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annotate generate_test.py @ 4:bd5ffc799c16 draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
author tduigou
date Mon, 15 Sep 2025 12:57:08 +0000
parents cfa70e3fe1a4
children
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
parents:
diff changeset
1 import hashlib
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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2 import subprocess
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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3 import tempfile
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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4 from typing import List
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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7 def compute_md5(path: str):
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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8 hash_md5 = hashlib.md5()
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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9 with open(path, "rb") as f:
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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10 for chunk in iter(lambda: f.read(4096), b""):
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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11 hash_md5.update(chunk)
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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12 return hash_md5.hexdigest()
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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15 def run_cmd(subcommand: str, sub_cmd: List):
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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16 with tempfile.NamedTemporaryFile() as fd:
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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17 cmd = ["python", "query.py"]
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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18 cmd.append(subcommand)
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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19 cmd.append("--output-data-json")
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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20 cmd.append(fd.name)
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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21 cmd.extend(sub_cmd)
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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23 print("Cmd:", " ".join(cmd))
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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24 ret = subprocess.run(cmd)
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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25 if ret.returncode != 0:
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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26 msg = f"Command failed: {' '.join(cmd)}\n"
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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27 if ret.stdout:
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
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28 msg += "Stdout:", ret.stdout + "\n"
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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29 if ret.stderr:
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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30 msg += "Stderr:", ret.stderr + "\n"
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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31 raise Exception()
0
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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33 return compute_md5(path=fd.name)
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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36 if __name__ == "__main__":
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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38 print("=" * 50)
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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39 print("templates")
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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40 smarts_str = "[O]-[C](=[O])"
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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41 cmd = ["--input-smarts-str", smarts_str, "--input-limit-int", "5"]
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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42 value = run_cmd(subcommand="templates", sub_cmd=cmd)
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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43 print("Test:", " ".join(cmd), "md5:", value)
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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45 print("=" * 50)
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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47 print("templates-summary")
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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48 template_id = "RR:03-27BC85-19184A-A71018"
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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49 cmd = ["--input-template-id-str", template_id]
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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50 value = run_cmd(subcommand="templates-summary", sub_cmd=cmd)
0
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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51 print("Test:", " ".join(cmd), "md5:", value)
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
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53 print("=" * 50)
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
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55 print("templates-sources")
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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56 template_id = "RR:03-27BC85-19184A-A71018"
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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57 cmd = ["--input-template-id-str", template_id]
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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58 value = run_cmd(subcommand="templates-sources", sub_cmd=cmd)
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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59 print("Test:", " ".join(cmd), "md5:", value)
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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61 print("=" * 50)
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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63 print("templates-count")
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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64 smarts_str = "[O]-[C](=[O])"
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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65 cmd = ["--input-smarts-str", smarts_str]
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bd5ffc799c16 planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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66 value = run_cmd(subcommand="templates-count", sub_cmd=cmd)
0
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
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67 print("Test:", " ".join(cmd), "md5:", value)
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
parents:
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55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
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69 print("=" * 50)
3
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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70 """
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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71 print("templates-export")
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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72 smarts_str = "[O]-[C](=[O])"
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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73 cmd = ["--input-smarts-str", smarts_str]
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
parents: 0
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74 value = run_cmd(subcommand="templates-export", sub_cmd=cmd)
0
55307a982baf planemo upload for repository https://github.com/brsynth/galaxytools commit a78c222aa38bc456809ade9fa22eb4b887185efd
tduigou
parents:
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75 print("Test:", " ".join(cmd), "md5:", value)
3
cfa70e3fe1a4 planemo upload for repository https://github.com/brsynth/galaxytools commit 09bda59fbe67d1546dc4f04a2a2a8672d520b194-dirty
tduigou
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76 """