Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy
changeset 5:9de2fb1ce1fb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
| author | iuc |
|---|---|
| date | Sun, 22 Nov 2020 12:48:48 +0000 |
| parents | d6acd5cd497b |
| children | 6dd9e00dea95 |
| files | data_manager/data_manager.py data_manager/ncbi_taxonomy_fetcher.xml test-data/ncbi_taxonomy.loc test-data/taxonomy.json tool-data/ncbi_taxonomy.loc.sample tool_data_table_conf.xml.test |
| diffstat | 6 files changed, 35 insertions(+), 11 deletions(-) [+] |
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--- a/data_manager/data_manager.py Mon Jul 06 20:06:21 2020 -0400 +++ b/data_manager/data_manager.py Sun Nov 22 12:48:48 2020 +0000 @@ -5,12 +5,7 @@ import shutil import tarfile import zipfile -try: - # For Python 3.0 and later - from urllib.request import Request, urlopen -except ImportError: - # Fall back to Python 2 imports - from urllib2 import Request, urlopen +from urllib.request import Request, urlopen def url_download(url, workdir): @@ -50,14 +45,15 @@ data_manager_entry['name'] = args.name data_manager_entry['path'] = '.' data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry)) - params = json.loads(open(args.output).read()) + with open(args.output) as fh: + params = json.load(fh) target_directory = params['output_data'][0]['extra_files_path'] os.mkdir(target_directory) output_path = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy')) for filename in os.listdir(workdir): shutil.move(os.path.join(output_path, filename), target_directory) - with open(args.output, 'w') as out: - out.write(json.dumps(data_manager_json, sort_keys=True)) + with open(args.output, 'w') as fh: + json.dump(data_manager_json, fh, sort_keys=True) if __name__ == '__main__':
--- a/data_manager/ncbi_taxonomy_fetcher.xml Mon Jul 06 20:06:21 2020 -0400 +++ b/data_manager/ncbi_taxonomy_fetcher.xml Sun Nov 22 12:48:48 2020 +0000 @@ -1,6 +1,9 @@ <?xml version="1.0"?> -<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.1"> +<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.2"> <description>taxonomy downloader</description> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/data_manager.py' --out '${out_file}' @@ -19,4 +22,15 @@ <outputs> <data name="out_file" format="data_manager_json" /> </outputs> + <tests> + <test> + <param name="database_name" value="tax_name"/> + <param name="database_id" value="tax_id"/> + <output name="out_file" value="taxonomy.json"/> + </test> + </tests> + <help> + Download a taxonomy dump from a provided URL. + The default URL is the latest dump from NCBI taxonomy. + </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy.loc Sun Nov 22 12:48:48 2020 +0000 @@ -0,0 +1,5 @@ +# Tab separated fields where +# value is unique key +# name is descriptive name +# path is path to directory containing names.dmp and nodes.dmp files +#value name path
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy.json Sun Nov 22 12:48:48 2020 +0000 @@ -0,0 +1,1 @@ +{"data_tables": {"ncbi_taxonomy": {"name": "tax_name", "path": ".", "value": "tax_name"}}} \ No newline at end of file
--- a/tool-data/ncbi_taxonomy.loc.sample Mon Jul 06 20:06:21 2020 -0400 +++ b/tool-data/ncbi_taxonomy.loc.sample Sun Nov 22 12:48:48 2020 +0000 @@ -2,4 +2,4 @@ # value is unique key # name is descriptive name # path is path to directory containing names.dmp and nodes.dmp files -#value name path +#value name path
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sun Nov 22 12:48:48 2020 +0000 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" /> + </table> +</tables>