Mercurial > repos > iuc > data_manager_selection_background

annotate data_manager/data_manager_selection_background.py @ 3:10ac95ec81d9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
author iuc
date Wed, 25 Aug 2021 21:07:59 +0000
parents e4f07770b340
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
1 # -*- coding: utf-8 -*-
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
2 import argparse
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
3 import bz2
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
4 import gzip
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
5 import json
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
6 import os
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
7 import shutil
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
8 import sys
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
9 import uuid
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
10 import zipfile
1
0bd1cd5eac51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 56142b399aae44a46fb6a588603eda2286cf73b2"
iuc
parents: 0
diff changeset
11 from urllib.request import urlretrieve
0
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
12
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
13 # Nice solution to opening compressed files (zip/bz2/gz) transparently
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
14 # https://stackoverflow.com/a/13045892/638445
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
15
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
16
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
17 class CompressedFile(object):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
18 magic = None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
19 file_type = None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
20 mime_type = None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
21 proper_extension = None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
22
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
23 def __init__(self, f):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
24 # f is an open file or file like object
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
25 self.f = f
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
26 self.accessor = self.open()
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
27
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
28 @classmethod
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
29 def is_magic(self, data):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
30 return data.startswith(self.magic)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
31
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
32 def open(self):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
33 return None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
34
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
35
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
36 class ZIPFile(CompressedFile):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
37 magic = '\x50\x4b\x03\x04'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
38 file_type = 'zip'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
39 mime_type = 'compressed/zip'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
40
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
41 def open(self):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
42 return zipfile.ZipFile(self.f)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
43
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
44
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
45 class BZ2File(CompressedFile):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
46 magic = '\x42\x5a\x68'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
47 file_type = 'bz2'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
48 mime_type = 'compressed/bz2'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
49
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
50 def open(self):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
51 return bz2.BZ2File(self.f)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
52
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
53
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
54 class GZFile(CompressedFile):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
55 magic = '\x1f\x8b\x08'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
56 file_type = 'gz'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
57 mime_type = 'compressed/gz'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
58
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
59 def open(self):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
60 return gzip.GzipFile(self.f)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
61
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
62
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
63 # factory function to create a suitable instance for accessing files
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
64 def get_compressed_file(filename):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
65 with open(filename, 'rb') as f:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
66 start_of_file = f.read(1024)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
67 f.seek(0)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
68 for cls in (ZIPFile, BZ2File, GZFile):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
69 if cls.is_magic(start_of_file):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
70 f.close()
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
71 return cls(filename)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
72
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
73 return None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
74
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
75
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
76 def url_download(url):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
77 """Attempt to download gene annotation file from a given url
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
78 :param url: full url to gene annotation file
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
79 :type url: str.
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
80 :returns: name of downloaded gene annotation file
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
81 :raises: ContentDecodingError, IOError
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
82 """
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
83
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
84 # Generate file_name
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
85 file_name = url.split('/')[-1]
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
86
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
87 try:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
88 # download URL (FTP and HTTP work, probably local and data too)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
89 urlretrieve(url, file_name)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
90
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
91 # uncompress file if needed
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
92 cf = get_compressed_file(file_name)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
93 if cf is not None:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
94 uncompressed_file_name = os.path.splitext(file_name)[0]
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
95 with open(uncompressed_file_name, 'w+') as uncompressed_file:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
96 shutil.copyfileobj(cf.accessor, uncompressed_file)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
97 os.remove(file_name)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
98 file_name = uncompressed_file_name
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
99 except IOError as e:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
100 sys.stderr.write('Error occured downloading reference file: %s' % e)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
101 os.remove(file_name)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
102 return file_name
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
103
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
104
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
105 def main():
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
106 parser = argparse.ArgumentParser(description='Create data manager JSON.')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
107 parser.add_argument('--output', dest='output', action='store', required=True, help='JSON filename')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
108 parser.add_argument('--dbkey', dest='dbkey', action='store', default=uuid.uuid4(), help='Data table entry unique ID')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
109 parser.add_argument('--label', dest='label', action='store', required=True, help='Label to display')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
110 parser.add_argument('--uri', dest='uri', action='store', help='URI for the sequences')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
111 parser.add_argument('--dataset', dest='dataset', action='store', help='Path for the sequences')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
112
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
113 args = parser.parse_args()
3
10ac95ec81d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
iuc
parents: 2
diff changeset
114 dbkey = str(args.dbkey)
0
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
115
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
116 if args.uri is not None:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
117 background_fasta = url_download(args.uri)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
118 else:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
119 background_fasta = args.dataset
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
120
3
10ac95ec81d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
iuc
parents: 2
diff changeset
121 with open(args.output) as fh:
10ac95ec81d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
iuc
parents: 2
diff changeset
122 params = json.load(fh)
10ac95ec81d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
iuc
parents: 2
diff changeset
123 target_directory = params['output_data'][0]['extra_files_path']
10ac95ec81d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
iuc
parents: 2
diff changeset
124 os.makedirs(target_directory, exist_ok=True)
10ac95ec81d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
iuc
parents: 2
diff changeset
125 table_entry = '%s.fa' % dbkey
10ac95ec81d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
iuc
parents: 2
diff changeset
126 shutil.copy(background_fasta, os.path.join(target_directory, table_entry))
0
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
127
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
128 # Update Data Manager JSON and write to file
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
129 data_manager_entry = {
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
130 'data_tables': {
3
10ac95ec81d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
iuc
parents: 2
diff changeset
131 'selection_background': {'value': dbkey, 'label': args.label, 'path': table_entry}
0
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
132 }
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
133 }
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
134
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
135 with open(os.path.join(args.output), 'w+') as fh:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
136 json.dump(data_manager_entry, fh, sort_keys=True)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
137
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
138
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
139 if __name__ == '__main__':
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
140 main()