Mercurial > repos > iuc > data_manager_metaphlan_database_downloader

--- a/data_manager/data_manager_metaphlan_download.py	Fri Jun 14 21:14:55 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,147 +0,0 @@
-#!/usr/bin/env python
-#
-# Data manager for reference data for the MetaPhlAn Galaxy tools
-import argparse
-import json
-import subprocess
-from datetime import date
-from pathlib import Path
-
-
-# Utility functions for interacting with Galaxy JSON
-def read_input_json(json_fp):
-    """Read the JSON supplied from the data manager tool
-
-    Returns a tuple (param_dict,extra_files_path)
-
-    'param_dict' is an arbitrary dictionary of parameters
-    input into the tool; 'extra_files_path' is the path
-    to a directory where output files must be put for the
-    receiving data manager to pick them up.
-
-    NB the directory pointed to by 'extra_files_path'
-    doesn't exist initially, it is the job of the script
-    to create it if necessary.
-
-    """
-    with open(json_fp) as fh:
-        params = json.load(fh)
-    return (params['param_dict'],
-            Path(params['output_data'][0]['extra_files_path']))
-
-
-# Utility functions for creating data table dictionaries
-#
-# Example usage:
-# >>> d = create_data_tables_dict()
-# >>> add_data_table(d,'my_data')
-# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
-# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
-# >>> print(json.dumps(d))
-def create_data_tables_dict():
-    """Return a dictionary for storing data table information
-
-    Returns a dictionary that can be used with 'add_data_table'
-    and 'add_data_table_entry' to store information about a
-    data table. It can be converted to JSON to be sent back to
-    the data manager.
-
-    """
-    d = {
-        'data_tables': {}
-    }
-    return d
-
-
-def add_data_table(d, table):
-    """Add a data table to the data tables dictionary
-
-    Creates a placeholder for a data table called 'table'.
-
-    """
-    d['data_tables'][table] = []
-
-
-def add_data_table_entry(d, table, entry):
-    """Add an entry to a data table
-
-    Appends an entry to the data table 'table'. 'entry'
-    should be a dictionary where the keys are the names of
-    columns in the data table.
-
-    Raises an exception if the named data table doesn't
-    exist.
-
-    """
-    try:
-        d['data_tables'][table].append(entry)
-    except KeyError:
-        raise Exception("add_data_table_entry: no table '%s'" % table)
-
-
-def download_metaphlan_db(data_tables, index, table_name, target_dp):
-    """Download MetaPhlAn database
-
-    Creates references to the specified file(s) on the Galaxy
-    server in the appropriate data table (determined from the
-    file extension).
-
-    The 'data_tables' dictionary should have been created using
-    the 'create_data_tables_dict' and 'add_data_table' functions.
-
-    Arguments:
-      data_tables: a dictionary containing the data table info
-      index: version
-      table_name: name of the table
-      target_dp: directory to put copy or link to the data file
-
-    """
-    db_dp = target_dp / Path(index)
-    cmd = "metaphlan --install --index %s --bowtie2db %s" % (index, db_dp)
-    subprocess.check_call(cmd, shell=True)
-    add_data_table_entry(
-        data_tables,
-        table_name,
-        dict(
-            dbkey=index,
-            value='%s-%s' % (index, date.today().strftime("%d%m%Y")),
-            name="MetaPhlAn clade-specific marker genes (%s)" % index,
-            path=str(db_dp),
-            db_version='SGB' if 'SGB' in index else 'legacy'))
-
-
-if __name__ == "__main__":
-    print("Starting...")
-
-    # Read command line
-    parser = argparse.ArgumentParser(description='Download and build MetaPhlan database')
-    parser.add_argument('--index', help="Version of the database")
-    parser.add_argument('--json', help="Path to JSON file")
-    args = parser.parse_args()
-    print("args   : %s" % args)
-
-    # Read the input JSON
-    json_fp = Path(args.json)
-    params, target_dp = read_input_json(json_fp)
-
-    # Make the target directory
-    print("Making %s" % target_dp)
-    target_dp.mkdir(parents=True, exist_ok=True)
-
-    # Set up data tables dictionary
-    data_tables = create_data_tables_dict()
-    add_data_table(data_tables, "metaphlan_database_versioned")
-
-    # Fetch data from specified data sources
-    print("Download and build database")
-    download_metaphlan_db(
-        data_tables,
-        args.index,
-        "metaphlan_database_versioned",
-        target_dp)
-
-    # Write output JSON
-    print("Outputting JSON")
-    with open(json_fp, 'w') as fh:
-        json.dump(data_tables, fh, sort_keys=True)
-    print("Done.")
--- a/data_manager/data_manager_metaphlan_download.xml	Fri Jun 14 21:14:55 2024 +0000
+++ b/data_manager/data_manager_metaphlan_download.xml	Mon Jul 29 07:13:31 2024 +0000
@@ -12,10 +12,32 @@
         <exit_code range="1:" level="fatal" description="Error"/>
     </stdio>
     <command><![CDATA[
-python '$__tool_directory__/data_manager_metaphlan_download.py'
-    --index '$index'
-    --json '$out_file'
+        metaphlan --install --index '$index' --bowtie2db '$out_file.extra_files_path/$index' &&
+        cp '$dmjson' '$out_file'
     ]]></command>
+     <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import date
+{
+  "data_tables":{
+    "genomad":[
+      {
+        "dbkey": "$index",
+        "value": "${index}-#echo date.today().strftime('%d%m%Y')#",
+        "name": "MetaPhlAn clade-specific marker genes ($index)",
+        "path": "$out_file.extra_files_path/$index",
+        "db_version": #slurp
+#if "SGB" in str($index)
+"SGB"#slurp
+#else
+"legacy"#slurp
+#end if
+      }
+    ]
+  }
+}]]>
+        </configfile>
+    </configfiles>
     <inputs>
         <param name="index" type="select" label="Version">
             <option value="mpa_vOct22_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202403</option>
@@ -34,8 +56,11 @@
             <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
             <output name="out_file">
                 <assert_contents>
-                    <has_text text="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
-                    <has_text text="MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"/>
+                    <has_text text='"db_version": "SGB"'/>
+                    <has_text text='"dbkey": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"'/>
+                    <has_text_matching expression='"value": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103-[0-9]{8}"'/>
+                    <has_text text='"name": "MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"'/>
+                    <has_text_matching expression='.*"path": ".*/mpa_vJan21_TOY_CHOCOPhlAnSGB_202103".*'/>
                 </assert_contents>
             </output>
         </test>
--- a/test-data/metaphlan_database_versioned.loc	Fri Jun 14 21:14:55 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of metagenomics files.
-#file has this format (white space characters are TAB characters)
-#mpa_v30_CHOCOPhlAn_201901-20210420	MetaPhlAn clade-specific marker genes (mpa_v30_CHOCOPhlAn_201901)	mpa_v30_CHOCOPhlAn_201901	/path/to/data	SGB_or_legacy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metaphlan_database_versioned.loc.test	Mon Jul 29 07:13:31 2024 +0000
@@ -0,0 +1,4 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.
+#file has this format (white space characters are TAB characters)
+#mpa_v30_CHOCOPhlAn_201901-20210420	MetaPhlAn clade-specific marker genes (mpa_v30_CHOCOPhlAn_201901)	mpa_v30_CHOCOPhlAn_201901	/path/to/data	SGB_or_legacy
--- a/tool_data_table_conf.xml.test	Fri Jun 14 21:14:55 2024 +0000
+++ b/tool_data_table_conf.xml.test	Mon Jul 29 07:13:31 2024 +0000
@@ -1,6 +1,6 @@
 <tables>
     <table name="metaphlan_database_versioned" comment_char="#">
         <columns>value, name, dbkey, path, db_version</columns>
-        <file path="${__HERE__}/test-data/metaphlan_database_versioned.loc"/>
+        <file path="${__HERE__}/test-data/metaphlan_database_versioned.loc.test"/>
     </table>
 </tables>