Merge branch 'release_18.05' into dev

galaxyproject · May 21, 2018 · a992637 · a992637
2 parents d0cb1d6 + 805854a
commit a992637
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Showing 4 changed files with 5 additions and 3 deletions.
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -39,7 +39,7 @@ var ANY_COLLECTION_TYPE_DESCRIPTION = {
         return "AnyCollectionType[]";
     },
     append: function() {
-        throw "Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION";
+        return ANY_COLLECTION_TYPE_DESCRIPTION;
     },
     equal: function(other) {
         return other === this;

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
@@ -52,6 +52,7 @@
       <converter file="len_to_linecount.xml" target_datatype="linecount"/>
     </datatype>
     <datatype extension="dmnd" type="galaxy.datatypes.binary:DMND" display_in_upload="false"/>
+    <datatype extension="idat" type="galaxy.datatypes.binary:Idat" display_in_upload="true"/>
     <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
       <display file="ucsc/bigbed.xml"/>
       <display file="igb/bb.xml"/>
@@ -708,6 +709,7 @@
     <sniffer type="galaxy.datatypes.binary:Fast5Archive"/>
     <sniffer type="galaxy.datatypes.binary:PostgresqlArchive"/>
     <sniffer type="galaxy.datatypes.binary:ICM"/>
+    <sniffer type="galaxy.datatypes.binary:Idat"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -118,7 +118,7 @@ sqlalchemy-utils==0.33.2
 sqlalchemy==1.2.6
 sqlparse==0.2.4
 stevedore==1.28.0
-subprocess32==3.2.7; python_version < '3.0'
+subprocess32==3.5.0; python_version < '3.0'
 svgwrite==1.1.12
 tempita==0.5.2
 tzlocal==1.5.1

diff --git a/lib/galaxy/tools/errors.py b/lib/galaxy/tools/errors.py
@@ -163,7 +163,7 @@ def create_report(self, user, email='', message='', redact_user_details_in_bugre
         hda_id_encoded = self.app.security.encode_id(hda.id)
         hda_show_params_link = web.url_for(controller="dataset", action="show_params", dataset_id=hda_id_encoded, qualified=True)
         # Build the email message
-        if self.redact_user_details_in_bugreport:
+        if redact_user_details_in_bugreport:
             # This is sub-optimal but it is hard to solve fully. This affects
             # the github posting method more than the traditional email plugin.
             # There is no way around CCing the person with the traditional