Mercurial > repos > pimarin > data_manager_bakta
changeset 25:9adbf01a8929 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit ed22b0f3b7b651e240154a08c9313585def1cfe5
| author | pimarin |
|---|---|
| date | Mon, 13 Feb 2023 11:36:50 +0000 |
| parents | 9d4bc7853eca |
| children | 0408796bce2a |
| files | data_manager/bakta_build_database.py data_manager_conf.xml test-data/bakta_test.loc test-data/bakta_test_data_manager.json test-data/bakta_test_data_manager_test2.json tool-data/bakta_database.loc |
| diffstat | 6 files changed, 15 insertions(+), 15 deletions(-) [+] |
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--- a/data_manager/bakta_build_database.py Thu Feb 09 09:53:53 2023 +0000 +++ b/data_manager/bakta_build_database.py Mon Feb 13 11:36:50 2023 +0000 @@ -78,13 +78,13 @@ def get_data_manager(self, bakta_database_info): self.bakta_table_list = self.get_data_table_format() - bakta_name = f"V{bakta_database_info['major']}." \ - f"{bakta_database_info['minor']}_" \ - f"{bakta_database_info['date']}" + bakta_value = f"V{bakta_database_info['major']}." \ + f"{bakta_database_info['minor']}_" \ + f"{bakta_database_info['date']}" tool_version = str(f"{bakta_database_info['software-min']['major']}." f"{bakta_database_info['software-min']['minor']}") - data_info = dict(value=bakta_name, - dbkey=bakta_database_info['record'], + data_info = dict(value=bakta_database_info['record'], + dbkey=bakta_value, bakta_version=tool_version, path="db") self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
--- a/data_manager_conf.xml Thu Feb 09 09:53:53 2023 +0000 +++ b/data_manager_conf.xml Mon Feb 13 11:36:50 2023 +0000 @@ -8,9 +8,9 @@ <column name="path" output_ref="output_file"> <move type="directory" relativize_symlinks="True"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bakta_database/${dbkey}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bakta_database/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bakta_database/${dbkey}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bakta_database/${value}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- a/test-data/bakta_test.loc Thu Feb 09 09:53:53 2023 +0000 +++ b/test-data/bakta_test.loc Mon Feb 13 11:36:50 2023 +0000 @@ -5,7 +5,7 @@ # # for example 7197299 V0.0_date_test 0.0 ${__HERE__} -V1.0_2022-10-12 7197299 1.4 /tmp/tmpiyh6lcqw/galaxy-dev/tool-data/bakta_database/7197299 -V2.0_2022-11-25 7360139 1.5 /tmp/tmpiyh6lcqw/galaxy-dev/tool-data/bakta_database/7360139 -V1.0_2022-10-12 7197299 1.4 /tmp/tmpv364f06x/galaxy-dev/tool-data/bakta_database/7197299 -V2.0_2022-11-25 7360139 1.5 /tmp/tmpv364f06x/galaxy-dev/tool-data/bakta_database/7360139 +7197299 V1.0_2022-10-12 1.4 /tmp/tmpxrkfnuec/galaxy-dev/tool-data/bakta_database/7197299 +7360139 V2.0_2022-11-25 1.5 /tmp/tmpxrkfnuec/galaxy-dev/tool-data/bakta_database/7360139 +7197299 V1.0_2022-10-12 1.4 /tmp/tmpwe9n4gyg/galaxy-dev/tool-data/bakta_database/7197299 +7360139 V2.0_2022-11-25 1.5 /tmp/tmpwe9n4gyg/galaxy-dev/tool-data/bakta_database/7360139
--- a/test-data/bakta_test_data_manager.json Thu Feb 09 09:53:53 2023 +0000 +++ b/test-data/bakta_test_data_manager.json Mon Feb 13 11:36:50 2023 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"bakta_database": [{"bakta_version": "1.4", "dbkey": "7197299", "path": "db", "value": "V1.0_2022-10-12"}]}} \ No newline at end of file +{"data_tables": {"bakta_database": [{"bakta_version": "1.4", "dbkey": "V1.0_2022-10-12", "path": "db", "value": "7197299"}]}} \ No newline at end of file
--- a/test-data/bakta_test_data_manager_test2.json Thu Feb 09 09:53:53 2023 +0000 +++ b/test-data/bakta_test_data_manager_test2.json Mon Feb 13 11:36:50 2023 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"bakta_database": [{"bakta_version": "1.5", "dbkey": "7360139", "path": "db", "value": "V2.0_2022-11-25"}]}} \ No newline at end of file +{"data_tables": {"bakta_database": [{"bakta_version": "1.5", "dbkey": "V2.0_2022-11-25", "path": "db", "value": "7360139"}]}} \ No newline at end of file
--- a/tool-data/bakta_database.loc Thu Feb 09 09:53:53 2023 +0000 +++ b/tool-data/bakta_database.loc Mon Feb 13 11:36:50 2023 +0000 @@ -1,7 +1,7 @@ # this is a tab separated file describing the location of bakta database # # the columns are: -# name, dbkey, bakta_version, path +# value, dbkey, bakta_version, path # # for example -#V0.0_date_test 7197299 0.0 ${__HERE__} +#7197299 V0.0_date_test 0.0 ${__HERE__}