Add interactive table

bin/create_interactive_table.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+
+import argparse
+
+import pandas as pd
+
+# TODO maybe allow comunities to modify
+COLUMNS = [
+    "Expand",
+    "Galaxy wrapper id",
+    "Galaxy wrapper version",
+    "Conda version",
+    "Conda id",
+    "Status",
+    "bio.tool id",
+    "bio.tool name",
+    "EDAM operation",
+    "EDAM topic",
+    "Description",
+    "bio.tool description",
+    "Status",
+    "Source",
+    "ToolShed categories",
+    "ToolShed id",
+    "Galaxy wrapper owner",
+    "Galaxy wrapper source",
+]
+
+
+def generate_table(
+    tsv_path: str,
+    template_path: str,
+    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)
+    table = df.to_html(border=0, table_id="dataframe", classes=["display", "nowrap"], index=False)
+
+    with open(template_path) as template_file:
+        template = template_file.read()
+
+    final_html_output = template.replace("COMMUNITY_TABLE", table)
+
+    with open(output_path, "w") as output:
+        output.write(final_html_output)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Create interactive table from \
+            TSV file using a template, where COMMUNITY_TABLE is replaced \
+            by the rendered table"
+    )
+    parser.add_argument(
+        "--table",
+        "-ta",
+        required=True,
+        help="Path to TSV file with tools",
+    )
+    parser.add_argument(
+        "--template",
+        "-te",
+        required=True,
+        help="Path to HTML template",
+    )
+    parser.add_argument(
+        "--output",
+        "-out",
+        required=True,
+        help="Path to HTML output",
+    )
+
+    args = parser.parse_args()
+    generate_table(args.table, args.template, args.output)

bin/filter_microgalaxy_tools.sh → bin/get_microgalaxy_tools.sh

@@ -18,4 +18,9 @@ python bin/extract_galaxy_tools.py \
         --filtered_tools 'results/microgalaxy/tools.tsv' \
         --categories "data/microgalaxy/categories" \
         --exclude "data/microgalaxy/tools_to_exclude" \
-        --keep "data/microgalaxy/tools_to_keep"
+        --keep "data/microgalaxy/tools_to_keep"
+
+python bin/create_interactive_table.py \
+        --table 'results/microgalaxy/tools.tsv' \
+        --template 'data/interactive_table_template.html' \
+        --output 'results/microgalaxy/index.html'

data/datatable_template.html

@@ -0,0 +1,58 @@
+<script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+<script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+<script src="https://cdn.datatables.net/searchbuilder/1.6.0/js/dataTables.searchBuilder.min.js"></script>
+<script src="https://cdn.datatables.net/datetime/1.5.1/js/dataTables.dateTime.min.js"></script>
+
+<script src="https://cdn.datatables.net/responsive/2.5.0/js/dataTables.responsive.min.js"></script>
+
+<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/responsive/2.2.3/css/responsive.dataTables.min.css">
+
+<link rel="stylesheet" href="https://cdn.datatables.net/1.13.6/css/jquery.dataTables.min.css">
+<link rel="stylesheet" href="https://cdn.datatables.net/searchbuilder/1.6.0/css/searchBuilder.dataTables.min.css">
+<link rel="stylesheet" href="https://cdn.datatables.net/datetime/1.5.1/css/dataTables.dateTime.min.css">
+
+<link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" />
+<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
+
+<style type="text/css">
+  .tooltip {
+    font-family: Georgia;
+    font-size: 18px;
+  }
+  .tooltip .tooltip-inner {
+    background-color: #00FFFF;
+    color: #000000;
+    min-width: 400px;
+  }   
+  </style>
+
+<script>
+    $(document).ready(function() {
+    $('#dataframe').DataTable( {
+        "sScrollX": "100%",
+        "dom": "Qlfrtip",
+
+        responsive: {
+            details: {
+                type: 'column'
+            }
+        },
+        "bAutoWidth": false,
+        columnDefs: [ {
+            className: 'control',
+            orderable: false,
+            targets:   [ 0 ],
+            width: 100,
+        },
+        { type: 'natural', targets: 1 } // allow normal sorting
+        ],
+
+    });
+});
+</script>
+
+<div class="display nowrap" style="width:80%" width="100%">
+
+COMMUNITY_TABLE
+
+</div>

data/interactive_table_template.html

@@ -0,0 +1,58 @@
+<script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+<script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+<script src="https://cdn.datatables.net/searchbuilder/1.6.0/js/dataTables.searchBuilder.min.js"></script>
+<script src="https://cdn.datatables.net/datetime/1.5.1/js/dataTables.dateTime.min.js"></script>
+
+<script src="https://cdn.datatables.net/responsive/2.5.0/js/dataTables.responsive.min.js"></script>
+
+<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/responsive/2.2.3/css/responsive.dataTables.min.css">
+
+<link rel="stylesheet" href="https://cdn.datatables.net/1.13.6/css/jquery.dataTables.min.css">
+<link rel="stylesheet" href="https://cdn.datatables.net/searchbuilder/1.6.0/css/searchBuilder.dataTables.min.css">
+<link rel="stylesheet" href="https://cdn.datatables.net/datetime/1.5.1/css/dataTables.dateTime.min.css">
+
+<link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" />
+<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
+
+<style type="text/css">
+  .tooltip {
+    font-family: Georgia;
+    font-size: 18px;
+  }
+  .tooltip .tooltip-inner {
+    background-color: #00FFFF;
+    color: #000000;
+    min-width: 400px;
+  }   
+  </style>
+
+<script>
+    $(document).ready(function() {
+    $('#dataframe').DataTable( {
+        "sScrollX": "100%",
+        "dom": "Qlfrtip",
+
+        responsive: {
+            details: {
+                type: 'column'
+            }
+        },
+        "bAutoWidth": false,
+        columnDefs: [ {
+            className: 'control',
+            orderable: false,
+            targets:   [ 0 ],
+            width: 100,
+        },
+        { type: 'natural', targets: 1 } // allow normal sorting
+        ],
+
+    });
+});
+</script>
+
+<div class="display nowrap" style="width:80%" width="100%">
+
+COMMUNITY_TABLE
+
+</div>

data/microgalaxy/tools_to_exclude

@@ -139,6 +139,7 @@ inforna
 intarna
 kinwalker
 locarna
+mea
 mqc
 nastiseq
 paralyzer

data/microgalaxy/tools_to_keep

@@ -47,7 +47,6 @@ nucleosome_prediction
 pfamscan
 racon
 infernal
-mea
 rRNA
 reago
 sortmerna