From beafe2c099b6cbd7b6b9d5f25f7923862f4c5990 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 27 Sep 2024 11:34:50 -0400
Subject: [PATCH] Drop python wrapper

---
 .../data_manager/bwa_mem2_index_builder.py    | 83 -------------------
 .../data_manager/bwa_mem2_index_builder.xml   | 49 ++++++++---
 .../test-data/bwa_mem2_data_manager.1.json    | 12 +++
 .../test-data/bwa_mem2_data_manager.2.json    | 12 +++
 .../test-data/bwa_mem2_data_manager.json      |  1 -
 5 files changed, 62 insertions(+), 95 deletions(-)
 delete mode 100644 data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.py
 create mode 100644 data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.1.json
 create mode 100644 data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.2.json
 delete mode 100644 data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.json

diff --git a/data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.py b/data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.py
deleted file mode 100644
index 79444e63809..00000000000
--- a/data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.py
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env python
-# Based heavily on the bwa-mem data manager wrapper script by Dan Blankenberg
-from __future__ import print_function
-
-import argparse
-import json
-import os
-import subprocess
-import sys
-
-DEFAULT_DATA_TABLE_NAME = "bwa_mem2_indexes"
-
-
-def get_id_name(params, dbkey, fasta_description=None):
-    # TODO: ensure sequence_id is unique and does not already appear in location file
-    sequence_id = params['param_dict']['sequence_id']
-    if not sequence_id:
-        sequence_id = dbkey
-
-    sequence_name = params['param_dict']['sequence_name']
-    if not sequence_name:
-        sequence_name = fasta_description
-        if not sequence_name:
-            sequence_name = dbkey
-    return sequence_id, sequence_name
-
-
-def build_bwa_mem2_index(data_manager_dict, options, params, sequence_id, sequence_name):
-    data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
-    target_directory = params['output_data'][0]['extra_files_path']
-    if not os.path.exists(target_directory):
-        os.mkdir(target_directory)
-    fasta_base_name = os.path.split(options.fasta_filename)[-1]
-    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
-    os.symlink(options.fasta_filename, sym_linked_fasta_filename)
-    args = ['bwa-mem2', 'index', sym_linked_fasta_filename]
-    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
-    return_code = proc.wait()
-    if return_code:
-        print("Error building index.", file=sys.stderr)
-        sys.exit(return_code)
-    data_table_entry = dict(value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=fasta_base_name)
-    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
-
-
-def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
-    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
-    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
-    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
-    return data_manager_dict
-
-
-def main():
-    # Parse Command Line
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--output', dest='output', action='store', type=str, default=None)
-    parser.add_argument('--fasta_filename', dest='fasta_filename', action='store', type=str, default=None)
-    parser.add_argument('--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None)
-    parser.add_argument('--fasta_description', dest='fasta_description', action='store', type=str, default=None)
-    parser.add_argument('--data_table_name', dest='data_table_name', action='store', type=str, default='bwa_mem2_indexes')
-    options = parser.parse_args()
-
-    filename = options.output
-
-    with open(filename) as fh:
-        params = json.load(fh)
-    data_manager_dict = {}
-
-    if options.fasta_dbkey in [None, '', '?']:
-        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (options.fasta_dbkey))
-
-    sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)
-
-    # build the index
-    build_bwa_mem2_index(data_manager_dict, options, params, sequence_id, sequence_name)
-
-    # save info to json file
-    with open(filename, 'w') as fh:
-        json.dump(data_manager_dict, fh, sort_keys=True)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.xml b/data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.xml
index 69145e91fe2..1d7af2d5099 100644
--- a/data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.xml
+++ b/data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.xml
@@ -1,18 +1,39 @@
-<tool id="bwa_mem2_index_builder_data_manager" name="BWA-MEM2 index" tool_type="manage_data" version="0.0.1" profile="19.05">
-    <description>builder</description>
+<tool id="bwa_mem2_index_builder_data_manager" name="Build BWA-MEM2 indexes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
+    <description></description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.2.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="2.2.1">bwa-mem2</requirement>
-        <requirement type="package" version="3.9">python</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/bwa_mem2_index_builder.py'
-        --output '${out_file}'
-        --fasta_filename '${all_fasta_source.fields.path}'
-        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
-        --fasta_description '${all_fasta_source.fields.name}'
-        --data_table_name bwa_mem2_indexes
+        #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
+        mkdir -p '${out_file.extra_files_path}' &&
+        ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
+        bwa-mem2 index '${out_file.extra_files_path}/${fasta_file_name}' &&
+        cp '$dmjson' '$out_file'
         ]]>
     </command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[#slurp
+#set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
+#set $value = $sequence_id or $all_fasta_source.fields.dbkey
+#set $name = $sequence_name or $all_fasta_source.fields.name
+{
+  "data_tables":{
+    "bwa_mem2_indexes":[
+      {
+        "value": "${value}",
+        "dbkey": "${all_fasta_source.fields.dbkey}",
+        "name": "${name}",
+        "path": "${fasta_file_name}"
+      }
+    ]
+  }
+}
+]]></configfile>
+    </configfiles>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
@@ -26,7 +47,13 @@
     <tests>
         <test>
             <param name="all_fasta_source" value="phiX174"/>
-            <output name="out_file" file="bwa_mem2_data_manager.json"/>
+            <output name="out_file" file="bwa_mem2_data_manager.1.json"/>
+        </test>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="sequence_name" value="Galeocerdo cuvier"/>
+            <param name="sequence_id" value="fooBar1"/>
+            <output name="out_file" file="bwa_mem2_data_manager.2.json"/>
         </test>
     </tests>
     <help>
diff --git a/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.1.json b/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.1.json
new file mode 100644
index 00000000000..344c77f9b7e
--- /dev/null
+++ b/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.1.json
@@ -0,0 +1,12 @@
+{
+  "data_tables":{
+    "bwa_mem2_indexes":[
+      {
+        "value": "phiX174",
+        "dbkey": "phiX174",
+        "name": "phiX174",
+        "path": "phiX174.fasta"
+      }
+    ]
+  }
+}
diff --git a/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.2.json b/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.2.json
new file mode 100644
index 00000000000..259853414c6
--- /dev/null
+++ b/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.2.json
@@ -0,0 +1,12 @@
+{
+  "data_tables":{
+    "bwa_mem2_indexes":[
+      {
+        "value": "fooBar1",
+        "dbkey": "phiX174",
+        "name": "Galeocerdo cuvier",
+        "path": "phiX174.fasta"
+      }
+    ]
+  }
+}
diff --git a/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.json b/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.json
deleted file mode 100644
index 413fb8c3992..00000000000
--- a/data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.json
+++ /dev/null
@@ -1 +0,0 @@
-{"data_tables": {"bwa_mem2_indexes": [{"dbkey": "phiX174", "name": "phiX174", "path": "phiX174.fasta", "value": "phiX174"}]}}
\ No newline at end of file