Merge pull request #26 from bebatut/script-community-tools

thanks @bebatut
galaxyproject · Nov 2, 2023 · 86de36b · 86de36b
2 parents c1da781 + 2d8ad6e
commit 86de36b
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Showing 9 changed files with 27,189 additions and 87 deletions.
diff --git a/bin/create_interactive_table.py b/bin/create_interactive_table.py
@@ -33,7 +33,10 @@ def generate_table(
     output_path: str,
 ) -> None:
     df = pd.read_csv(tsv_path, sep="\t").assign(Expand=lambda df: "").fillna("")
-    df = df[df["To keep"]].loc[:, COLUMNS].reindex(columns=COLUMNS)
+    if "To keep" in df.columns:
+        df["To keep"] = df["To keep"].replace("", True)
+        df = df.query("`To keep`")
+    df = df.loc[:, COLUMNS].reindex(columns=COLUMNS)
     table = df.to_html(border=0, table_id="dataframe", classes=["display", "nowrap"], index=False)
 
     with open(template_path) as template_file:

diff --git a/bin/extract_all_tools.sh b/bin/extract_all_tools.sh
@@ -5,4 +5,9 @@ mkdir -p 'results/'
 python bin/extract_galaxy_tools.py \
         extractools \
         --api $GITHUB_API_KEY \
-        --all_tools 'results/all_tools.tsv'
+        --all_tools 'results/all_tools.tsv'
+
+python bin/create_interactive_table.py \
+        --table "results/all_tools.tsv" \
+        --template "data/interactive_table_template.html" \
+        --output "results/index.html"
diff --git a/bin/get_community_tools.sh b/bin/get_community_tools.sh
@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+
+
+for com_data_fp in data/* ; do
+        if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then
+                community=`basename "$com_data_fp"`
+
+                echo "$community";
+
+                if [[ "$community" == *"microgalaxy"* ]]; then
+                        curl \
+                                -L \
+                                "https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hfSg3zu9L4/export?format=tsv&gid=1533244711" \
+                                -o "data/$community/tools_to_keep"
+
+                        curl \
+                                -L \
+                                "https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hfSg3zu9L4/export?format=tsv&gid=672552331" \
+                                -o "data/$community/tools_to_exclude"
+                fi;
+
+
+                mkdir -p "results/$community"
+
+                python bin/extract_galaxy_tools.py \
+                        filtertools \
+                        --tools "results/all_tools.tsv" \
+                        --filtered_tools "results/$community/tools.tsv" \
+                        --categories "data/$community/categories" \
+                        --exclude "data/$community/tools_to_exclude" \
+                        --keep "data/$community/tools_to_keep"
+
+                python bin/create_interactive_table.py \
+                        --table "results/$community/tools.tsv" \
+                        --template "data/interactive_table_template.html" \
+                        --output "results/$community/index.html"
+
+  fi;
+done
diff --git a/bin/get_microgalaxy_tools.sh b/bin/get_microgalaxy_tools.sh
diff --git a/data/datatable_template.html b/data/datatable_template.html
diff --git a/data/interactive_table_template.html b/data/interactive_table_template.html
@@ -23,7 +23,7 @@
     background-color: #00FFFF;
     color: #000000;
     min-width: 400px;
-  }   
+  }
   </style>
 
 <script>