# HG changeset patch
# User iuc
# Date 1763416023 0
# Node ID 2649aece3781e6c5ee9344b488745c2c606ee3fb
# Parent  34a5799a65fa13494a36fe708f441236370b37fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_fetch_ncbi_taxonomy commit cf8607692417bdc4f663c726aea34c1056dd9c48

diff -r 34a5799a65fa -r 2649aece3781 data_manager/data_manager.py
--- a/data_manager/data_manager.py	Tue May 21 07:36:09 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-import argparse
-import datetime
-import json
-import os
-import shutil
-import tarfile
-import zipfile
-from urllib.request import Request, urlopen
-
-
-def url_download(url, workdir):
-    file_path = os.path.join(workdir, 'download.dat')
-    if not os.path.exists(workdir):
-        os.makedirs(workdir)
-    src = None
-    dst = None
-    try:
-        req = Request(url)
-        src = urlopen(req)
-        with open(file_path, 'wb') as dst:
-            while True:
-                chunk = src.read(2**10)
-                if chunk:
-                    dst.write(chunk)
-                else:
-                    break
-    finally:
-        if src:
-            src.close()
-    if tarfile.is_tarfile(file_path):
-        fh = tarfile.open(file_path, 'r:*')
-    elif zipfile.is_zipfile(file_path):
-        fh = zipfile.ZipFile(file_path, 'r')
-    else:
-        return
-    fh.extractall(workdir)
-    os.remove(file_path)
-
-
-def download_name_maps(url, workdir, partial):
-
-    if partial:
-        map_files = [
-            'pdb.accession2taxid.gz',
-        ]
-    else:
-        map_files = [
-            'dead_nucl.accession2taxid.gz',
-            'dead_prot.accession2taxid.gz',
-            'dead_wgs.accession2taxid.gz',
-            'nucl_gb.accession2taxid.gz',
-            'nucl_wgs.accession2taxid.gz',
-            'pdb.accession2taxid.gz',
-            'prot.accession2taxid.gz',
-            'prot.accession2taxid.FULL.gz'
-        ]
-
-    if not os.path.exists(workdir):
-        os.makedirs(workdir)
-
-    for map in map_files:
-        src = "{}{}".format(url, map)
-        dest = os.path.join(workdir, map)
-
-        print("Downloading taxonomy accession2taxid file from {} to {}".format(src, dest))
-
-        try:
-            req = Request(src)
-            src = urlopen(req)
-            with open(dest, 'wb') as dst:
-                while True:
-                    chunk = src.read(2**10)
-                    if chunk:
-                        dst.write(chunk)
-                    else:
-                        break
-        finally:
-            if src:
-                src.close()
-
-
-def move_files_to_final_dir(workdir, target_directory, copy=False):
-    for filename in os.listdir(workdir):
-        if copy:
-            shutil.copy(os.path.join(workdir, filename), target_directory)
-        else:
-            shutil.move(os.path.join(workdir, filename), target_directory)
-
-
-def main(args):
-    workdir = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy'))
-    url_download(args.url, workdir)
-
-    data_manager_entry = {}
-    data_manager_entry['value'] = args.name.lower()
-    data_manager_entry['name'] = args.name
-    data_manager_entry['path'] = '.'
-    data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry))
-
-    with open(args.output) as fh:
-        params = json.load(fh)
-
-    if args.name_maps:
-        workdir_a2t = os.path.join(os.getcwd(), 'accession2taxid')
-        download_name_maps("ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/", workdir_a2t, args.partial)
-
-        target_directory_a2t = os.path.join(params['output_data'][0]['extra_files_path'], "accession2taxid")
-        os.makedirs(target_directory_a2t)
-        move_files_to_final_dir(workdir_a2t, target_directory_a2t)
-
-        # Also copy taxonomy data to accession2taxid dir
-        move_files_to_final_dir(workdir, target_directory_a2t, copy=True)
-
-        data_manager_json['data_tables']['ncbi_accession2taxid'] = data_manager_entry
-
-    target_directory_tax = os.path.join(params['output_data'][0]['extra_files_path'], "taxonomy")
-    os.makedirs(target_directory_tax)
-
-    move_files_to_final_dir(workdir, target_directory_tax)
-
-    with open(args.output, 'w') as fh:
-        json.dump(data_manager_json, fh, sort_keys=True)
-
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Create data manager json.')
-    parser.add_argument('--out', dest='output', action='store', help='JSON filename')
-    parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID')
-    parser.add_argument('--url', dest='url', action='store', default='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz', help='Download URL')
-    parser.add_argument('--name-maps', dest='name_maps', action='store_true', help='')
-    parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
-    args = parser.parse_args()
-
-    main(args)
diff -r 34a5799a65fa -r 2649aece3781 data_manager/ncbi_taxonomy_fetcher.xml
--- a/data_manager/ncbi_taxonomy_fetcher.xml	Tue May 21 07:36:09 2024 +0000
+++ b/data_manager/ncbi_taxonomy_fetcher.xml	Mon Nov 17 21:47:03 2025 +0000
@@ -1,26 +1,68 @@
-<?xml version="1.0"?>
-<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.4" profile="23.0">
+<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.1" profile="24.0">
     <description>taxonomy downloader</description>
     <requirements>
-        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="1.25.0">wget</requirement>
     </requirements>
     <command detect_errors="exit_code">
     <![CDATA[
-        python '$__tool_directory__/data_manager.py' --out '${out_file}'
-        #if $taxonomy_url:
-            --url '${taxonomy_url}'
+        set -o pipefail;
+
+        mkdir -p '$out_file.extra_files_path/taxonomy/' &&
+        wget -O - '$taxonomy_url' | tar -xz -C '$out_file.extra_files_path/taxonomy/' &&
+        if [[ ! -f '$out_file.extra_files_path/taxonomy/nodes.dmp' ]]; then >&2 echo "nodes.dmp missing"; exit 1; fi &&
+
+        #if $name_maps
+            mkdir -p '$out_file.extra_files_path/accession2taxid/' &&
+            #if $partial_data
+                #set files = ['pdb.accession2taxid']
+            #else
+                #set files = ['dead_nucl.accession2taxid', 'dead_prot.accession2taxid', 'dead_wgs.accession2taxid', 'nucl_gb.accession2taxid', 'nucl_wgs.accession2taxid', 'pdb.accession2taxid', 'prot.accession2taxid', 'prot.accession2taxid.FULL']
+            #end if
+            #for file in files
+                wget -O - ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/${file}.gz | gunzip -c > '$out_file.extra_files_path/accession2taxid/${file}' &&
+            #end for
         #end if
-        #if $database_name:
-            --name '${database_name}'
-        #end if
-        $name_maps
-        $partial_data
+        cp '$dmjson' '$out_file'
     ]]>
     </command>
+        <configfiles>
+        <configfile name="dmjson"><![CDATA[#slurp
+#if $database_name == ""
+    #import datetime
+    #import os.path
+    #set now = datetime.datetime.now().strftime("%Y-%m-%d-%H%M%S")
+    #set basename = os.path.basename(str($taxonomy_url))[:-7]
+    #set value = basename + "_" + now
+    #set name = basename + " " + now
+#else
+    #set value = $database_name.lower()
+    #set name = $database_name
+#end if
+{
+  "data_tables":{
+    "ncbi_taxonomy":[
+      {
+        "value": "$value",
+        "name": "$name",
+        "path": "."
+      }
+    ]
+#if $name_maps
+    ,"ncbi_accession2taxid":[
+      {
+        "value": "$value",
+        "name": "$name",
+        "path": "."
+      }
+    ]
+#end if
+  }
+}]]></configfile>
+    </configfiles>
     <inputs>
-        <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
+        <param name="database_name" type="text" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
         <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" />
-        <param name="name_maps" type="boolean" truevalue="--name-maps" falsevalue="" label="Also download accession2taxid data" checked="false" />
+        <param name="name_maps" type="boolean" label="Also download accession2taxid data" checked="false" />
         <param name="partial_data" type="hidden" value="" help="Used for testing"/>
     </inputs>
     <outputs>
@@ -32,6 +74,14 @@
             <output name="out_file" value="taxonomy.json"/>
         </test>
         <test>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text_matching expression='"value": "taxdump_\d\d\d\d-\d\d-\d\d-\d\d\d\d\d\d"'/>
+                    <has_text_matching expression='"name": "taxdump \d\d\d\d-\d\d-\d\d-\d\d\d\d\d\d"'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
             <param name="database_name" value="tax_name"/>
             <param name="name_maps" value="true"/>
             <param name="partial_data" value="--partial"/>
diff -r 34a5799a65fa -r 2649aece3781 test-data/ncbi_accession2taxid.loc
--- a/test-data/ncbi_accession2taxid.loc	Tue May 21 07:36:09 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-# Tab separated fields where
-# value is unique key
-# name is descriptive name
-# path is path to directory containing accession2taxid files
-#value	name	path
diff -r 34a5799a65fa -r 2649aece3781 test-data/ncbi_taxonomy.loc
--- a/test-data/ncbi_taxonomy.loc	Tue May 21 07:36:09 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-# Tab separated fields where
-# value is unique key
-# name is descriptive name
-# path is path to directory containing names.dmp and nodes.dmp files
-#value	name	path
diff -r 34a5799a65fa -r 2649aece3781 test-data/taxonomy.json
--- a/test-data/taxonomy.json	Tue May 21 07:36:09 2024 +0000
+++ b/test-data/taxonomy.json	Mon Nov 17 21:47:03 2025 +0000
@@ -1,1 +1,11 @@
-{"data_tables": {"ncbi_taxonomy": {"name": "tax_name", "path": ".", "value": "tax_name"}}}
\ No newline at end of file
+{
+  "data_tables":{
+    "ncbi_taxonomy":[
+      {
+        "value": "tax_name",
+        "name": "tax_name",
+        "path": "."
+      }
+    ]
+  }
+}
\ No newline at end of file
diff -r 34a5799a65fa -r 2649aece3781 test-data/taxonomy_with_accession2taxid.json
--- a/test-data/taxonomy_with_accession2taxid.json	Tue May 21 07:36:09 2024 +0000
+++ b/test-data/taxonomy_with_accession2taxid.json	Mon Nov 17 21:47:03 2025 +0000
@@ -1,1 +1,18 @@
-{"data_tables": {"ncbi_accession2taxid": {"name": "tax_name", "path": ".", "value": "tax_name"}, "ncbi_taxonomy": {"name": "tax_name", "path": ".", "value": "tax_name"}}}
\ No newline at end of file
+{
+  "data_tables":{
+    "ncbi_taxonomy":[
+      {
+        "value": "tax_name",
+        "name": "tax_name",
+        "path": "."
+      }
+    ]
+    ,"ncbi_accession2taxid":[
+      {
+        "value": "tax_name",
+        "name": "tax_name",
+        "path": "."
+      }
+    ]
+  }
+}
\ No newline at end of file