# HG changeset patch
# User iuc
# Date 1616190222 0
# Node ID 6dd9e00dea958a5e15eb50a7d52dce765c69f7f2
# Parent  9de2fb1ce1fb1881641fbcfe4c0e0a5ffa289ffb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 3d78021971b83d585c432830cee0488ada7bd257"

diff -r 9de2fb1ce1fb -r 6dd9e00dea95 data_manager/data_manager.py
--- a/data_manager/data_manager.py	Sun Nov 22 12:48:48 2020 +0000
+++ b/data_manager/data_manager.py	Fri Mar 19 21:43:42 2021 +0000
@@ -37,21 +37,87 @@
     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.join(os.getcwd(), 'taxonomy')
+    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)
-    target_directory = params['output_data'][0]['extra_files_path']
-    os.mkdir(target_directory)
-    output_path = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy'))
-    for filename in os.listdir(workdir):
-        shutil.move(os.path.join(output_path, filename), target_directory)
+
+    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)
 
@@ -61,6 +127,8 @@
     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 9de2fb1ce1fb -r 6dd9e00dea95 data_manager/ncbi_taxonomy_fetcher.xml
--- a/data_manager/ncbi_taxonomy_fetcher.xml	Sun Nov 22 12:48:48 2020 +0000
+++ b/data_manager/ncbi_taxonomy_fetcher.xml	Fri Mar 19 21:43:42 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.2">
+<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.3">
     <description>taxonomy downloader</description>
     <requirements>
         <requirement type="package" version="3.7">python</requirement>
@@ -13,11 +13,15 @@
         #if $database_name:
             --name '${database_name}'
         #end if
+        $name_maps
+        $partial_data
     ]]>
     </command>
     <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="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="partial_data" type="hidden" value="" help="Used for testing"/>
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />
@@ -28,9 +32,17 @@
             <param name="database_id" value="tax_id"/>
             <output name="out_file" value="taxonomy.json"/>
         </test>
+        <test>
+            <param name="database_name" value="tax_name"/>
+            <param name="database_id" value="tax_id"/>
+            <param name="name_maps" value="true"/>
+            <param name="partial_data" value="--partial"/>
+            <output name="out_file" value="taxonomy_with_accession2taxid.json"/>
+        </test>
     </tests>
     <help>
         Download a taxonomy dump from a provided URL.
         The default URL is the latest dump from NCBI taxonomy.
+        The accession2taxid data comes from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ and can be used by the Diamond data_manager (uses ~20Gb as of 2021).
     </help>
 </tool>
diff -r 9de2fb1ce1fb -r 6dd9e00dea95 data_manager_conf.xml
--- a/data_manager_conf.xml	Sun Nov 22 12:48:48 2020 +0000
+++ b/data_manager_conf.xml	Fri Mar 19 21:43:42 2021 +0000
@@ -1,12 +1,13 @@
 <?xml version="1.0"?>
 <data_managers>
-    <data_manager tool_file="data_manager/ncbi_taxonomy_fetcher.xml" id="ncbi_taxonomy_fetcher" version="1.0.0">
+    <data_manager tool_file="data_manager/ncbi_taxonomy_fetcher.xml" id="ncbi_taxonomy_fetcher" version="1.0.3">
         <data_table name="ncbi_taxonomy">
             <output>
                 <column name="value" />
                 <column name="name" />
                 <column name="path" output_ref="out_file">
                     <move type="directory" relativize_symlinks="True">
+                        <source>${path}/taxonomy</source>
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ncbi_taxonomy/${value}</target>
                     </move>
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ncbi_taxonomy/${value}</value_translation>
@@ -14,5 +15,19 @@
                 </column>
             </output>
         </data_table>
+        <data_table name="ncbi_accession2taxid">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="path" output_ref="out_file">
+                    <move type="directory" relativize_symlinks="True">
+                        <source>${path}/accession2taxid</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ncbi_accession2taxid/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ncbi_accession2taxid/${value}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
     </data_manager>
 </data_managers>
diff -r 9de2fb1ce1fb -r 6dd9e00dea95 test-data/ncbi_accession2taxid.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ncbi_accession2taxid.loc	Fri Mar 19 21:43:42 2021 +0000
@@ -0,0 +1,5 @@
+# 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 9de2fb1ce1fb -r 6dd9e00dea95 test-data/taxonomy_with_accession2taxid.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_with_accession2taxid.json	Fri Mar 19 21:43:42 2021 +0000
@@ -0,0 +1,1 @@
+{"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
diff -r 9de2fb1ce1fb -r 6dd9e00dea95 tool-data/ncbi_accession2taxid.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ncbi_accession2taxid.loc.sample	Fri Mar 19 21:43:42 2021 +0000
@@ -0,0 +1,5 @@
+# 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 9de2fb1ce1fb -r 6dd9e00dea95 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sun Nov 22 12:48:48 2020 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Mar 19 21:43:42 2021 +0000
@@ -5,4 +5,8 @@
         <columns>value, name, path</columns>
         <file path="tool-data/ncbi_taxonomy.loc" />
     </table>
+    <table name="ncbi_accession2taxid" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/ncbi_accession2taxid.loc" />
+    </table>
 </tables>
diff -r 9de2fb1ce1fb -r 6dd9e00dea95 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Sun Nov 22 12:48:48 2020 +0000
+++ b/tool_data_table_conf.xml.test	Fri Mar 19 21:43:42 2021 +0000
@@ -5,4 +5,8 @@
         <columns>value, name, path</columns>
         <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" />
     </table>
+    <table name="ncbi_accession2taxid" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/ncbi_accession2taxid.loc" />
+    </table>
 </tables>