Add microgalaxy wf tag and fix scripts

galaxyproject · Oct 11, 2024 · d37af5e · d37af5e
1 parent a5c95d3
commit d37af5e
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Showing 4 changed files with 45 additions and 29 deletions.
diff --git a/communities/microgalaxy/metadata/workflow_tags b/communities/microgalaxy/metadata/workflow_tags
@@ -1 +1,15 @@
-microgalaxy
+name:microgalaxy
+bacteria
+bacterial-genomics
+antimicrobial-resistance
+metagenomics
+virology
+amr
+microbiome
+asaim
+pathogfair
+abromics
+bacterial
+microgalaxy
+name:metatranscriptomics
+name:amplicon
diff --git a/sources/bin/extract_all_workflows.sh b/sources/bin/extract_all_workflows.sh
@@ -2,12 +2,12 @@
 
 if [ ! -z $1 ] 
 then
-        python bin/extract_galaxy_workflows.py extract \
-                --all results/workflows.json \
-                --tools results/all_tools.json \
+        python sources/bin/extract_galaxy_workflows.py extract \
+                --all communities/all/resources/workflows.json \
+                --tools communities/all/resources/tools.json \
                 --test
 else
-        python bin/extract_galaxy_workflows.py extract \
-                --all results/workflows.json \
-                --tools results/all_tools.json
+        python sources/bin/extract_galaxy_workflows.py extract \
+                --all communities/all/resources/workflows.json \
+                --tools communities/all/resources/tools.json
 fi
diff --git a/sources/bin/extract_galaxy_workflows.py b/sources/bin/extract_galaxy_workflows.py
@@ -148,8 +148,6 @@ def add_workflows_from_workflowhub(self) -> None:
         )
         print(f"Workflows from WorkflowHub: {len(wfhub_wfs['data'])}")
         data = wfhub_wfs["data"]
-        if self.test:
-            data = data[:1]
         for wf in data:
             wfhub_wf = shared.get_request_json(
                 f"https://workflowhub.eu{wf['links']['self']}",
@@ -158,6 +156,7 @@ def add_workflows_from_workflowhub(self) -> None:
             wf = Workflow()
             wf.init_from_search(wf=wfhub_wf, source="WorkflowHub", tools=self.tools)
             self.workflows.append(wf)
+        print(len(self.workflows))
 
     def add_workflows_from_a_server(self, server: str) -> None:
         """
@@ -193,7 +192,7 @@ def add_workflows_from_public_servers(self) -> None:
             "https://usegalaxy.org.au",
         ]
         if self.test:
-            server_urls = server_urls[:2]
+            server_urls = server_urls[2:3]
         for url in server_urls:
             print(url)
             self.add_workflows_from_a_server(url)
@@ -208,10 +207,13 @@ def filter_workflows_by_tags(self, tags: list) -> None:
         """
         Filter workflows by tags
         """
+        to_keep_wf = []
         for w in self.workflows:
-            matches = set(w.tags) & set(tags)
-            if len(matches) == 0:
-                self.workflows.remove(w)
+            wf_tags = [w.lower() for w in w.tags]
+            matches = set(wf_tags) & set(tags)
+            if len(matches) != 0:
+                to_keep_wf.append(w)
+        self.workflows = to_keep_wf
 
     def export_workflows_to_tsv(self, output_fp: str) -> None:
         """

diff --git a/sources/bin/get_community_workflows.sh b/sources/bin/get_community_workflows.sh
@@ -2,16 +2,16 @@
 
 if [ ! -z $1 ] 
 then
-        python bin/extract_galaxy_workflows.py \
+        python sources/bin/extract_galaxy_workflows.py \
                 filter \
-                --all "results/workflows.json" \
-                --filtered "results/microgalaxy/test_workflows.tsv" \
-                --tags "data/communities/microgalaxy/workflow_tags"
+                --all "communities/all/resources/workflows.json" \
+                --filtered "communities/microgalaxy/resources/workflows.tsv" \
+                --tags "communities/microgalaxy/metadata/workflow_tags"
 
-        python bin/create_interactive_table.py \
-                --input "results/microgalaxy/workflows.tsv" \
-                --template "data/interactive_table_template.html" \
-                --output "results/microgalaxy/workflows.html"
+        python sources/bin/create_interactive_table.py \
+                --input "communities/microgalaxy/resources/workflows.tsv" \
+                --template "sources/data/interactive_table_template.html" \
+                --output "communities/microgalaxy/resources/workflows.html"
 
 else
         for com_data_fp in data/communities/* ; do
@@ -23,16 +23,16 @@ else
                         if [[ -f "data/communities/$community/workflow_tags" ]]; then
                                 mkdir -p "results/$community/"
 
-                                python bin/extract_galaxy_workflows.py \
+                                python sources/bin/extract_galaxy_workflows.py \
                                         filter \
-                                        --all "results/workflows.json" \
-                                        --filtered "results/$community/workflows.tsv" \
-                                        --tags "data/communities/$community/workflow_tags"
+                                        --all "communities/all/resources/workflows.json" \
+                                        --filtered "communities/$community/resources/workflows.tsv" \
+                                        --tags "communities/$community/metadata/workflow_tags"
 
-                                python bin/create_interactive_table.py \
-                                        --input "results/$community/workflows.tsv" \
-                                        --template "data/interactive_table_template.html" \
-                                        --output "results/$community/workflows.html"
+                                python sources/bin/create_interactive_table.py \
+                                        --input "communities/$community/resources/workflows.tsv" \
+                                        --template "sources/data/interactive_table_template.html" \
+                                        --output "communities/$community/resources/workflows.html"
                         fi;
                 fi;
         done