| Previous changeset 1:e60fc2879221 (2018-11-05) Next changeset 3:6be23757c5d5 (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_add_biomaterial.xml macros.xml |
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| diff -r e60fc2879221 -r ecf81582c5cc chado.py --- a/chado.py Mon Nov 05 12:19:38 2018 -0500 +++ b/chado.py Fri Nov 23 11:14:54 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 e60fc2879221 -r ecf81582c5cc expression_add_biomaterial.xml --- a/expression_add_biomaterial.xml Mon Nov 05 12:19:38 2018 -0500 +++ b/expression_add_biomaterial.xml Fri Nov 23 11:14:54 2018 -0500 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool id="expression_add_biomaterial" name="Chado biomaterial add" version="@WRAPPER_VERSION@.0"> - <description></description> + <description></description> <macros> <import>macros.xml</import> </macros> @@ -41,12 +41,12 @@ <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" /> <!-- options --> - <param name="description" label="Description" argument="description" type="text" help="Description of the biomaterial" optional="true" /> - <param name="biomaterial_provider" label="Biomaterial Provider" argument="biomaterial_provider" type="text" help="Biomaterial provider name" optional="true" /> - <param name="biosample_accession" label="Biosample Accession" argument="biosample_accession" type="text" help="Biosample accession number" optional="true" /> - <param name="sra_accession" label="Sra Accession" argument="sra_accession" type="text" help="SRA accession number" optional="true" /> - <param name="bioproject_accession" label="Bioproject Accession" argument="bioproject_accession" type="text" help="Bioproject accession number" optional="true" /> - <param name="attributes" label="Attributes" argument="attributes" type="data" format="json" help="Custom attributes (In JSON dict form)" optional="true" /> + <param name="description" label="Description" argument="--description" type="text" help="Description of the biomaterial" optional="true" /> + <param name="biomaterial_provider" label="Biomaterial Provider" argument="--biomaterial_provider" type="text" help="Biomaterial provider name" optional="true" /> + <param name="biosample_accession" label="Biosample Accession" argument="--biosample_accession" type="text" help="Biosample accession number" optional="true" /> + <param name="sra_accession" label="Sra Accession" argument="--sra_accession" type="text" help="SRA accession number" optional="true" /> + <param name="bioproject_accession" label="Bioproject Accession" argument="--bioproject_accession" type="text" help="Bioproject accession number" optional="true" /> + <param name="attributes" label="Attributes" argument="--attributes" type="data" format="json" help="Custom attributes (In JSON dict form)" optional="true" /> <expand macro="wait_for"/> |
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| diff -r e60fc2879221 -r ecf81582c5cc macros.xml --- a/macros.xml Mon Nov 05 12:19:38 2018 -0500 +++ b/macros.xml Fri Nov 23 11:14:54 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> |