# HG changeset patch
# User gga
# Date 1542989747 18000
# Node ID 4451447ae06537a9ebaddb09dd4ee0b7e612391c
# Parent 60d7b4054865c358a0a53d2b6458f3b4687dfdcd
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
diff -r 60d7b4054865 -r 4451447ae065 chado.py
--- a/chado.py Mon Nov 05 12:20:09 2018 -0500
+++ b/chado.py Fri Nov 23 11:15:47 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
diff -r 60d7b4054865 -r 4451447ae065 feature_load_gff.xml
--- a/feature_load_gff.xml Mon Nov 05 12:20:09 2018 -0500
+++ b/feature_load_gff.xml Fri Nov 23 11:15:47 2018 -0500
@@ -2,7 +2,7 @@
- macros.xml
+ macros.xml
@@ -19,15 +19,15 @@
#end if
#if $prot_naming.method == 'regex'
- #if $re_protein:
- --re_protein '$re_protein'
+ #if $prot_naming.re_protein:
+ --re_protein '$prot_naming.re_protein'
#end if
- #if $re_protein_capture:
- --re_protein_capture '$re_protein_capture'
+ #if $prot_naming.re_protein_capture:
+ --re_protein_capture '$prot_naming.re_protein_capture'
#end if
#elif $prot_naming.method == "attr"
- #if $protein_id_attr:
- --protein_id_attr '$protein_id_attr'
+ #if $prot_naming.protein_id_attr:
+ --protein_id_attr '$prot_naming.protein_id_attr'
#end if
#end if
@@ -43,20 +43,14 @@
> $results
]]>
-
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-
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+
@@ -66,30 +60,30 @@
-
+
-
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-
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-
-
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+
Load features from a gff file
@HELP@
-
+
diff -r 60d7b4054865 -r 4451447ae065 macros.xml
--- a/macros.xml Mon Nov 05 12:20:09 2018 -0500
+++ b/macros.xml Fri Nov 23 11:15:47 2018 -0500
@@ -2,7 +2,7 @@
- python-chado
+ python-chadojq
@@ -16,7 +16,7 @@
- 2.2.2
+ 2.2.3