| Previous changeset 1:87d423ea58f4 (2018-11-05) Next changeset 3:d30230d3eb0d (2019-01-24) |
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Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5 |
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modified:
chado.py expression_get_biomaterials.xml macros.xml |
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| diff -r 87d423ea58f4 -r 3df5eaa8ae44 chado.py --- a/chado.py Mon Nov 05 12:22:00 2018 -0500 +++ b/chado.py Fri Nov 23 11:18:22 2018 -0500 |
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| @@ -406,6 +406,7 @@ # there. data = _list_organisms(ci, *args, **kwargs) cache[cacheKey] = data + ci.session.close() return data try: # The cache key may or may not be in the cache at this point, it @@ -413,12 +414,14 @@ # when we checked above and now, so we reference the object from the # cache in preparation to return. data = cache[cacheKey] + ci.session.close() return data except KeyError: # If access fails due to eviction, we will fail over and can ensure that # data is inserted. data = _list_organisms(ci, *args, **kwargs) cache[cacheKey] = data + ci.session.close() return data @@ -447,6 +450,7 @@ data = _list_analyses(ci, *args, **kwargs) cache[cacheKey] = data + ci.session.close() return data try: # The cache key may or may not be in the cache at this point, it @@ -454,12 +458,14 @@ # when we checked above and now, so we reference the object from the # cache in preparation to return. data = cache[cacheKey] + ci.session.close() return data except KeyError: # If access fails due to eviction, we will fail over and can ensure that # data is inserted. data = _list_analyses(ci, *args, **kwargs) cache[cacheKey] = data + ci.session.close() return data |
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| diff -r 87d423ea58f4 -r 3df5eaa8ae44 expression_get_biomaterials.xml --- a/expression_get_biomaterials.xml Mon Nov 05 12:22:00 2018 -0500 +++ b/expression_get_biomaterials.xml Fri Nov 23 11:18:22 2018 -0500 |
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| @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool id="expression_get_biomaterials" name="Chado biomaterial get" version="@WRAPPER_VERSION@.0"> - <description></description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <code file="chado.py"/> - <command detect_errors="aggressive"><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ @AUTH@ chakin expression get_biomaterials @@ -29,22 +29,22 @@ | jq -S . > $results ]]></command> - <inputs> - <!-- options --> - <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" /> - <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" optional="true" /> - <param name="provider_id" label="Provider Id" argument="provider_id" type="text" help="Limit query to the selected provider" optional="true" /> - <param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="text" help="Limit query to the selected biomaterial id" optional="true" /> - <param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Limit query to the selected biomaterial name" optional="true" /> + <inputs> + <!-- options --> + <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" /> + <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" optional="true" /> + <param name="provider_id" label="Provider Id" argument="provider_id" type="text" help="Limit query to the selected provider" optional="true" /> + <param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="text" help="Limit query to the selected biomaterial id" optional="true" /> + <param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Limit query to the selected biomaterial name" optional="true" /> - <expand macro="wait_for"/> - </inputs> - <outputs> - <data format="json" name="results"/> - </outputs> - <help> + <expand macro="wait_for"/> + </inputs> + <outputs> + <data format="json" name="results"/> + </outputs> + <help> List biomaterials in the database @HELP@ - </help> + </help> </tool> |
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| diff -r 87d423ea58f4 -r 3df5eaa8ae44 macros.xml --- a/macros.xml Mon Nov 05 12:22:00 2018 -0500 +++ b/macros.xml Fri Nov 23 11:18:22 2018 -0500 |
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| @@ -2,7 +2,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2.2">python-chado</requirement> + <requirement type="package" version="2.2.3">python-chado</requirement> <requirement type="package" version="1.5">jq</requirement> <yield/> </requirements> @@ -16,7 +16,7 @@ </stdio> </xml> - <token name="@WRAPPER_VERSION@">2.2.2</token> + <token name="@WRAPPER_VERSION@">2.2.3</token> <xml name="citation"> <citations> |