Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy
changeset 4:d6acd5cd497b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 79946a95eb9a4c98fde04fa2cb3bc6a31a28e407"
| author | iuc |
|---|---|
| date | Mon, 06 Jul 2020 20:06:21 -0400 |
| parents | bdd8632fa9fb |
| children | 9de2fb1ce1fb |
| 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, 8 insertions(+), 31 deletions(-) [+] |
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--- a/data_manager/data_manager.py Mon Jul 06 19:32:35 2020 -0400 +++ b/data_manager/data_manager.py Mon Jul 06 20:06:21 2020 -0400 @@ -5,7 +5,12 @@ import shutil import tarfile import zipfile -from urllib.request import Request, urlopen +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 def url_download(url, workdir):
--- a/data_manager/ncbi_taxonomy_fetcher.xml Mon Jul 06 19:32:35 2020 -0400 +++ b/data_manager/ncbi_taxonomy_fetcher.xml Mon Jul 06 20:06:21 2020 -0400 @@ -1,9 +1,6 @@ <?xml version="1.0"?> -<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.2"> +<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.1"> <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}' @@ -22,15 +19,4 @@ <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>
--- a/test-data/ncbi_taxonomy.loc Mon Jul 06 19:32:35 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -# 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
--- a/test-data/taxonomy.json Mon Jul 06 19:32:35 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"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 19:32:35 2020 -0400 +++ b/tool-data/ncbi_taxonomy.loc.sample Mon Jul 06 20:06:21 2020 -0400 @@ -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
--- a/tool_data_table_conf.xml.test Mon Jul 06 19:32:35 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -<?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>