Mercurial > repos > gga > chado_expression_add_biomaterial

changeset 2:ecf81582c5cc draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
author gga
date Fri, 23 Nov 2018 11:14:54 -0500
parents e60fc2879221
children 6be23757c5d5
files chado.py expression_add_biomaterial.xml macros.xml
diffstat 3 files changed, 15 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/chado.py	Mon Nov 05 12:19:38 2018 -0500
+++ b/chado.py	Fri Nov 23 11:14:54 2018 -0500
@@ -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
 
 
--- 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
@@ -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"/>
 
--- a/macros.xml	Mon Nov 05 12:19:38 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:14:54 2018 -0500
@@ -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>