Mercurial > repos > iuc > data_manager_bakta
changeset 1:bb463043c93e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit fb13b466a4c529d701a181535568b5f73e7f832f
| author | iuc |
|---|---|
| date | Thu, 02 Mar 2023 14:47:02 +0000 |
| parents | a19189a128cb |
| children | adfd6bf710bd |
| 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 tool-data/bakta_database.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 8 files changed, 19 insertions(+), 21 deletions(-) [+] |
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--- a/data_manager/bakta_build_database.py Sat Dec 10 21:52:28 2022 +0000 +++ b/data_manager/bakta_build_database.py Thu Mar 02 14:47:02 2023 +0000 @@ -78,13 +78,13 @@ def get_data_manager(self, bakta_database_info): self.bakta_table_list = self.get_data_table_format() - bakta_value = f"V{bakta_database_info['major']}." \ - f"{bakta_database_info['minor']}_" \ - f"{bakta_database_info['date']}" + bakta_name = 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_database_info['record'], - dbkey=bakta_value, + data_info = dict(value=bakta_name, + dbkey=bakta_database_info['record'], bakta_version=tool_version, path="db") self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
--- a/data_manager_conf.xml Sat Dec 10 21:52:28 2022 +0000 +++ b/data_manager_conf.xml Thu Mar 02 14:47:02 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/${value}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bakta_database/${dbkey}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bakta_database/${value}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bakta_database/${dbkey}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- a/test-data/bakta_test.loc Sat Dec 10 21:52:28 2022 +0000 +++ b/test-data/bakta_test.loc Thu Mar 02 14:47:02 2023 +0000 @@ -5,7 +5,5 @@ # # for example 7197299 V0.0_date_test 0.0 ${__HERE__} -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 +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
--- a/test-data/bakta_test_data_manager.json Sat Dec 10 21:52:28 2022 +0000 +++ b/test-data/bakta_test_data_manager.json Thu Mar 02 14:47:02 2023 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"bakta_database": [{"bakta_version": "1.4", "dbkey": "V1.0_2022-10-12", "path": "db", "value": "7197299"}]}} \ No newline at end of file +{"data_tables": {"bakta_database": [{"bakta_version": "1.4", "dbkey": "7197299", "path": "db", "value": "V1.0_2022-10-12"}]}} \ No newline at end of file
--- a/test-data/bakta_test_data_manager_test2.json Sat Dec 10 21:52:28 2022 +0000 +++ b/test-data/bakta_test_data_manager_test2.json Thu Mar 02 14:47:02 2023 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"bakta_database": [{"bakta_version": "1.5", "dbkey": "V2.0_2022-11-25", "path": "db", "value": "7360139"}]}} \ No newline at end of file +{"data_tables": {"bakta_database": [{"bakta_version": "1.5", "dbkey": "7360139", "path": "db", "value": "V2.0_2022-11-25"}]}} \ No newline at end of file
--- a/tool-data/bakta_database.loc Sat Dec 10 21:52:28 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -# this is a tab separated file describing the location of bakta database -# -# the columns are: -# value, dbkey, bakta_version, path -# -# for example -#7197299 V0.0_date_test 0.0 ${__HERE__}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bakta_database.loc.sample Thu Mar 02 14:47:02 2023 +0000 @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of bakta database +# +# the columns are: +# name, dbkey, bakta_version, path +# +# for example +#V0.0_date_test 7197299 0.0 ${__HERE__}
--- a/tool_data_table_conf.xml.sample Sat Dec 10 21:52:28 2022 +0000 +++ b/tool_data_table_conf.xml.sample Thu Mar 02 14:47:02 2023 +0000 @@ -2,6 +2,6 @@ <!-- Locations of bakta database in the required format --> <table name="bakta_database" comment_char="#"> <columns>value, dbkey, bakta_version, path</columns> - <file path="tool-data/bakta_database.loc" /> + <file path="tool-data/bakta_database.loc.sample" /> </table> </tables>