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annotate generate_test.py @ 4:815748762646 draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools commit d7030c1af6fe06a1d45af115756ee775721e39b5
author tduigou
date Thu, 02 Oct 2025 14:27:31 +0000
parents 95b4196b4ded
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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1 import hashlib
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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2 import subprocess
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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3 import tempfile
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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4 from typing import List
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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7 def compute_md5(path: str):
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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8 hash_md5 = hashlib.md5()
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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9 with open(path, "rb") as f:
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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10 for chunk in iter(lambda: f.read(4096), b""):
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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11 hash_md5.update(chunk)
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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12 return hash_md5.hexdigest()
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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15 def run_cmd(subcommand: str, sub_cmd: List):
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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16 with tempfile.NamedTemporaryFile() as fd:
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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17 cmd = ["python", "query.py"]
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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18 cmd.append(subcommand)
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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19 cmd.append("--output-data-json")
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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20 cmd.append(fd.name)
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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21 cmd.extend(sub_cmd)
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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23 print("Cmd:", " ".join(cmd))
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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24 ret = subprocess.run(cmd)
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95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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25 if ret.returncode != 0:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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26 msg = f"Command failed: {' '.join(cmd)}\n"
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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27 if ret.stdout:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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28 msg += "Stdout:", ret.stdout + "\n"
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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29 if ret.stderr:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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30 msg += "Stderr:", ret.stderr + "\n"
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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31 raise Exception()
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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33 return compute_md5(path=fd.name)
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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36 if __name__ == "__main__":
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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38 print("=" * 50)
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95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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39 print("templates")
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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40 smarts_str = "[O]-[C](=[O])"
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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41 cmd = ["--input-smarts-str", smarts_str, "--input-limit-int", "5"]
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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42 value = run_cmd(subcommand="templates", sub_cmd=cmd)
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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43 print("Test:", " ".join(cmd), "md5:", value)
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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45 print("=" * 50)
3
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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47 print("templates-summary")
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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48 template_id = "RR:03-27BC85-19184A-A71018"
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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49 cmd = ["--input-template-id-str", template_id]
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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50 value = run_cmd(subcommand="templates-summary", sub_cmd=cmd)
0
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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51 print("Test:", " ".join(cmd), "md5:", value)
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815748762646 planemo upload for repository https://github.com/brsynth/galaxytools commit d7030c1af6fe06a1d45af115756ee775721e39b5
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53 print("=" * 50)
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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55 print("templates-sources")
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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56 template_id = "RR:03-27BC85-19184A-A71018"
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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57 cmd = ["--input-template-id-str", template_id]
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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58 value = run_cmd(subcommand="templates-sources", sub_cmd=cmd)
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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59 print("Test:", " ".join(cmd), "md5:", value)
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815748762646 planemo upload for repository https://github.com/brsynth/galaxytools commit d7030c1af6fe06a1d45af115756ee775721e39b5
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61 print("=" * 50)
4
815748762646 planemo upload for repository https://github.com/brsynth/galaxytools commit d7030c1af6fe06a1d45af115756ee775721e39b5
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62
3
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63 print("templates-count")
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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64 smarts_str = "[O]-[C](=[O])"
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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65 cmd = ["--input-smarts-str", smarts_str]
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
parents: 0
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66 value = run_cmd(subcommand="templates-count", sub_cmd=cmd)
0
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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67 print("Test:", " ".join(cmd), "md5:", value)
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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69 print("=" * 50)
3
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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70 """
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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71 print("templates-export")
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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72 smarts_str = "[O]-[C](=[O])"
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
parents: 0
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73 cmd = ["--input-smarts-str", smarts_str]
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
parents: 0
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74 value = run_cmd(subcommand="templates-export", sub_cmd=cmd)
0
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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75 print("Test:", " ".join(cmd), "md5:", value)
4
815748762646 planemo upload for repository https://github.com/brsynth/galaxytools commit d7030c1af6fe06a1d45af115756ee775721e39b5
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76 """