Mercurial > repos > gga > chado_organism_add_organism

changeset 7:ad220cb1ce2b 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 11:05:58 -0500
parents 476d0fc00c75
children cd397cc9f0e5
files chado.py macros.xml organism_add_organism.xml
diffstat 3 files changed, 10 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/chado.py	Mon Nov 05 12:14:45 2018 -0500
+++ b/chado.py	Fri Nov 23 11:05:58 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 12:14:45 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:05:58 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_add_organism.xml	Mon Nov 05 12:14:45 2018 -0500
+++ b/organism_add_organism.xml	Fri Nov 23 11:05:58 2018 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool id="organism_add_organism" name="Chado organism add" version="@WRAPPER_VERSION@.0">
- <description></description>
+    <description></description>
 	<macros>
 		<import>macros.xml</import>
 	</macros>
@@ -28,7 +28,7 @@
 	<param name="abbr" label="Abbr" argument="abbr" type="text" help="The abbreviation of the organism" />
 
     <!-- options -->
-	<param name="comment" label="Comment" argument="comment" type="text" help="A comment / description" />
+	<param name="comment" label="Comment" argument="--comment" type="text" help="A comment / description" />
 
 	</inputs>
 	<outputs>