Mercurial > repos > iuc > data_manager_pangolearn

changeset 1:112bb7a9da3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolearn commit 1f7b91c7bbd72d30ab47c64d0796ce9825edcaf9"
author iuc
date Wed, 02 Jun 2021 16:06:25 +0000
parents 3eac657893fe
children ed7a967cb11b
files data_manager/pangolearn_dm.py data_manager/pangolearn_dm.xml test-data/pangolearn.loc
diffstat 3 files changed, 26 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/pangolearn_dm.py	Sat Apr 24 20:56:04 2021 +0000
+++ b/data_manager/pangolearn_dm.py	Wed Jun 02 16:06:25 2021 +0000
@@ -93,7 +93,7 @@
     parser.add_argument("--start_date", type=parse_date)
     parser.add_argument("--end_date", type=parse_date)
     parser.add_argument("--overwrite", default=False, action="store_true")
-    parser.add_argument('--pangolearn_format_version', default="1.0")
+    parser.add_argument('--pangolearn_format_version')
     parser.add_argument("datatable_name")
     parser.add_argument("galaxy_datamanager_filename")
     args = parser.parse_args()
@@ -139,11 +139,20 @@
     ]
     for release in releases_to_download:
         tag = download_and_unpack(release["tarball_url"], output_directory)
+        release_date = parse_date(tag)
+        if args.pangolearn_format_version is not None:
+            version = args.pangolearn_format_version
+        else:
+            # 2021-05-27 was the first release of pangoLEARN for pangolin 3, which changed DB format
+            if release_date >= datetime.datetime(2021, 5, 27):
+                version = '3.0'
+            else:
+                version = '1.0'
         data_manager_dict["data_tables"][args.datatable_name].append(
             dict(
                 value=tag,
                 description=release["name"],
-                format_version=args.pangolearn_format_version,
+                format_version=version,
                 path=output_directory + "/" + tag,
             )
         )
--- a/data_manager/pangolearn_dm.xml	Sat Apr 24 20:56:04 2021 +0000
+++ b/data_manager/pangolearn_dm.xml	Wed Jun 02 16:06:25 2021 +0000
@@ -50,9 +50,22 @@
             <output name="output_file">
                 <assert_contents>
                     <has_text text="pangoLEARN data release 2021-04-01"/>
+                    <has_text text='"format_version": "1.0"'/>
                 </assert_contents>
             </output>        
         </test>
+        <test>
+            <conditional name="release">
+                <param name="which" value="date_range" />
+                <param name="start_date" value="2021-05-27" />
+                <param name="end_date" value="2021-05-27" />
+            </conditional>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text='"format_version": "3.0"'/>
+                </assert_contents>
+            </output>        
+        </test>        
     </tests>
     <help><![CDATA[
         This data managers fetches models (from the pangoLEARN_ repository) for the pangolin_
--- a/test-data/pangolearn.loc	Sat Apr 24 20:56:04 2021 +0000
+++ b/test-data/pangolearn.loc	Wed Jun 02 16:06:25 2021 +0000
@@ -5,4 +5,5 @@
 # value  description format_version	path
 #
 # for example
-# 2021-04-14	pangoLEARN data release 2021-04-14		1.0	/tmp/database/pangolearn/pangolearn/2021-04-14
+# 2021-04-14	pangoLEARN data release 2021-04-14	1.0	/tmp/database/pangolearn/2021-04-14
+# 2021-05-27	pangoLEARN data release 2021-05-27	3.0	/tmp/database/pangolearn/2021-05-27