	512 raise ConfigException(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	513 "No token provided. We will not be able to connect to peakforest."
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	514 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	515
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	516 if os.path.exists(arguments.input):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	517 single_file = True
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	518 file_paths = [arguments.input]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	519 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	520 path_list = arguments.input.split(',')
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	521 if all(map(os.path.exists, path_list)):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	522 single_file = False
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	523 file_paths = path_list
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	524 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	525 raise ValueError(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	526 f"Some files cannot be found: "
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	527 + ', '.join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	528 path for path in path_list
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	529 if not os.path.exists(path)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	530 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	531 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	532 arguments["input"] = list(map(os.path.abspath, file_paths))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	533
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	534 if single_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	535 arguments["name"] = [arguments.name]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	536 arguments["raw_metadata"] = [arguments.raw_metadata]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	537 parameters.logger.info(f"Single file processing: {arguments.input}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	538 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	539 parameters.logger.info(f"Multiple file processing:")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	540 arguments["raw_metadata"] = arguments.raw_metadata.split(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	541 arguments.raw_metadata_sep
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	542 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	543 if not arguments.name:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	544 arguments["name"] = arguments["raw_metadata"]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	545 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	546 arguments["name"] = arguments.name.split(',')
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	547 for i in range(len(arguments.name)):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	548 parameters.logger.info(f" - file: {arguments.input[i]}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	549 parameters.logger.info(f" - name: {arguments.name[i]}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	550 parameters.logger.info(f" - metadata: {arguments.raw_metadata[i]}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	551 parameters.logger.info(f" ")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	552 if (
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	553 len(arguments.name) != len(arguments.raw_metadata)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	554 or len(arguments.name) != len(arguments.input)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	555 ):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	556 raise ValueError(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	557 "name, raw_metadata and input parameters have different lengths: \n"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	558 f"input is {len(arguments.input)} elements long, "
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	559 f"raw_metadata is {len(arguments.raw_metadata)} elements long "
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	560 f"and name is {len(arguments.name)} elements long."
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	561 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	562 if arguments.spectrum_type == "LC_MS":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	563 arguments["scan_type"] = "ms"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	564 elif arguments.spectrum_type == "LC_MSMS":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	565 arguments["scan_type"] = "ms2"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	566 if arguments.method == "test":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	567 if arguments.spectrum_type == "LC_MS":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	568 arguments["method"] = "cf_pfem_urine_qtof"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	569 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	570 arguments["method"] = "cf_pfem_urine_method1_qtof-msms"
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	571 arguments["method"] = "toulouse-metatoul-agromix__ft-esi__msms"
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	572 if arguments["sample_type"] == COMPOUND_MIX:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	573 check_mix_compound_files(parameters)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	574 more_info_in_logs(parameters)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	575 return parameters
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	576
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	577 def check_mix_compound_files(parameters):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	578 arguments = parameters.arguments
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	579 try:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	580 numbarz = [
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	581 list(map(int, os.path.basename(metadata).split("_", 1)[0].split("-")))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	582 for metadata in arguments.raw_metadata
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	583 ]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	584 except ValueError:
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	585 ## file does not start with `[0-9]+-[0-9]+_.*`: probably
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	586 ## a ms2snoop file.
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	587 return
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	588 # parameters.logger.error(
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	589 # "Metadata/file names does not start with `[0-9]+-[0-9]+_.*` . "
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	590 # "This is necessary in the case of compounds mix."
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	591 # )
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	592 # sys.exit(-1)
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	593 runs, samples = zip(*numbarz)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	594 if not all(runs[0] == i for i in runs[1:]):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	595 parameters.logger.error(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	596 "Run numbers in metadata/file names are not identical. "
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	597 "You mixed some files."
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	598 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	599 sys.exit(-1)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	600 length = len(samples)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	601 if list(sorted(samples)) != list(range(1, length+1)):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	602 if not all(samples.count(i) == 1 for i in samples):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	603 parameters.logger.error("Some samples are duplicated. ")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	604 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	605 parameters.logger.error("Some samples files are missing. ")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	606 sys.exit(-1)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	607
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	608 def more_info_in_logs(config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	609 arguments = config.arguments
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	610 if arguments.embed_js:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	611 config.logger.info(f"JS will be embed in HTML page to form a HTML bundle.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	612 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	613 config.logger.info(f"JS are separated files, needed to be served.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	614 config.logger.info(f"Choosen parameters:")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	615 config.logger.info(f" - method: {arguments.method}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	616 config.logger.info(f" - peakforest instance: {arguments.peakforest.url}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	617 config.logger.info(f" - polarity instance: {arguments.polarity}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	618 config.logger.info(f" - spectrum type: {arguments.spectrum_type}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	619 config.logger.info(f" - scan type: {arguments.scan_type}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	620 config.logger.info(f" - produce JSON: {arguments.produce_json}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	621 config.logger.info(f" - sample type: {arguments.sample_type}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	622
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	623 def process_all_files(config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	624 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	625 for each file and its metadata, read and process them,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	626 then fills the meta html template file with the whole result.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	627 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	628 arguments = config.arguments
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	629 extra_defaults = [
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	630 process_fragnot_metadata(metadata, config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	631 for metadata in arguments.raw_metadata
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	632 ]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	633 for i, name in enumerate(arguments.name):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	634 extra_defaults[i]["name"] = name
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	635
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	636 if not extra_defaults:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	637 extra_defaults = [{}] * len(arguments.input)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	638
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	639 index = 0
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	640 for input_path, extra_default in zip(arguments.input, extra_defaults):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	641 config.logger.info(f"Processing file at {input_path}...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	642 curent_defaults = arguments.copy()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	643 curent_defaults.update(extra_default)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	644 if config.arguments.verbose:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	645 config.logger.info(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	646 "[VERBOSE] Defaults for curent file: "
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	647 + ';'.join(f"{key}={value}" for key, value in curent_defaults.items())
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	648 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	649 tsv_content, tsv_data_extractor = read_input(input_path, config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	650 index = process_tsv(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	651 tsv_content,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	652 tsv_data_extractor,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	653 config,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	654 defaults_data = curent_defaults,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	655 index = index+1,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	656 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	657 if arguments.embed_js:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	658 config.logger.info(f"Embeding JS in HTML file... ")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	659 for index in range(len(config.tab_list)):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	660 config.placeholders[EMBED_JS_PLACEHOLDER] += "<script type='text/javascript'>"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	661 with open(f"add-one-spectrum-{index+1}.js") as js_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	662 config.placeholders[EMBED_JS_PLACEHOLDER] += js_file.read()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	663 config.placeholders[EMBED_JS_PLACEHOLDER] += "</script>"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	664 config.placeholders[EMBED_JS_PLACEHOLDER] += "\n"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	665 config.logger.info(f" - add-one-spectrum-{index+1}.js embed.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	666 config.placeholders[TAB_LIST_PLACEHOLDER] = "\n".join(config.tab_list)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	667 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	668 config.placeholders[EMBED_JS_PLACEHOLDER] += "<script type='text/javascript'>"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	669 config.placeholders[EMBED_JS_PLACEHOLDER] += "</script>"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	670 config.placeholders[EMBED_JS_PLACEHOLDER] += "\n".join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	671 [""] + [
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	672 " "*12 + f"<script src=\"./add-one-spectrum-{index+1}.js\"></script>"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	673 for index in range(len(config.tab_list))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	674 ]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	675 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	676 config.placeholders[EMBED_JS_PLACEHOLDER] += "\n"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	677 config.placeholders[TAB_LIST_PLACEHOLDER] = "\n".join(config.tab_list)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	678
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	679 fill_template("meta_template", "pf_path", config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	680
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	681 def fill_template(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	682 template_name,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	683 output_name,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	684 config,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	685 additional_placeholders=dict()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	686 ):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	687 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	688 Fills a template, replaces the placeholders.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	689 Either outputs the result in a given file, or returns it if path is none.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	690 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	691 template_path = config[template_name]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	692 config.logger.debug(f"Filling template {template_name} at {template_path}...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	693 with open(template_path) as template_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	694 template_content = template_file.read()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	695 placeholders = config.placeholders.copy()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	696 placeholders.update(additional_placeholders)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	697 for placeholder, replacement in placeholders.items():
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	698 if not placeholder.startswith(config.templates.placeholders.start):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	699 placeholder = placeholder.join((
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	700 config.templates.placeholders.start,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	701 config.templates.placeholders.stop
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	702 ))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	703 template_content = template_content.replace(placeholder, replacement)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	704 if output_name is None:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	705 config.logger.debug(f"Returning template content")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	706 return template_content
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	707 output_path = config[output_name]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	708 if "{{ index }}" in output_path:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	709 index_value = additional_placeholders["{{ index }}"]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	710 config.logger.debug(f"Changing index value for {index_value}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	711 output_path = output_path.replace("{{ index }}", index_value)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	712 config.logger.debug(f"Full output path {output_path}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	713 with open(output_path, "w") as output_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	714 output_file.write(template_content)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	715
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	716 def read_input(input_path, config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	717 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	718 reads a tsv file and determin its processor, based on its header.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	719 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	720 with open(input_path) as input_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	721 config.logger.info(f"Reading {input_path}...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	722 tsv_file = csv.reader(input_file, delimiter='\t')
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	723 header = next(tsv_file)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	724 tsv_file = list(tsv_file)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	725 config.logger.info(f"Header is: {', '.join(header)}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	726 if header == list(FRAGNOT_HEADER):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	727 config.logger.info(f"Fragnot recognized.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	728 processor = fragnot_extractor
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	729 return uniformize_fragnot(tsv_file, header), processor
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	730 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	731 config.logger.info(f"MS2Snoop recognized.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	732 processor = ms2snoop_extractor
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	733 return uniformize_ms2snoop(tsv_file, header), processor
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	734
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	735 def uniformize_fragnot(content, header):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	736 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	737 sorts fragnot data so they appear always in the same order
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	738 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	739 return sorted(content, key=lambda x:(float(x[0]), float(x[4])))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	740
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	741 def uniformize_ms2snoop(content, header):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	742 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	743 sorts ms2snoop data so they appear always in the same order
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	744 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	745 return sorted(content, key=lambda x:(x[0], float(x[4])))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	746
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	747 def process_fragnot_metadata(raw_metadata, config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	748 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	749 Tries to extract informations from the metadata provided by fragnot
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	750 files names.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	751 Heavily based on regex defined in conf file.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	752 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	753 regex = config.regex.copy()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	754 del regex["values"]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	755 result = {}
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	756 config.logger.info(f"Extracting info from {raw_metadata}...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	757 count = 0
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	758 for name, expression in regex.items():
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	759 if (match := re.search(expression, raw_metadata)):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	760 result[name] = match[name]
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	761 count += 1
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	762 did = "+ did"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	763 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	764 did = "- did not"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	765 if config.arguments.verbose:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	766 config.logger.info(f" {did} match {expression}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	767 config.logger.info(f"{count} useful informations extracted.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	768 return result
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	769
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	770 def process_tsv(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	771 tsv_content,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	772 tsv_data_extractor,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	773 config,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	774 defaults_data={},
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	775 index=1
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	776 ):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	777 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	778 processes one tsv file, containing one or multiple compounds.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	779 Creation of the peak table for each compound
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	780 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	781 tsv_content = list(tsv_content)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	782 curent_name, ms_data = get_ms_data(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	783 tsv_content[0],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	784 tsv_data_extractor,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	785 defaults_data,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	786 config
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	787 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	788 _, second_ms_data = get_ms_data(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	789 tsv_content[1],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	790 tsv_data_extractor,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	791 defaults_data,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	792 config
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	793 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	794 ms_peak_table = []
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	795 config.logger.info(f"Processing compound {curent_name}...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	796
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	797 for line in tsv_content:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	798 name, new_ms_data = get_ms_data(line, tsv_data_extractor, defaults_data, config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	799 if name != curent_name:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	800 new_compound(curent_name, index, ms_data, config, ms_peak_table)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	801 curent_name = name
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	802 index += 1
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	803 config.logger.info(f"Processing compound {curent_name}...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	804 ms_peak_table = []
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	805 ms_data = new_ms_data
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	806 ms_peak_table.append(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	807 ", ".join(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	808 f'"{value}"' if value not in ("na", "NA")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	809 else '""'
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	810 for value in (
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	811 ms_data["fragment_mz"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	812 ms_data["abs_intensity"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	813 ms_data["rel_intensity"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	814 ms_data["ppm"],
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	815 ms_data["fragment"],
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	816 ms_data["composition"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	817 str(ms_data["valid_corelation"] == "TRUE").lower(),
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	818 "true" if ms_data.get("correlation") == "1" else "false"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	819 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	820 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	821 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	822 new_compound(curent_name, index, ms_data, config, ms_peak_table)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	823 return index
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	824
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	825 def get_ms_data(line, extractor, defaults, config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	826 ms_data = defaults.copy()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	827 ms_data.update(extractor(config, *line))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	828 return ms_data["name"], ms_data
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	829
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	830 def new_compound(name, index, ms_data, config, ms_peak_table):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	831 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	832 aggregates informations to form the peak table,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	833 adds the compound to the tab list,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	834 creates the js file for this tab
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	835 """
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	836 ignore_multiple_parent_ion(ms_peak_table)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	837 determine_min_max_mz(ms_peak_table)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	838 guess_relative_intensities(ms_peak_table)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	839 accept_all_fragments_if_all_false(ms_peak_table)
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	840 config.placeholders[MS_PEAK_VALUES_PLACEHOLDER] = f"""[
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	841 {','.join('['+line+']' for line in ms_peak_table)}
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	842 ]"""
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	843 tab_list = fill_template(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	844 "tab_list_template",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	845 None,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	846 config, {
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	847 COMPOUND_NAME_PLACEHOLDER: name,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	848 TAB_INDEX_PLACEHOLDER: str(index),
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	849 })
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	850 config.tab_list.append(tab_list)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	851 create_js_file(index, ms_data, config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	852 config.placeholders[ADD_SPECTRUM_FORM] += fill_template(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	853 "form_template",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	854 None,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	855 config,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	856 {TAB_INDEX_PLACEHOLDER: str(index)},
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	857 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	858 if index == 1:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	859 config.placeholders[ACTIVE_TAB_PLACEHOLDER] = ""
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	860
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	861 def determine_min_max_mz(ms_peak_table):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	862 mz_list = [
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	863 float(ms_peak_table[i].split(", ")[0].strip("\""))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	864 for i in range(len(ms_peak_table))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	865 ]
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	866 config.placeholders["DEFAULT_MIN_MZ"] = str(min(mz_list))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	867 config.placeholders["DEFAULT_MAX_MZ"] = str(max(mz_list))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	868
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	869 def guess_relative_intensities(ms_peak_table):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	870 if all(
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	871 ms_peak_table[i].split(", ")[2].strip("\"") == ""
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	872 for i in range(len(ms_peak_table))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	873 ):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	874 absolute_intensities = [
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	875 float(ms_peak_table[i].split(", ")[1].strip("\""))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	876 for i in range(len(ms_peak_table))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	877 ]
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	878 greatest = float(max(absolute_intensities))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	879 relative_intensities = [
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	880 intensity / greatest * 100
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	881 for intensity in absolute_intensities
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	882 ]
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	883 replace_ms_table_value(ms_peak_table, 2, relative_intensities)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	884
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	885 def ignore_multiple_parent_ion(ms_peak_table):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	886 if len([
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	887 None for x in ms_peak_table
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	888 if x.split(", ")[7].strip("\"") == "true"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	889 ]) > 1:
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	890 ## if more than one is the precursor, then none is the precursor
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	891 replace_ms_table_value(ms_peak_table, 7, "\"false\"")
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	892
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	893 def accept_all_fragments_if_all_false(ms_peak_table):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	894 if all(
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	895 ms_peak_table[i].split(", ")[6].strip("\"") == "false"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	896 for i in range(len(ms_peak_table))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	897 ):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	898 replace_ms_table_value(ms_peak_table, 6, "true")
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	899
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	900 def replace_ms_table_value(ms_peak_table, index, value, sep=", "):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	901 length = len(ms_peak_table)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	902 if not isinstance(value, list):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	903 if isinstance(value, str):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	904 value = [value.join('""')] * length
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	905 else:
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	906 value = [str(value)] * length
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	907 if not isinstance(value[0], str):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	908 value = [str(x) for x in value]
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	909 count = ms_peak_table[0].count(sep)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	910 endindex = count - index
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	911 neg_endindex = -endindex
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	912 for i in range(length):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	913 ms_peak_table[i] = sep.join((
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	914 *ms_peak_table[i].split(sep, index)[:index],
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	915 value[i],
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	916 *ms_peak_table[i].rsplit(sep, endindex)[neg_endindex:]
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	917 ))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	918
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	919 def fragnot_extractor(config, *line):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	920 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	921 Fragnot processor - extracts one fragnot line of content and
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	922 produces a uniformised output.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	923 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	924 fragnot_data = {
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	925 FRAGNOT_HEADER[header]: line[i].strip()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	926 for i, header in enumerate(FRAGNOT_HEADER)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	927 }
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	928 # fragnot_data["composition"] = "unknown"
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	929 fragnot_data["valid_corelation"] = config.arguments.validation
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	930 return fragnot_data
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	931
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	932 def ms2snoop_extractor(config, *line):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	933 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	934 Fragnot processor - extracts one ms2snoop line of content and
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	935 produces a uniformised output.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	936 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	937 ms2snoop_data = {
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	938 header: MS_2_SNOOP_HEADER[header](line[i])
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	939 for i, header in enumerate(MS_2_SNOOP_HEADER)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	940 }
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	941 return ms2snoop_data
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	942
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	943 def create_js_file(index, ms_data, config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	944 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	945 fills the js template file for one tab (compound)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	946 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	947 if (method := ms_data["method"]):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	948 method = f'"{method}"'
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	949 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	950 method = "null"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	951 if config.arguments.verbose:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	952 config.logger.info(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	953 "[VERBOSE] "
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	954 + ';'.join(f"{key}={value}" for key, value in ms_data.items())
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	955 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	956 fill_template(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	957 "js_template",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	958 "js_file",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	959 config,
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	960 {
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	961 TAB_INDEX_PLACEHOLDER: str(index),
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	962 "INCHIKEY_PLACEHOLDER": ms_data["inchikey"],
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	963 "DEFAULT_DATA": f"""{{
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	964 name: "{ms_data["name"]}",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	965 inchikey: "{ms_data["inchikey"]}",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	966 method: {method},
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	967 spectrum_type: "{ms_data["spectrum_type"]}",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	968 scan_type: "{ms_data["scan_type"]}",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	969 polarity: "{ms_data["polarity"]}",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	970 resolution: "{ms_data["resolution"]}",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	971 sample_type: "{ms_data["sample_type"]}",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	972 }}""",
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	973 "{{ index }}": str(index)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	974 },
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	975 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	976
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	977 def prepare_workplace(config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	978 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	979 prepares the directory we will work in.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	980 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	981 if config.workdir.work_in_tmp:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	982 os.chdir(config.workdir.tmp_dir)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	983 config.logger.info(f"Moving to {os.getcwd()}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	984 if config.workdir.generate_in_tmp:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	985 gen_dir = config.workdir.tmp_dir
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	986 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	987 gen_dir = tempfile.gettempdir()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	988 config.workdir.tmp_dir = gen_dir
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	989 shutil.copy(os.path.join(config["root_dir"], "src", "common.js"), gen_dir)
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	990 config.logger.info(f"Outputs will be generated in {config.workdir.tmp_dir}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	991 return gen_dir
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	992
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	993 def get_hander_for(directory, config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	994 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	995 generates the handler class for the directory we provide.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	996 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	997 config["json_result"] = [{}] * len(config.tab_list)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	998
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	999 class HTTPHandler(http.server.SimpleHTTPRequestHandler):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1000
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1001 def __init__(self, args, *kwargs):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1002 super().__init__(args, *kwargs, directory=directory)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1003
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1004 def do_POST(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1005 content_length = int(self.headers.get("Content-Length"))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1006 json_bytes = self.rfile.read(content_length).decode("utf-8")
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1007 # json_list = json.loads(json_bytes)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1008 # for i, obj in enumerate(json_list):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1009 # print(obj)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1010 # if obj:
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1011 # config["json_result"][i] = obj
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1012 json_obj = json.loads(json_bytes)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1013 config["json_result"][json_obj["index"]] = json_obj["object"]
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1014 save_json(config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1015 self.send_head()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1016 self.wfile.write(json_bytes.encode("utf-8"))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1017 return
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1018
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1019 def do_GET(self):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1020 if self.path == "/quit":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1021 self.path = "/"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1022 super().do_GET()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1023 exit(0)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1024 self.path = os.path.join(directory, self.path)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1025 if self.path == "/":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1026 self.path = config.generated.html
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1027 return super().do_GET()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1028
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1029 return HTTPHandler
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1030
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1031
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1032 def save_json(config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1033 json_string = json.dumps(config["json_result"])
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1034 print(json_string)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1035 with open(config.arguments.output_json, "w") as json_file:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1036 json_file.write(json_string)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1037
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1038 def run_server(config):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1039 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1040 prepare and runs the server, with the handler for the given directory
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1041 """
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1042 ip, port = config.arguments.ip, int(config.arguments.port)
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1043 config.logger.debug(f"IP and port: {ip}:{port}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1044 socketserver.TCPServer.allow_reuse_address = True
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1045 config.logger.debug(f"Allow reuse adress.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1046 handler = get_hander_for(config.workdir.tmp_dir, config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1047 config.logger.debug(f"Created server handler for {config.workdir.tmp_dir}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1048 config.logger.debug(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1049 f"Content of directory {config.workdir.tmp_dir}: "
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1050 + "\n"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1051 + '\n'.join(sorted(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1052 f" - {path}"for path in os.listdir(config.workdir.tmp_dir)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1053 ))
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1054 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1055 config.logger.debug(f"Creating TCP server...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1056 server = socketserver.TCPServer((ip, port), handler)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1057 if ip == "0.0.0.0":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1058 displayed_ip = "localhost"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1059 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1060 displayed_ip = ip
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1061 config.logger.debug(f"Serving...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1062 print()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1063 print(f"http://{displayed_ip}:{port}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1064 server.serve_forever()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1065
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1066 def get_logger(config, dummy=False):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1067 dummy_log = lambda msg:dummy and config.logger.info(msg)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1068 arguments = config.arguments
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1069 if not dummy:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1070 logger = logging.getLogger(__file__)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1071 if arguments.debug:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1072 dummy_log(f"Output debug info.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1073 level = logging.DEBUG
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1074 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1075 level = logging.INFO
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1076 if not dummy:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1077 logger.setLevel(level)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1078 formatter = logging.Formatter(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1079 "%(asctime)s - %(levelname)s - %(message)s"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1080 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1081 if arguments.logging.std == "err":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1082 dummy_log(f"Handler added to output logs in stderr.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1083 if not dummy:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1084 handler = logging.StreamHandler(sys.stderr)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1085 handler.setLevel(level)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1086 handler.setFormatter(formatter)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1087 logger.addHandler(handler)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1088 elif arguments.logging.std == "out":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1089 dummy_log(f"Handler added to output logs in stdout.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1090 if not dummy:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1091 handler = logging.StreamHandler(sys.stdout)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1092 handler.setLevel(level)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1093 handler.setFormatter(formatter)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1094 logger.addHandler(handler)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1095 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1096 dummy_log(f"Logs will not be output in stderr not stdout.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1097 if (path := arguments.logging.file.path):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1098 dummy_log(f"Add log file: {arguments.logging.file.path}.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1099 if not arguments.logging.file.append:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1100 dummy_log(f"Log file content cleaned.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1101 with open(path, "w"):pass
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1102 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1103 dummy_log(f"Logs appended to log file.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1104 if not dummy:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1105 file_handler = logging.FileHandler(filename=path)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1106 file_handler.setLevel(level)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1107 file_handler.setFormatter(formatter)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1108 logger.addHandler(file_handler)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1109 if not dummy:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1110 config["logger"] = logger
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1111 starting_sequence(logger)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1112 get_logger(config, dummy=True)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1113 return logger
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1114
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1115 def starting_sequence(logger):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1116 logger.info("bip bop")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1117 logger.info("starting...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1118 logger.info("program...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1119 logger.info("MS2PF is running...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1120 logger.info("bip bop am a robot")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1121 atexit.register(stoping_sequence, logger)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1122
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1123 def stoping_sequence(logger):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1124 logger.info("bip bop")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1125 logger.info("ending...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1126 logger.info("program...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1127 logger.info("MS2PF is shuting down...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1128 logger.info("...robot")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1129 logger.info("bip bop")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1130 logger.info("shutdown")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1131 logger.info("...")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1132
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1133 if __name__ == "__main__":
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1134 print(os.listdir("test-data"))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1135
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1136 if not os.path.exists("config.yml"):
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1137 shutil.copy("config.default.yml", "config.yml")
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1138
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1139 base_config = parse_config()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1140 config = parse_parameters(base_config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1141
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1142 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1143 The config contains result of the parsed config file.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1144 """
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1145 arguments = config.arguments
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1146
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1147 if arguments.pid:
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1148 print(arguments.pid)
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1149 with open(arguments.pid, "w") as pid_file:
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1150 pid_file.write(str(os.getpid()))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1151 atexit.register(lambda:os.unlink(arguments.pid))
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	1152
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1153 config.logger.info(f"Starting MS2PF from {os.getcwd()}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1154
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1155 gen_dir = prepare_workplace(config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1156
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1157 config["pf_path"] = os.path.join(gen_dir, config.generated.html)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1158 config.logger.info(f"HTML output file will be {config.pf_path}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1159 config["js_file"] = os.path.join(gen_dir, config.generated.js)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1160 config.logger.info(f"JS output files will like {config.js_file}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1161 config.placeholders["PF_URL_PLACEHOLDER"] = arguments.peakforest.url
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1162 config.placeholders["PF_TOKEN_PLACEHOLDER"] = (
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1163 arguments.peakforest.token
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1164 or config.token.value
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1165 )
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1166 if (token := config.placeholders.PF_TOKEN_PLACEHOLDER):
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1167 config.logger.info(f"Using a token for authentification - length: {len(token)}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1168 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1169 config.logger.info(f"No token provided for peakforest authentification.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1170
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1171 process_all_files(config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1172
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1173 if not arguments.do_run_dry:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1174 config.logger.debug(f"Running the server.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1175 if arguments.firefox or arguments.chromium:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1176 config.logger.debug(f"Running the server.")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1177 import threading
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1178 import time
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1179 if arguments.firefox:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1180 browser = "firefox"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1181 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1182 browser = "chromium"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1183 if (ip := config.network.ip) == "0.0.0.0":
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1184 ip = "localhost"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1185 adress = f"http://{ip}:{config.network.port}"
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1186 threading.Thread(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1187 target=lambda:(
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1188 time.sleep(1),
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1189 os.system(f"{browser} {adress}")
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1190 ),
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1191 daemon=True
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1192 ).start()
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1193 run_server(config)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1194 else:
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1195 config.logger.debug(f"Server not run.")

Mercurial > repos > lain > ms_to_peakforest_it

annotate server.py @ 1:7e3085fc60c1 draft default tip