Mercurial > repos > gga > chado_organism_get_organisms

changeset 7:05e1fd17832b 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 11:14:04 -0500
parents 8fbc70518b2b
children 8304d3bfc5b1
files chado.py macros.xml organism_get_organisms.xml
diffstat 3 files changed, 15 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/chado.py	Mon Nov 05 12:19:01 2018 -0500
+++ b/chado.py	Fri Nov 23 11:14:04 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/macros.xml	Mon Nov 05 12:19:01 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:14:04 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>
--- a/organism_get_organisms.xml	Mon Nov 05 12:19:01 2018 -0500
+++ b/organism_get_organisms.xml	Fri Nov 23 11:14:04 2018 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool id="organism_get_organisms" name="Chado organism get" version="@WRAPPER_VERSION@.0">
- <description></description>
+    <description></description>
 	<macros>
 		<import>macros.xml</import>
 	</macros>
@@ -35,12 +35,12 @@
     <!-- arguments -->
 
     <!-- options -->
-	<param name="organism_id" label="Organism Id" argument="organism_id" type="integer" help="organism_id filter" optional="True" />
-	<param name="genus" label="Genus" argument="genus" type="text" help="genus filter" optional="True" />
-	<param name="species" label="Species" argument="species" type="text" help="species filter" optional="True" />
-	<param name="common" label="Common" argument="common" type="text" help="common filter" optional="True" />
-	<param name="abbr" label="Abbr" argument="abbr" type="text" help="abbr filter" optional="True" />
-	<param name="comment" label="Comment" argument="comment" type="text" help="comment filter" optional="True" />
+	<param name="organism_id" label="Organism Id" argument="--organism_id" type="integer" help="organism_id filter" optional="True" />
+	<param name="genus" label="Genus" argument="--genus" type="text" help="genus filter" optional="True" />
+	<param name="species" label="Species" argument="--species" type="text" help="species filter" optional="True" />
+	<param name="common" label="Common" argument="--common" type="text" help="common filter" optional="True" />
+	<param name="abbr" label="Abbr" argument="--abbr" type="text" help="abbr filter" optional="True" />
+	<param name="comment" label="Comment" argument="--comment" type="text" help="comment filter" optional="True" />
 
 	</inputs>
 	<outputs>