From 4ee41c7832dc8c697d900e61a30f644ef5fc1ba3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Thu, 7 Nov 2024 11:01:13 +0100 Subject: [PATCH] Fix wf and tutorial extraction --- sources/bin/extract_all_tutorials.sh | 2 +- sources/bin/extract_all_workflows.sh | 2 +- sources/bin/shared.py | 10 +++++----- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/sources/bin/extract_all_tutorials.sh b/sources/bin/extract_all_tutorials.sh index 3a9cbd37..67af83f3 100644 --- a/sources/bin/extract_all_tutorials.sh +++ b/sources/bin/extract_all_tutorials.sh @@ -5,7 +5,7 @@ then python sources/bin/extract_gtn_tutorials.py \ extract \ --all "communities/all/resources/test_tutorials.json" \ - --tools "communities/all/resources/tools.json" \ + --tools "communities/all/resources/test_tools.json" \ --api $PLAUSIBLE_API_KEY \ --test else diff --git a/sources/bin/extract_all_workflows.sh b/sources/bin/extract_all_workflows.sh index c89e79b4..09f64727 100644 --- a/sources/bin/extract_all_workflows.sh +++ b/sources/bin/extract_all_workflows.sh @@ -4,7 +4,7 @@ if [ ! -z $1 ] then python sources/bin/extract_galaxy_workflows.py extract \ --all communities/all/resources/test_workflows.json \ - --tools communities/all/resources/tools.json \ + --tools communities/all/resources/test_tools.json \ --test else python sources/bin/extract_galaxy_workflows.py extract \ diff --git a/sources/bin/shared.py b/sources/bin/shared.py index 611436bc..a804502a 100644 --- a/sources/bin/shared.py +++ b/sources/bin/shared.py @@ -83,11 +83,11 @@ def read_suite_per_tool_id(tool_fp: str) -> Dict: tool_suites = load_json(tool_fp) tools = {} for suite in tool_suites: - for tool in suite["Galaxy tool ids"]: + for tool in suite["Suite ID"]: tools[tool] = { - "Galaxy wrapper id": suite["Galaxy wrapper id"], - "Galaxy wrapper owner": suite["Galaxy wrapper id"], - "EDAM operation": suite["EDAM operation"], + "Suite ID": suite["Suite ID"], + "Suite owner": suite["Suite owner"], + "EDAM operations": suite["EDAM operations"], } return tools @@ -154,7 +154,7 @@ def get_edam_operation_from_tools(selected_tools: list, all_tools: dict) -> List edam_operation = set() for t in selected_tools: if t in all_tools: - edam_operation.update(set(all_tools[t]["EDAM operation"])) + edam_operation.update(set(all_tools[t]["EDAM operations"])) else: print(f"{t} not found in all tools") return list(edam_operation)