Extract tools from curated workflows and upload a first JSON with tools #20
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agnesbrnb
commented
Nov 7, 2025
agnesbrnb
commented
- Script to extract tools from curated workflows
- Upload a first JSON with tools extract from the 62 workflows kept after manual curation. Since tools name could be extracted from WorkflowHub steps description, the JSON file will need some curation.
bebatut
reviewed
Jan 5, 2026
Contributor
There was a problem hiding this comment.
Thanks a lot @agnesbrnb. Looks great. I only put one comment
Comment on lines
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| matches_topic = set(self.edam_topic) & set(edam_keywords["topics"]) | ||
| matches_operation = set(self.edam_operation) & set(edam_keywords["operations"]) | ||
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| if len(matches_topic) != 0 or len(matches_operation) != 0: | ||
| self.filtered_on = "edam" | ||
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| return len(matches_topic) != 0 or len(matches_operation) != 0 |
Contributor
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Could you create a has_edam_terms function in utils.py:
def has_edam_terms(edam_topics, edam_operations, edam_keywords):
matches_topic = set(edam_topic) & set(edam_keywords["topics"])
matches_operation = set(edam_operations) & set(edam_keywords["operations"])
return len(matches_topic) != 0 or len(matches_operation) != 0
And change the function here as:
has_edam_terms = utils.has_edam_terms(self.edam_topic, self.edam_operation, edam_keywords)
if has_edam_terms:
self.filtered_on = "edam"
return has_edam_terms
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