From e1f1bad8079b0a2f0977b5c7cb73350a8372f4f3 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 11 Sep 2019 15:36:36 -0400
Subject: [PATCH 1/9] Allow user to switch to alternative toolshed if main
 toolshed is offline

---
 .../scripts/components/Toolshed/Index.vue     | 29 ++++++++++---------
 lib/galaxy/webapps/galaxy/api/toolshed.py     |  5 +++-
 2 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/client/galaxy/scripts/components/Toolshed/Index.vue b/client/galaxy/scripts/components/Toolshed/Index.vue
index c5788beb546..e45d8630e01 100644
--- a/client/galaxy/scripts/components/Toolshed/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/Index.vue
@@ -1,21 +1,21 @@
 <template>
     <div class="overflow-auto h-100 p-1" @scroll="onScroll">
+        <b-input
+            class="mb-3"
+            placeholder="search repositories"
+            v-model="queryInput"
+            @input="delayQuery"
+            @change="setQuery"
+        />
+        <serverselection
+            :toolshedUrl="toolshedUrl"
+            :toolshedUrls="toolshedUrls"
+            :total="total"
+            :loading="loading"
+            @onToolshed="setToolshed"
+        />
         <div v-if="error" class="alert alert-danger">{{ error }}</div>
         <div v-else>
-            <b-input
-                class="mb-3"
-                placeholder="search repositories"
-                v-model="queryInput"
-                @input="delayQuery"
-                @change="setQuery"
-            />
-            <serverselection
-                :toolshedUrl="toolshedUrl"
-                :toolshedUrls="toolshedUrls"
-                :total="total"
-                :loading="loading"
-                @onToolshed="setToolshed"
-            />
             <repositories
                 :query="query"
                 :scrolled="scrolled"
@@ -102,6 +102,7 @@ export default {
             this.query = this.queryInput = query;
         },
         setToolshed(url) {
+            this.error = null;
             this.toolshedUrl = url;
         },
         setTotal(total) {
diff --git a/lib/galaxy/webapps/galaxy/api/toolshed.py b/lib/galaxy/webapps/galaxy/api/toolshed.py
index f16c03862b4..8a41c42c9ae 100644
--- a/lib/galaxy/webapps/galaxy/api/toolshed.py
+++ b/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.")

From 008246becab71326a4fb45eab778f4124cb6b9a1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 11 Sep 2019 15:41:01 -0400
Subject: [PATCH 2/9] Add category search option to toolshed component

---
 client/galaxy/scripts/components/Toolshed/Categories.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/Toolshed/Categories.vue b/client/galaxy/scripts/components/Toolshed/Categories.vue
index 27e034ccedd..dd4144bc9dc 100644
--- a/client/galaxy/scripts/components/Toolshed/Categories.vue
+++ b/client/galaxy/scripts/components/Toolshed/Categories.vue
@@ -65,7 +65,7 @@ export default {
                 });
         },
         onCategory(category) {
-            this.$emit("onCategory", category);
+            this.$emit("onCategory", `category:${category}`);
         }
     }
 };

From 729c40fd3c2d712a9573376382910d3e6b5b5857 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 11 Sep 2019 15:54:08 -0400
Subject: [PATCH 3/9] Use quotes to wrap category search terms in toolshed
 client

---
 client/galaxy/scripts/components/Toolshed/Categories.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/components/Toolshed/Categories.vue b/client/galaxy/scripts/components/Toolshed/Categories.vue
index dd4144bc9dc..305df4f9aeb 100644
--- a/client/galaxy/scripts/components/Toolshed/Categories.vue
+++ b/client/galaxy/scripts/components/Toolshed/Categories.vue
@@ -65,7 +65,7 @@ export default {
                 });
         },
         onCategory(category) {
-            this.$emit("onCategory", `category:${category}`);
+            this.$emit("onCategory", `category:'${category}'`);
         }
     }
 };

From 33399500c6715e38f52bd308276fd76d205ac651 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 12 Sep 2019 14:54:54 -0400
Subject: [PATCH 4/9] Add clear search option to toolshed search text field

---
 .../scripts/components/Toolshed/Index.vue     | 22 ++++++++++++-------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/client/galaxy/scripts/components/Toolshed/Index.vue b/client/galaxy/scripts/components/Toolshed/Index.vue
index e45d8630e01..17ec592f63b 100644
--- a/client/galaxy/scripts/components/Toolshed/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/Index.vue
@@ -1,12 +1,18 @@
 <template>
     <div class="overflow-auto h-100 p-1" @scroll="onScroll">
-        <b-input
-            class="mb-3"
-            placeholder="search repositories"
-            v-model="queryInput"
-            @input="delayQuery"
-            @change="setQuery"
-        />
+        <b-input-group class="mb-3">
+            <b-input
+                placeholder="search repositories"
+                v-model="queryInput"
+                @input="delayQuery"
+                @change="setQuery"
+            />
+            <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"
@@ -111,7 +117,7 @@ export default {
         setLoading(loading) {
             this.loading = loading;
         },
-        onScroll: function({ target: { scrollTop, clientHeight, scrollHeight } }) {
+        onScroll({ target: { scrollTop, clientHeight, scrollHeight } }) {
             this.scrolled = scrollTop + clientHeight >= scrollHeight;
         }
     }

From 3b5416befc6cf407dafc4f1370b0dfba3e514895 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 12 Sep 2019 16:14:24 -0400
Subject: [PATCH 5/9] fix and refactor the allow query filters for TS searching

thanks to @jmchilton for the idea
---
 .../webapps/tool_shed/search/repo_search.py   | 39 ++++++++-----------
 1 file changed, 16 insertions(+), 23 deletions(-)

diff --git a/lib/galaxy/webapps/tool_shed/search/repo_search.py b/lib/galaxy/webapps/tool_shed/search/repo_search.py
index c5474ddd97d..436732d995a 100644
--- a/lib/galaxy/webapps/tool_shed/search/repo_search.py
+++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py
@@ -170,6 +170,8 @@ 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("abyss category:assembly")
         (And([Term('categories', 'assembly')]), 'abyss')
         >>> rs._parse_reserved_filters("abyss category:assembly greg")
@@ -181,28 +183,19 @@ 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|owner):(\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

From 29df0c3fa43042ff55846c02727acf268edffa35 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 12 Sep 2019 16:19:14 -0400
Subject: [PATCH 6/9] drop unused var; extend test, fix shorthands usage

---
 lib/galaxy/webapps/tool_shed/search/repo_search.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/tool_shed/search/repo_search.py b/lib/galaxy/webapps/tool_shed/search/repo_search.py
index 436732d995a..94ab0793b7c 100644
--- a/lib/galaxy/webapps/tool_shed/search/repo_search.py
+++ b/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")
@@ -172,6 +171,8 @@ class RepoSearch(object):
         (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")
@@ -186,7 +187,7 @@ class RepoSearch(object):
         allow_terms = []
         search_term_without_filters = None
         search_space = search_term.replace('"', "'")
-        reserved = re.compile(r"(category|owner):(\w+|\'.*?\')")
+        reserved = re.compile(r"(category|c|owner|o):(\w+|\'.*?\')")
         while True:
             match = reserved.search(search_space)
             if match is None:

From f593b146414284dd52f85e1d817de45ccd140a6f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 13 Sep 2019 10:12:55 +0100
Subject: [PATCH 7/9] Change MySQL from deprecated to unsupported

Follow-up on https://github.com/galaxyproject/galaxy/pull/8407
---
 doc/source/admin/production.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/source/admin/production.md b/doc/source/admin/production.md
index c7ea2f4b5b2..afa14d22584 100644
--- a/doc/source/admin/production.md
+++ b/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:
 ```

From 69bd851a63e0b4da7657daa5d0053b6d19ef5ddf Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 13 Sep 2019 12:12:55 -0400
Subject: [PATCH 8/9] Reset input in toolshed search input on escape key

---
 client/galaxy/scripts/components/Toolshed/Index.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/galaxy/scripts/components/Toolshed/Index.vue b/client/galaxy/scripts/components/Toolshed/Index.vue
index 17ec592f63b..ce2c48253e6 100644
--- a/client/galaxy/scripts/components/Toolshed/Index.vue
+++ b/client/galaxy/scripts/components/Toolshed/Index.vue
@@ -6,6 +6,7 @@
                 v-model="queryInput"
                 @input="delayQuery"
                 @change="setQuery"
+                @keydown.esc="setQuery()"
             />
             <b-input-group-append>
                 <b-btn :disabled="!queryInput" @click="setQuery()">

From 1da8e7d8cf8f48878cf90287771df713ee2abab0 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 16 Sep 2019 09:38:24 -0400
Subject: [PATCH 9/9] Bugfix for reports with output collections.

Reported by bgruening:

```
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 282, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/galaxy/api/workflows.py", line 887, in show_invocation_report
    trans, workflow_invocation, runtime_report_config_json=runtime_report_config_json, plugin_type=generator_plugin_type
  File "lib/galaxy/workflow/reports/__init__.py", line 11, in generate_report_json
    return plugin.generate_report_json(trans, invocation, runtime_report_config_json=runtime_report_config_json)
  File "lib/galaxy/workflow/reports/generators/__init__.py", line 45, in generate_report_json
    internal_markdown = resolve_invocation_markdown(trans, invocation, workflow_markdown)
  File "lib/galaxy/managers/markdown_util.py", line 236, in resolve_invocation_markdown
    workflow_markdown,
  File "lib/galaxy/managers/markdown_util.py", line 329, in _remap_galaxy_markdown_calls
    return _remap_galaxy_markdown_containers(_remap_container, markdown)
  File "lib/galaxy/managers/markdown_util.py", line 297, in _remap_galaxy_markdown_containers
    (replacement, whole_block) = func(match.group(1))
  File "lib/galaxy/managers/markdown_util.py", line 327, in _remap_container
    return func(match.group(1), matching_line + "\n")
  File "lib/galaxy/managers/markdown_util.py", line 163, in _section_remap
    if not output_assoc.workflow_output.label:
AttributeError: 'HistoryDatasetCollectionAssociation' object has no attribute 'workflow_output'
```
---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index b93c268b351..fca2071ad2e 100644
--- a/lib/galaxy/model/__init__.py
+++ b/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