Merge branch 'release_19.09' into dev

client/galaxy/scripts/components/Toolshed/Categories.vue

@@ -65,7 +65,7 @@ export default {
                 });
         },
         onCategory(category) {
-            this.$emit("onCategory", category);
+            this.$emit("onCategory", `category:'${category}'`);
         }
     }
 };

client/galaxy/scripts/components/Toolshed/Index.vue

@@ -1,21 +1,28 @@
 <template>
     <div class="overflow-auto h-100 p-1" @scroll="onScroll">
-        <div v-if="error" class="alert alert-danger">{{ error }}</div>
-        <div v-else>
+        <b-input-group class="mb-3">
             <b-input
-                class="mb-3"
                 placeholder="search repositories"
                 v-model="queryInput"
                 @input="delayQuery"
                 @change="setQuery"
+                @keydown.esc="setQuery()"
             />
-            <serverselection
-                :toolshedUrl="toolshedUrl"
-                :toolshedUrls="toolshedUrls"
-                :total="total"
-                :loading="loading"
-                @onToolshed="setToolshed"
-            />
+            <b-input-group-append>
+                <b-btn :disabled="!queryInput" @click="setQuery()">
+                    <i class="fa fa-times"/>
+                </b-btn>
+            </b-input-group-append>
+        </b-input-group>
+        <serverselection
+            :toolshedUrl="toolshedUrl"
+            :toolshedUrls="toolshedUrls"
+            :total="total"
+            :loading="loading"
+            @onToolshed="setToolshed"
+        />
+        <div v-if="error" class="alert alert-danger">{{ error }}</div>
+        <div v-else>
             <repositories
                 :query="query"
                 :scrolled="scrolled"
@@ -102,6 +109,7 @@ export default {
             this.query = this.queryInput = query;
         },
         setToolshed(url) {
+            this.error = null;
             this.toolshedUrl = url;
         },
         setTotal(total) {
@@ -110,7 +118,7 @@ export default {
         setLoading(loading) {
             this.loading = loading;
         },
-        onScroll: function({ target: { scrollTop, clientHeight, scrollHeight } }) {
+        onScroll({ target: { scrollTop, clientHeight, scrollHeight } }) {
             this.scrolled = scrollTop + clientHeight >= scrollHeight;
         }
     }

doc/source/admin/production.md

@@ -75,11 +75,11 @@ postgresql:///mydatabase?host=/var/run/postgresql
 
 For more hints on available options for the database URL, see the [SQLAlchemy documentation](https://docs.sqlalchemy.org/en/latest/core/engines.html#database-urls).
 
-#### Deprecated MySQL support
+#### MySQL database server (unsupported)
 
-Postgres database backend is more used and better tested, please use it if you can.
+Postgres database backend is far more used and better tested, please use it if you can.
 
-In the past Galaxy supported [MySQL](https://dev.mysql.com/) but currently there are nontrivial problems associated with it so expect amount of troubleshooting when using it.
+In the past Galaxy supported [MySQL](https://dev.mysql.com/), but currently there may be nontrivial problems associated with it, so expect some amount of troubleshooting when using it.
 
 Connection string example:
 ```

lib/galaxy/model/__init__.py

@@ -5071,7 +5071,7 @@ class WorkflowInvocation(UsesCreateAndUpdateTime, Dictifiable, RepresentById):
         for output_dataset_assoc in self.output_datasets:
             outputs.append(output_dataset_assoc)
         for output_dataset_collection_assoc in self.output_dataset_collections:
-            outputs.append(output_dataset_collection_assoc.dataset_collection)
+            outputs.append(output_dataset_collection_assoc)
         return outputs
 
     @property

lib/galaxy/webapps/galaxy/api/toolshed.py

@@ -335,6 +335,9 @@ class ToolShedController(BaseAPIController):
                 pathspec.append(params.pop("id"))
             if "action" in params:
                 pathspec.append(params.pop("action"))
-            return json.loads(util.url_get(tool_shed_url, params=dict(params), pathspec=pathspec))
+            try:
+                return json.loads(util.url_get(tool_shed_url, params=dict(params), pathspec=pathspec))
+            except Exception as e:
+                raise MessageException("Invalid server response. %s." % str(e))
         else:
             raise MessageException("Invalid toolshed url.")

lib/galaxy/webapps/tool_shed/search/repo_search.py

@@ -15,7 +15,6 @@ from galaxy.exceptions import ObjectNotFound
 if sys.version_info > (3,):
     long = int
 
-RESERVED_SEARCH_TERMS = ["category", "owner"]
 log = logging.getLogger(__name__)
 
 schema = Schema(
@@ -159,7 +158,7 @@ class RepoSearch(object):
         :returns allow_query: whoosh Query object used for filtering
             results of searching in index
         :returns search_term_without_filters: str that represents user's
-            search phrase without the wildcards
+            search phrase without the filters
 
         >>> rs = RepoSearch()
         >>> rs._parse_reserved_filters("category:assembly")
@@ -170,6 +169,10 @@ class RepoSearch(object):
         (And([Term('categories', 'Climate Analysis')]), 'psy_maps')
         >>> rs._parse_reserved_filters("climate category:'Climate Analysis' owner:'bjoern gruening' psy_maps")
         (And([Term('categories', 'Climate Analysis'), Term('repo_owner_username', 'bjoern gruening')]), 'climate psy_maps')
+        >>> rs._parse_reserved_filters("climate category:'John Says This Fails' owner:'bjoern gruening' psy_maps")
+        (And([Term('categories', 'John Says This Fails'), Term('repo_owner_username', 'bjoern gruening')]), 'climate psy_maps')
+        >>> rs._parse_reserved_filters("climate o:'bjoern gruening' middle strings c:'John Says This Fails' psy_maps")
+        (And([Term('repo_owner_username', 'bjoern gruening'), Term('categories', 'John Says This Fails')]), 'climate middle strings psy_maps')
         >>> rs._parse_reserved_filters("abyss category:assembly")
         (And([Term('categories', 'assembly')]), 'abyss')
         >>> rs._parse_reserved_filters("abyss category:assembly greg")
@@ -181,28 +184,19 @@ class RepoSearch(object):
         >>> rs._parse_reserved_filters("meaningoflife:42")
         (None, 'meaningoflife:42')
         """
-        allow_query = None
         allow_terms = []
-        # Split query string on spaces that are not followed by <anytext>singlequote_space_
-        # to allow for quoting filtering values. Also unify double and single quotes into single quotes.
-        search_term_chunks = re.split(r"\s+(?!\w+'\s)", search_term.replace('"', "'"), re.MULTILINE)
-        reserved_terms = []
-        for term_chunk in search_term_chunks:
-            if ":" in term_chunk:
-                reserved_filter = term_chunk.split(":")[0]
-                # Remove the quotes used for delimiting values with space(s)
-                reserved_filter_value = term_chunk.split(":")[1].replace("'", "")
-                if reserved_filter in RESERVED_SEARCH_TERMS:
-                    reserved_terms.append(term_chunk)
-                    if reserved_filter == "category":
-                        allow_terms.append(Term('categories', reserved_filter_value))
-                    elif reserved_filter == "owner":
-                        allow_terms.append(Term('repo_owner_username', reserved_filter_value))
-                else:
-                    pass  # Treat unrecognized filter as normal search term.
-        if allow_terms:
-            allow_query = And(allow_terms)
-            search_term_without_filters = " ".join([chunk for chunk in search_term_chunks if chunk not in reserved_terms])
-        else:
-            search_term_without_filters = search_term
+        search_term_without_filters = None
+        search_space = search_term.replace('"', "'")
+        reserved = re.compile(r"(category|c|owner|o):(\w+|\'.*?\')")
+        while True:
+            match = reserved.search(search_space)
+            if match is None:
+                search_term_without_filters = ' '.join(search_space.split())
+                break
+            if match.groups()[0] in ["category", "c"]:
+                allow_terms.append(Term('categories', match.groups()[1].strip().replace("'", "")))
+            elif match.groups()[0] in ["owner", "o"]:
+                allow_terms.append(Term('repo_owner_username', match.groups()[1].strip().replace("'", "")))
+            search_space = search_space[0:match.start()] + search_space[match.end():]
+        allow_query = And(allow_terms) if allow_terms else None
         return allow_query, search_term_without_filters