Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/verify/test_data.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import hashlib |
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2 import os |
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3 import re |
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4 import subprocess |
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5 from string import Template |
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6 |
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7 from galaxy.util import ( |
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8 asbool, |
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9 in_directory, |
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10 smart_str |
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11 ) |
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12 |
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13 UPDATE_TEMPLATE = Template( |
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14 "git --work-tree $dir --git-dir $dir/.git fetch && " |
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15 "git --work-tree $dir --git-dir $dir/.git merge origin/master" |
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16 ) |
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17 |
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18 UPDATE_FAILED_TEMPLATE = Template( |
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19 "Warning failed to update test repository $dir - " |
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20 "update stdout was [$stdout] and stderr was [$stderr]." |
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21 ) |
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22 |
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23 |
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24 LIST_SEP = re.compile(r"\s*,\s*") |
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25 |
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26 |
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27 class TestDataResolver: |
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28 |
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29 def __init__(self, file_dirs=None, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ): |
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30 if file_dirs is None: |
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31 file_dirs = environ.get(env_var, None) |
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32 if file_dirs is None: |
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33 file_dirs = "test-data,https://github.com/galaxyproject/galaxy-test-data.git" |
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34 if file_dirs: |
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35 self.resolvers = [build_resolver(u, environ) for u in LIST_SEP.split(file_dirs)] |
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36 else: |
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37 self.resolvers = [] |
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38 |
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39 def get_filename(self, name): |
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40 for resolver in self.resolvers or []: |
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41 if not resolver.exists(name): |
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42 continue |
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43 filename = resolver.path(name) |
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44 if filename: |
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45 return os.path.abspath(filename) |
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46 |
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47 def get_filecontent(self, name): |
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48 filename = self.get_filename(name=name) |
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49 with open(filename, mode='rb') as f: |
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50 return f.read() |
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51 |
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52 def get_directory(self, name): |
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53 return self.get_filename(name=name) |
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54 |
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55 |
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56 def build_resolver(uri, environ): |
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57 if uri.startswith("http") and uri.endswith(".git"): |
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58 return GitDataResolver(uri, environ) |
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59 else: |
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60 return FileDataResolver(uri) |
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61 |
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62 |
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63 class FileDataResolver: |
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64 |
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65 def __init__(self, file_dir): |
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66 self.file_dir = file_dir |
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67 |
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68 def exists(self, filename): |
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69 path = os.path.abspath(self.path(filename)) |
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70 return os.path.exists(path) and in_directory(path, self.file_dir) |
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71 |
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72 def path(self, filename): |
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73 return os.path.join(self.file_dir, filename) |
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74 |
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75 |
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76 class GitDataResolver(FileDataResolver): |
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77 |
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78 def __init__(self, repository, environ): |
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79 self.repository = repository |
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80 self.updated = False |
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81 repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-cache") |
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82 m = hashlib.md5() |
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83 m.update(smart_str(repository)) |
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84 repo_path = os.path.join(repo_cache, m.hexdigest()) |
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85 super().__init__(repo_path) |
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86 # My preference would be for this to be false, but for backward compat |
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87 # will leave it as true for now. |
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88 self.fetch_data = asbool(environ.get("GALAXY_TEST_FETCH_DATA", "true")) |
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89 |
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90 def exists(self, filename): |
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91 exists_now = super().exists(filename) |
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92 if exists_now or not self.fetch_data or self.updated: |
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93 return exists_now |
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94 self.update_repository() |
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95 return super().exists(filename) |
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96 |
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97 def update_repository(self): |
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98 self.updated = True |
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99 if not os.path.exists(self.file_dir): |
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100 parent_dir = os.path.dirname(self.file_dir) |
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101 if not os.path.exists(parent_dir): |
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102 os.makedirs(parent_dir) |
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103 self.execute(f"git clone '{self.repository}' '{self.file_dir}'") |
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104 update_command = UPDATE_TEMPLATE.safe_substitute(dir=self.file_dir) |
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105 self.execute(update_command) |
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106 |
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107 def execute(self, cmd): |
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108 subprocess_kwds = dict( |
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109 shell=True, |
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110 stdout=subprocess.PIPE, |
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111 stderr=subprocess.PIPE, |
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112 ) |
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113 print("Executing %s" % cmd) |
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114 p = subprocess.Popen(cmd, **subprocess_kwds) |
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115 stdout, stderr = p.communicate() |
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116 if p.returncode != 0: |
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117 kwds = { |
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118 'dir': self.file_dir, |
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119 'stdout': stdout, |
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120 'stderr': stderr, |
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121 } |
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122 print(UPDATE_FAILED_TEMPLATE.substitute(**kwds)) |