Mercurial > repos > sh477 > data_manager_vep_cache_downloader
changeset 4:97cd72b5130e draft
Fixed several issues
| author | sh477 |
|---|---|
| date | Wed, 23 Feb 2022 12:26:11 +0000 |
| parents | a7f871f7d3df |
| children | a3dba0440f08 |
| files | data_manager/data_manager_vep_cache_download.py data_manager/data_manager_vep_cache_download.xml data_manager_conf.xml data_manager_conf.xml.sample data_manager_conf.xml.test test-data/from_test-meta.data_manager.json |
| diffstat | 6 files changed, 16 insertions(+), 14 deletions(-) [+] |
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--- a/data_manager/data_manager_vep_cache_download.py Tue Feb 22 17:27:55 2022 +0000 +++ b/data_manager/data_manager_vep_cache_download.py Wed Feb 23 12:26:11 2022 +0000 @@ -32,7 +32,7 @@ # Construct metadata for the new data table entry data_manager_dict = { 'data_tables': { - 'vep_cache_databases': [ + 'vep_versioned_caches': [ { 'value': params['param_dict']['file_name'].strip(".tar.gz"), 'dbkey': params['param_dict']['dbkey'], @@ -44,6 +44,8 @@ ] } } + + #assert 42 == 0, str(data_manager_dict) # Save metadata to out_file with open(sys.argv[1], 'w') as fh:
--- a/data_manager/data_manager_vep_cache_download.xml Tue Feb 22 17:27:55 2022 +0000 +++ b/data_manager/data_manager_vep_cache_download.xml Wed Feb 23 12:26:11 2022 +0000 @@ -1,5 +1,5 @@ -<tool id="data_manager_vep_cache_downloader" name="Download and install VEP cache" version="0.1" tool_type="manage_data"> - <description>the cache files required by VEP</description> +<tool id="data_manager_vep_cache_download" name="Download and install VEP cache" version="0.1" tool_type="manage_data"> + <description>ToDo:the cache files required by VEP</description> <requirements> <requirement type="package" version="3.9">python</requirement> </requirements> @@ -19,12 +19,12 @@ <data name="out_file" format="data_manager_json"/> </outputs> <tests> - <test> - <param name="dbkey" value="ce11"/> - <param name="url" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"/> - <param name="file_name" value="caenorhabditis_elegans_vep_105_WBcel235.tar.gz"/> - <param name="display_name" value="C. elegans c11 (V105)"/> - <output name="out_file" file="from_test-meta.data_manager.json"/> + <test> + <param name="dbkey" value="ce11"/> + <param name="url" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"/> + <param name="file_name" value="caenorhabditis_elegans_vep_105_WBcel235.tar.gz"/> + <param name="display_name" value="C. elegans ce11 (V105)"/> + <output name="out_file" file="from_test-meta.data_manager.json"/> </test> </tests> <help>
--- a/data_manager_conf.xml Tue Feb 22 17:27:55 2022 +0000 +++ b/data_manager_conf.xml Wed Feb 23 12:26:11 2022 +0000 @@ -18,4 +18,4 @@ </output> </data_table> </data_manager> -</data_managers> \ No newline at end of file +</data_managers>
--- a/data_manager_conf.xml.sample Tue Feb 22 17:27:55 2022 +0000 +++ b/data_manager_conf.xml.sample Wed Feb 23 12:26:11 2022 +0000 @@ -9,4 +9,4 @@ <columns>value, name, len_path</columns> <file path="tool-data/dbkeys.loc" /> </table> -</tables> \ No newline at end of file +</tables>
--- a/data_manager_conf.xml.test Tue Feb 22 17:27:55 2022 +0000 +++ b/data_manager_conf.xml.test Wed Feb 23 12:26:11 2022 +0000 @@ -1,6 +1,6 @@ <tables> <!-- Table of installed versioned vep cache data --> - <table name="versioned vep cache" comment_char="#"> + <table name="vep_versioned_caches" comment_char="#"> <columns>value, dbkey, version, cachetype, name, path</columns> <file path="${__HERE__}/test-data/vep_versioned_caches.loc" /> </table> @@ -9,4 +9,4 @@ <columns>value, name, len_path</columns> <file path="${__HERE__}/test-data/dbkeys.loc" /> </table> -</tables> \ No newline at end of file +</tables>
--- a/test-data/from_test-meta.data_manager.json Tue Feb 22 17:27:55 2022 +0000 +++ b/test-data/from_test-meta.data_manager.json Wed Feb 23 12:26:11 2022 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"vep_cache_databases": [{"value": "caenorhabditis_elegans_vep_105_WBcel235", "dbkey": "ce11", "version": "105", "cachetype": "default", "name": "C. elegans c11 (V105)", "path": "./caenorhabditis_elegans_vep_105_WBcel235"}]}} \ No newline at end of file +{"data_tables": {"vep_versioned_caches": [{"cachetype": "default", "dbkey": "ce11", "name": "C. elegans ce11 (V105)", "path": "./caenorhabditis_elegans_vep_105_WBcel235", "value": "caenorhabditis_elegans_vep_105_WBcel235", "version": "105"}]}} \ No newline at end of file