Merge pull request #10259 from mvdbeek/dev

Merge 20.05 into dev

client/src/components/Workflow/Editor/Node.vue

@@ -414,8 +414,6 @@ export default {
             }
             const outputName = output.name;
             const outputTerminal = this.outputTerminals[outputName];
-            outputTerminal.force_datatype = datatype;
-            output.force_datatype = datatype;
             if (datatype) {
                 this.postJobActions["ChangeDatatypeAction" + outputName] = {
                     action_arguments: { newtype: datatype },

client/src/components/Workflow/Editor/NodeOutput.vue

@@ -74,7 +74,6 @@ export default {
                 collection_type: collection_type,
                 collection_type_source: collection_type_source,
                 datatypes: output.extensions,
-                force_datatype: output.force_datatype,
                 optional: output.optional,
             });
         } else if (output.parameter) {
@@ -91,7 +90,6 @@ export default {
                 name: output.name,
                 element: this.$refs.terminal,
                 datatypes: output.extensions,
-                force_datatype: output.force_datatype,
                 optional: output.optional,
             });
         }

client/src/components/Workflow/Editor/modules/terminals.js

@@ -589,18 +589,14 @@ class BaseOutputTerminal extends Terminal {
         super(attr);
         this.datatypes = attr.datatypes;
         this.optional = attr.optional;
-        this.force_datatype = attr.force_datatype;
+    }
+    get force_datatype() {
+        const changeOutputDatatype = this.node.postJobActions["ChangeDatatypeAction" + this.name];
+        return changeOutputDatatype ? changeOutputDatatype.action_arguments["newtype"] : null;
     }
     update(output) {
         this.datatypes = output.datatypes || output.extensions;
         this.optional = output.optional;
-        this.force_datatype = output.force_datatype;
-        const changeOutputDatatype = this.node.postJobActions["ChangeOutputDatatype" + output.name];
-        if (changeOutputDatatype) {
-            this.node.outputTerminals[output.name].force_datatype = changeOutputDatatype.action_arguments["newtype"];
-        } else {
-            this.node.outputTerminals[output.name].force_datatype = null;
-        }
     }
 }
 

client/tests/qunit/tests/workflow_editor_tests.js

@@ -35,6 +35,7 @@ const nodeData = {
 class Node {
     constructor(attr = {}) {
         this.element = attr.element;
+        this.postJobActions = {};
         this.inputTerminals = {};
         this.outputTerminals = {};
     }
@@ -326,7 +327,7 @@ QUnit.test("Collection output can connect to same collection input type", functi
         datatypes: "txt",
         collection_type: "list",
     });
-    outputTerminal.node = {};
+    outputTerminal.node = {postJobActions: {}};
     assert.ok(
         inputTerminal.canAccept(outputTerminal).canAccept,
         "Input terminal " + inputTerminal + " can not accept " + outputTerminal

lib/galaxy/datatypes/binary.py

@@ -32,6 +32,9 @@ from galaxy.util.checkers import is_bz2, is_gzip
 from . import data, dataproviders
 
 log = logging.getLogger(__name__)
+# pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
+# Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
+pysam.set_verbosity(0)
 
 # Currently these supported binary data types must be manually set on upload
 
@@ -486,9 +489,9 @@ class Bam(BamNative):
             # we start another process and discard stderr.
             if index_flag == '-b':
                 # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
-                cmd = ['python', '-c', "import pysam; pysam.index('{}', '{}')".format(file_name, index_name)]
+                cmd = ['python', '-c', "import pysam; pysam.set_verbosity(0); pysam.index('{}', '{}')".format(file_name, index_name)]
             else:
-                cmd = ['python', '-c', "import pysam; pysam.index('{}', '{}', '{}')".format(index_flag, file_name, index_name)]
+                cmd = ['python', '-c', "import pysam; pysam.set_verbosity(0); pysam.index('{}', '{}', '{}')".format(index_flag, file_name, index_name)]
             with open(os.devnull, 'w') as devnull:
                 subprocess.check_call(cmd, stderr=devnull, shell=False)
             needs_sorting = False

lib/galaxy/visualization/data_providers/genome.py

@@ -27,6 +27,9 @@ from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and
 # Utility functions.
 #
 
+# pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
+# Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
+pysam.set_verbosity(0)
 PYSAM_INDEX_SYMLINK_NECESSARY = packaging.version.parse(pysam.__version__) <= packaging.version.parse('0.13.0')