Mercurial > repos > iuc > data_manager_pangolearn
comparison data_manager/pangolearn_dm.py @ 1:112bb7a9da3c draft
"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 | df30a2f1db55 |
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| 0:3eac657893fe | 1:112bb7a9da3c |
|---|---|
| 91 parser.add_argument("--testmode", default=False, action="store_true") | 91 parser.add_argument("--testmode", default=False, action="store_true") |
| 92 parser.add_argument("--latest", default=False, action="store_true") | 92 parser.add_argument("--latest", default=False, action="store_true") |
| 93 parser.add_argument("--start_date", type=parse_date) | 93 parser.add_argument("--start_date", type=parse_date) |
| 94 parser.add_argument("--end_date", type=parse_date) | 94 parser.add_argument("--end_date", type=parse_date) |
| 95 parser.add_argument("--overwrite", default=False, action="store_true") | 95 parser.add_argument("--overwrite", default=False, action="store_true") |
| 96 parser.add_argument('--pangolearn_format_version', default="1.0") | 96 parser.add_argument('--pangolearn_format_version') |
| 97 parser.add_argument("datatable_name") | 97 parser.add_argument("datatable_name") |
| 98 parser.add_argument("galaxy_datamanager_filename") | 98 parser.add_argument("galaxy_datamanager_filename") |
| 99 args = parser.parse_args() | 99 args = parser.parse_args() |
| 100 | 100 |
| 101 if args.testmode: | 101 if args.testmode: |
| 137 for release in releases | 137 for release in releases |
| 138 if release["tag_name"] not in existing_release_tags | 138 if release["tag_name"] not in existing_release_tags |
| 139 ] | 139 ] |
| 140 for release in releases_to_download: | 140 for release in releases_to_download: |
| 141 tag = download_and_unpack(release["tarball_url"], output_directory) | 141 tag = download_and_unpack(release["tarball_url"], output_directory) |
| 142 release_date = parse_date(tag) | |
| 143 if args.pangolearn_format_version is not None: | |
| 144 version = args.pangolearn_format_version | |
| 145 else: | |
| 146 # 2021-05-27 was the first release of pangoLEARN for pangolin 3, which changed DB format | |
| 147 if release_date >= datetime.datetime(2021, 5, 27): | |
| 148 version = '3.0' | |
| 149 else: | |
| 150 version = '1.0' | |
| 142 data_manager_dict["data_tables"][args.datatable_name].append( | 151 data_manager_dict["data_tables"][args.datatable_name].append( |
| 143 dict( | 152 dict( |
| 144 value=tag, | 153 value=tag, |
| 145 description=release["name"], | 154 description=release["name"], |
| 146 format_version=args.pangolearn_format_version, | 155 format_version=version, |
| 147 path=output_directory + "/" + tag, | 156 path=output_directory + "/" + tag, |
| 148 ) | 157 ) |
| 149 ) | 158 ) |
| 150 data_manager_dict["data_tables"][args.datatable_name].sort( | 159 data_manager_dict["data_tables"][args.datatable_name].sort( |
| 151 key=operator.itemgetter("value"), reverse=True | 160 key=operator.itemgetter("value"), reverse=True |