From 94328b9684244b5d6782b147130901504229d5fc Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Mon, 24 Jun 2019 14:08:03 +0200
Subject: [PATCH 01/31] merge dev into toolref

---
 client/galaxy/scripts/components/xrefs.vue    | 76 +++++++++++++++++++
 .../galaxy/scripts/mvc/tool/tool-form-base.js | 13 ++++
 doc/schema_template.md                        |  2 +
 lib/galaxy/config.py                          |  3 +-
 lib/galaxy/managers/xrefs.py                  | 31 ++++++++
 lib/galaxy/tool_util/parser/xml.py            |  6 ++
 lib/galaxy/tool_util/parser/yaml.py           |  3 +
 lib/galaxy/tool_util/xsd/galaxy.xsd           | 69 ++++++++++++++---
 lib/galaxy/tools/__init__.py                  | 20 +++++
 lib/galaxy/webapps/galaxy/api/tools.py        |  8 ++
 lib/galaxy/webapps/galaxy/buildapp.py         |  1 +
 11 files changed, 221 insertions(+), 11 deletions(-)
 create mode 100644 client/galaxy/scripts/components/xrefs.vue
 create mode 100644 lib/galaxy/managers/xrefs.py

diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue
new file mode 100644
index 00000000000..a6f925d6eb8
--- /dev/null
+++ b/client/galaxy/scripts/components/xrefs.vue
@@ -0,0 +1,76 @@
+<template>
+    <b-card>
+        <h4 slot="header" class="mb-0">
+            References
+        </h4>
+        <span v-html="content"></span>
+    </b-card>
+</template>
+<script>
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+export default {
+    props: {
+        source: {
+            type: String,
+            required: true
+        },
+        id: {
+            type: String,
+            required: true
+        },
+        type: {
+            type: String,
+            required: true
+        },
+        content: {
+            type: String,
+            required: true
+        },
+        viewRender: {
+            type: Boolean,
+            requried: false,
+            default: true
+        }
+    },
+    data() {
+        return {
+            xrefs: [],
+            errors: []
+        };
+    },
+    created: function() {
+        axios
+            .get(`${getAppRoot()}api/${this.source}/${this.id}/xrefs`)
+            .then(response => {
+                this.type = "";
+                this.content = "<table>";
+                for (var raw_xref of response.data) {
+                    try {
+                        this.type = raw_xref.reftype;
+                        this.content += "<tr>";
+                        this.content += "<th> - ";
+                        this.content += this.type;
+                        this.content += "</th>";
+                        this.content += "<td> : ";
+                        if (this.type == "bio.tools") {
+                            this.content += "<a href=\"https://bio.tools/" + raw_xref.content + "\" target=\"_blank\">" + raw_xref.content + "</a>";
+                        }
+                        else {
+                            this.content += raw_xref.content;
+                        }
+                        this.content += "</td>";
+                        this.content += "</tr>";
+                    } catch (err) {
+                        console.warn("Error parsing xref: " + err);
+                    }
+                }
+                this.content += "</table>";
+            })
+            .catch(e => {
+                console.error(e);
+            });
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index ceb1a0dd109..c2b47fe70d4 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -12,6 +12,7 @@ import Ui from "mvc/ui/ui-misc";
 import FormBase from "mvc/form/form-view";
 import Webhooks from "mvc/webhooks";
 import Citations from "components/Citations.vue";
+import xrefs from "components/xrefs.vue";
 import Vue from "vue";
 import axios from "axios";
 
@@ -268,6 +269,7 @@ export default FormBase.extend({
     _footer: function() {
         var options = this.model.attributes;
         var $el = $("<div/>").append(this._templateHelp(options));
+
         if (options.citations) {
             var citationInstance = Vue.extend(Citations);
             var vm = document.createElement("div");
@@ -279,6 +281,17 @@ export default FormBase.extend({
                 }
             }).$mount(vm);
         }
+	if (options.xrefs) {
+            var xrefInstance = Vue.extend(xrefs);
+            vm = document.createElement("div");
+            $el.append(vm);
+            new xrefInstance({
+                propsData: {
+                    id: options.id, 
+                    source: "tools"
+                }
+            }).$mount(vm);
+        }
         return $el;
     },
 
diff --git a/doc/schema_template.md b/doc/schema_template.md
index a08c3fc12ec..681ca56a5fe 100644
--- a/doc/schema_template.md
+++ b/doc/schema_template.md
@@ -18,6 +18,8 @@ $tag:tool|description://element[@name='tool']//element[@name='description']
 $tag:tool|macros://complexType[@name='Macros']
 $tag:tool|edam_topics://complexType[@name='EdamTopics']
 $tag:tool|edam_operations://complexType[@name='EdamOperations']
+$tag:tool|xrefs://complexType[@name='xrefs']
+$tag:tool|xrefs|xref://complexType[@name='xref']
 $tag:tool|requirements://complexType[@name='Requirements']
 $tag:tool|requirements|requirement://complexType[@name='Requirement']
 $tag:tool|requirements|container://complexType[@name='Container']
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index f81a2293e95..6a384b42df9 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -38,7 +38,6 @@ from .version import VERSION_MAJOR
 
 log = logging.getLogger(__name__)
 
-
 PATH_DEFAULTS = dict(
     auth_config_file=['config/auth_conf.xml', 'config/auth_conf.xml.sample'],
     data_manager_config_file=['config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample'],
@@ -1060,11 +1059,13 @@ class ConfiguresGalaxyMixin(object):
     def _configure_toolbox(self):
         from galaxy import tools
         from galaxy.managers.citations import CitationsManager
+        from galaxy.managers.xrefs import xrefsManager
         from galaxy.tool_util.deps import containers
         from galaxy.tool_util.deps.dependencies import AppInfo
         import galaxy.tools.search
 
         self.citations_manager = CitationsManager(self)
+        self.xrefs_manager = xrefsManager(self)
 
         from galaxy.managers.tools import DynamicToolManager
         self.dynamic_tools_manager = DynamicToolManager(self)
diff --git a/lib/galaxy/managers/xrefs.py b/lib/galaxy/managers/xrefs.py
new file mode 100644
index 00000000000..917c82b8571
--- /dev/null
+++ b/lib/galaxy/managers/xrefs.py
@@ -0,0 +1,31 @@
+
+class xrefsManager(object):
+
+    def __init__(self, app):
+        self.app = app
+
+    def parse_xref(self, xref_elem):
+        return parse_xref(xref_elem, self)
+
+    def _get_tool(self, tool_id):
+        tool = self.app.toolbox.get_tool(tool_id)
+        return tool
+
+
+def parse_xref(elem, tool_ref_manager):
+    """ Parse a xreference entry from the specified XML element."""
+    return xref(elem)
+
+
+class Base_xref(object):
+    def to_dict(self):
+        return dict(
+            reftype=self.reftype,
+            content=self.content,
+        )
+
+
+class xref(Base_xref):
+    def __init__(self, elem):
+        self.content = elem.text.strip()
+        self.reftype = elem.attrib.get('type', None)
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 24eca5a78a4..f65280298c9 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -95,6 +95,12 @@ class XmlToolSource(ToolSource):
             return []
         return [edam_topic.text for edam_topic in edam_topics.findall("edam_topic")]
 
+    def parse_xrefs(self):
+        xrefs = self.root.find("xrefs")
+        if xrefs is None:
+            return []
+        return [xref.text for xref in xrefs.findall("xref") if xref.get("type") in {'bio.tools'}]
+
     def parse_description(self):
         return xml_text(self.root, "description")
 
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index d13331cd768..76bbdc1e133 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -40,6 +40,9 @@ class YamlToolSource(ToolSource):
     def parse_edam_topics(self):
         return self.root_dict.get("edam_topics", [])
 
+    def parse_xrefs(self):
+        return self.root_dict.get("xrefs", [])
+
     def parse_is_multi_byte(self):
         return self.root_dict.get("is_multi_byte", self.default_is_multi_byte)
 
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index a9c208e62ca..3c753d87899 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -47,7 +47,8 @@ A ``data_source`` tool contains a few more relevant attributes.
         <xs:element name="macros" type="Macros" minOccurs="0"/>
         <xs:element name="edam_topics" type="EdamTopics" minOccurs="0"/>
         <xs:element name="edam_operations" type="EdamOperations" minOccurs="0"/>
-        <xs:element name="requirements" type="Requirements" minOccurs="0"/>
+        <xs:element name="xrefs" type="xrefs" minOccurs="0" />
+	<xs:element name="requirements" type="Requirements" minOccurs="0"/>
         <xs:element name="description" type="xs:string" minOccurs="0">
           <xs:annotation gxdocs:best_practices="tool-descriptions">
             <xs:documentation xml:lang="en"><![CDATA[The value is displayed in
@@ -5581,14 +5582,62 @@ A tool can have any number of EDAM operation references.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-        <xs:element name="edam_operation" minOccurs="0" maxOccurs="unbounded">
-          <xs:simpleType>
-            <xs:restriction base="xs:string">
-              <xs:pattern value="operation_[0-9]{4}"></xs:pattern>
-            </xs:restriction>
-          </xs:simpleType>
-        </xs:element>
-      </xs:sequence>
-    </xs:complexType>
+      <xs:element name="edam_operation" minOccurs="0" maxOccurs="unbounded">
+        <xs:simpleType>
+          <xs:restriction base="xs:string">
+            <xs:pattern value="operation_[0-9]{4}"></xs:pattern>
+          </xs:restriction>
+        </xs:simpleType>
+      </xs:element>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="xrefs">
+    <xs:annotation>
+      <xs:documentation xml:lang="en"><![CDATA[
+Container tag set for the ``<xref>`` tags.
+A tool can refer multiple reference IDs.
+	
+```xml
+   <!-- Example: this tool is seqtk -->
+   <xrefs>      
+	<xref type="bio.tools">seqtk</xref>
+   </xrefs>
+   <!-- https://bio.tools/seqtk -->
+```
+   
+]]></xs:documentation>
+    </xs:annotation>
+      <xs:sequence>
+        <xs:element name="xref" type="xref" minOccurs="0" maxOccurs="unbounded">
+      </xs:element>
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="xref">
+    <xs:annotation>
+      <xs:documentation xml:lang="en">Each xrefs element can contain one or
+more ``xref`` tag elements - each of which specifies reference information 
+according to a catalog or an other.
+  </xs:documentation>
+    </xs:annotation>
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute name="type" type="xrefType" use="required">
+          <xs:annotation>
+            <xs:documentation xml:lang="en">Type of reference - currently ``bio.tools``
+is the only supported options.</xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
+  <xs:simpleType name="xrefType">
+    <xs:annotation>
+      <xs:documentation xml:lang="en">Type of Reference.</xs:documentation>
+    </xs:annotation>
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="bio.tools"/>
+      <!--xs:enumeration value="whatelse"/-->
+    </xs:restriction>
+  </xs:simpleType>
 
 </xs:schema>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 920dec40203..782a8269c3a 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -808,6 +808,7 @@ class Tool(Dictifiable):
         self.containers = containers
 
         self.citations = self._parse_citations(tool_source)
+        self.xrefs = self._parse_xrefs(tool_source)
 
         # Determine if this tool can be used in workflows
         self.is_workflow_compatible = self.check_workflow_compatible(tool_source)
@@ -1079,6 +1080,24 @@ class Tool(Dictifiable):
                     citations.append(citation)
         return citations
 
+    def _parse_xrefs(self, tool_source):
+        if not hasattr(tool_source, 'root'):
+            return []
+        root = tool_source.root
+        xrefs = []
+        xrefs_elem = root.find("xrefs")
+        if xrefs_elem is None:
+            return xrefs
+
+        for xref_elem in xrefs_elem:
+            if xref_elem.tag != "xref":
+                pass
+            if hasattr(self.app, 'xrefs_manager'):
+                xref = self.app.xrefs_manager.parse_xref(xref_elem)
+                if xref:
+                    xrefs.append(xref)
+        return xrefs
+
     def parse_input_elem(self, page_source, enctypes, context=None):
         """
         Parse a parent element whose children are inputs -- these could be
@@ -1989,6 +2008,7 @@ class Tool(Dictifiable):
             'id'            : self.id,
             'help'          : tool_help,
             'citations'     : bool(self.citations),
+            'xrefs'         : bool(self.xrefs),
             'sharable_url'  : self.sharable_url,
             'message'       : tool_message,
             'warnings'      : tool_warnings,
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index d86a11d5b9b..6374169b0c2 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -403,6 +403,14 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
             rval.append(citation.to_dict('bibtex'))
         return rval
 
+    @expose_api_anonymous_and_sessionless
+    def xrefs(self, trans, id, **kwds):
+        tool = self._get_tool(id, user=trans.user)
+        rval = []
+        for xref in tool.xrefs:
+            rval.append(xref.to_dict())
+        return rval
+
     @web.legacy_expose_api_raw
     @web.require_admin
     def download(self, trans, id, **kwds):
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 8f9825ed845..a2145988d06 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -348,6 +348,7 @@ def populate_api_routes(webapp, app):
     webapp.mapper.connect('/api/tools/{id:.+?}/test_data', action='test_data', controller="tools")
     webapp.mapper.connect('/api/tools/{id:.+?}/diagnostics', action='diagnostics', controller="tools")
     webapp.mapper.connect('/api/tools/{id:.+?}/citations', action='citations', controller="tools")
+    webapp.mapper.connect('/api/tools/{id:.+?}/xrefs', action='xrefs', controller="tools")
     webapp.mapper.connect('/api/tools/{id:.+?}/download', action='download', controller="tools")
     webapp.mapper.connect('/api/tools/{id:.+?}/requirements', action='requirements', controller="tools")
     webapp.mapper.connect('/api/tools/{id:.+?}/install_dependencies', action='install_dependencies', controller="tools", conditions=dict(method=["POST"]))

From 17807f4ddd9499b71b5be7724fa10085a466f8b8 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Tue, 25 Jun 2019 09:44:55 +0200
Subject: [PATCH 02/31] advices from nsoranzo

---
 lib/galaxy/tool_util/xsd/galaxy.xsd    | 8 +++-----
 lib/galaxy/webapps/galaxy/api/tools.py | 5 +----
 2 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 3c753d87899..2f4e839d557 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -48,7 +48,7 @@ A ``data_source`` tool contains a few more relevant attributes.
         <xs:element name="edam_topics" type="EdamTopics" minOccurs="0"/>
         <xs:element name="edam_operations" type="EdamOperations" minOccurs="0"/>
         <xs:element name="xrefs" type="xrefs" minOccurs="0" />
-	<xs:element name="requirements" type="Requirements" minOccurs="0"/>
+        <xs:element name="requirements" type="Requirements" minOccurs="0"/>
         <xs:element name="description" type="xs:string" minOccurs="0">
           <xs:annotation gxdocs:best_practices="tool-descriptions">
             <xs:documentation xml:lang="en"><![CDATA[The value is displayed in
@@ -5614,10 +5614,8 @@ A tool can refer multiple reference IDs.
   </xs:complexType>
   <xs:complexType name="xref">
     <xs:annotation>
-      <xs:documentation xml:lang="en">Each xrefs element can contain one or
-more ``xref`` tag elements - each of which specifies reference information 
-according to a catalog or an other.
-  </xs:documentation>
+      <xs:documentation xml:lang="en">The ``xref`` element specifies reference 
+information according to a catalog.</xs:documentation>
     </xs:annotation>
     <xs:simpleContent>
       <xs:extension base="xs:string">
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 6374169b0c2..f62fc1bb619 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -406,10 +406,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
     @expose_api_anonymous_and_sessionless
     def xrefs(self, trans, id, **kwds):
         tool = self._get_tool(id, user=trans.user)
-        rval = []
-        for xref in tool.xrefs:
-            rval.append(xref.to_dict())
-        return rval
+        return [_.to_dict() for _ in tool.xrefs]
 
     @web.legacy_expose_api_raw
     @web.require_admin

From f9fa46670a2452d6a8f2ebc0e9d2cbefaeba1dde Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Tue, 25 Jun 2019 13:33:25 +0200
Subject: [PATCH 03/31] correct space insert

---
 client/galaxy/scripts/mvc/tool/tool-form-base.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index c2b47fe70d4..b98d5f1929b 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -269,7 +269,6 @@ export default FormBase.extend({
     _footer: function() {
         var options = this.model.attributes;
         var $el = $("<div/>").append(this._templateHelp(options));
-
         if (options.citations) {
             var citationInstance = Vue.extend(Citations);
             var vm = document.createElement("div");

From 8df9d5f8c0996b21cd42c514c4894469fe29e92c Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Tue, 25 Jun 2019 13:34:22 +0200
Subject: [PATCH 04/31] remove xref manager

---
 lib/galaxy/config.py         |  3 +--
 lib/galaxy/managers/xrefs.py | 31 -------------------------------
 lib/galaxy/tools/__init__.py | 10 +++++-----
 3 files changed, 6 insertions(+), 38 deletions(-)
 delete mode 100644 lib/galaxy/managers/xrefs.py

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 6a384b42df9..f81a2293e95 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -38,6 +38,7 @@ from .version import VERSION_MAJOR
 
 log = logging.getLogger(__name__)
 
+
 PATH_DEFAULTS = dict(
     auth_config_file=['config/auth_conf.xml', 'config/auth_conf.xml.sample'],
     data_manager_config_file=['config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample'],
@@ -1059,13 +1060,11 @@ class ConfiguresGalaxyMixin(object):
     def _configure_toolbox(self):
         from galaxy import tools
         from galaxy.managers.citations import CitationsManager
-        from galaxy.managers.xrefs import xrefsManager
         from galaxy.tool_util.deps import containers
         from galaxy.tool_util.deps.dependencies import AppInfo
         import galaxy.tools.search
 
         self.citations_manager = CitationsManager(self)
-        self.xrefs_manager = xrefsManager(self)
 
         from galaxy.managers.tools import DynamicToolManager
         self.dynamic_tools_manager = DynamicToolManager(self)
diff --git a/lib/galaxy/managers/xrefs.py b/lib/galaxy/managers/xrefs.py
deleted file mode 100644
index 917c82b8571..00000000000
--- a/lib/galaxy/managers/xrefs.py
+++ /dev/null
@@ -1,31 +0,0 @@
-
-class xrefsManager(object):
-
-    def __init__(self, app):
-        self.app = app
-
-    def parse_xref(self, xref_elem):
-        return parse_xref(xref_elem, self)
-
-    def _get_tool(self, tool_id):
-        tool = self.app.toolbox.get_tool(tool_id)
-        return tool
-
-
-def parse_xref(elem, tool_ref_manager):
-    """ Parse a xreference entry from the specified XML element."""
-    return xref(elem)
-
-
-class Base_xref(object):
-    def to_dict(self):
-        return dict(
-            reftype=self.reftype,
-            content=self.content,
-        )
-
-
-class xref(Base_xref):
-    def __init__(self, elem):
-        self.content = elem.text.strip()
-        self.reftype = elem.attrib.get('type', None)
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 782a8269c3a..349f7c6205f 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1088,14 +1088,14 @@ class Tool(Dictifiable):
         xrefs_elem = root.find("xrefs")
         if xrefs_elem is None:
             return xrefs
-
         for xref_elem in xrefs_elem:
             if xref_elem.tag != "xref":
                 pass
-            if hasattr(self.app, 'xrefs_manager'):
-                xref = self.app.xrefs_manager.parse_xref(xref_elem)
-                if xref:
-                    xrefs.append(xref)
+            xref = dict(
+                reftype=xref_elem.text.strip(),
+                content=xref_elem.attrib.get('type', None)
+            )
+            xrefs.append(xref)
         return xrefs
 
     def parse_input_elem(self, page_source, enctypes, context=None):

From 40e42b852262c8693cddca475e2a73d0ec368711 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Wed, 26 Jun 2019 10:11:16 +0200
Subject: [PATCH 05/31] correct reftype-content invert

---
 lib/galaxy/tools/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 349f7c6205f..6d70823fa84 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1092,8 +1092,8 @@ class Tool(Dictifiable):
             if xref_elem.tag != "xref":
                 pass
             xref = dict(
-                reftype=xref_elem.text.strip(),
-                content=xref_elem.attrib.get('type', None)
+                reftype=xref_elem.attrib.get('type', None),
+                content=xref_elem.text.strip()
             )
             xrefs.append(xref)
         return xrefs

From 3eacbeb794858fe5fa5fbda40344b5e9f61303ad Mon Sep 17 00:00:00 2001
From: Valentin Marcon <v.marcon@outlook.fr>
Date: Wed, 26 Jun 2019 17:15:30 +0200
Subject: [PATCH 06/31] Update lib/galaxy/tools/__init__.py

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 6d70823fa84..59ca8c21c17 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -808,7 +808,7 @@ class Tool(Dictifiable):
         self.containers = containers
 
         self.citations = self._parse_citations(tool_source)
-        self.xrefs = self._parse_xrefs(tool_source)
+        self.xrefs = tool_source.parse_xrefs()
 
         # Determine if this tool can be used in workflows
         self.is_workflow_compatible = self.check_workflow_compatible(tool_source)

From 7347e57509dc24b60bf3d6f9d77a59982068939b Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Thu, 27 Jun 2019 11:41:31 +0200
Subject: [PATCH 07/31] add parsing xml and yaml test

---
 test/unit/tools/test_parsing.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/test/unit/tools/test_parsing.py b/test/unit/tools/test_parsing.py
index 168bd09f0fd..ca04095367b 100644
--- a/test/unit/tools/test_parsing.py
+++ b/test/unit/tools/test_parsing.py
@@ -12,6 +12,9 @@ from galaxy.util import galaxy_directory
 TOOL_XML_1 = """
 <tool name="BWA Mapper" id="bwa" version="1.0.1" is_multi_byte="true" display_interface="true" require_login="true" hidden="true">
     <description>The BWA Mapper</description>
+    <xrefs>
+        <xref type="bio.tools">bwa</xref>
+    </xrefs>
     <version_command interpreter="python">bwa.py --version</version_command>
     <parallelism method="multi" split_inputs="input1" split_mode="to_size" split_size="1" merge_outputs="out_file1" />
     <command interpreter="python">bwa.py --arg1=42</command>
@@ -311,6 +314,10 @@ class XmlLoaderTestCase(BaseLoaderTestCase):
         assert attributes1["compare"] == "sim_size"
         assert attributes1["lines_diff"] == 4
 
+    def test_xrefs(self):
+        xrefs = self._tool_source.parse_xrefs()
+        assert xrefs[0] == "bwa"
+
     def test_exit_code(self):
         tool_source = self._get_tool_source(source_contents="""<tool id="bwa" name="bwa">
             <command detect_errors="exit_code">
@@ -468,6 +475,10 @@ class YamlLoaderTestCase(BaseLoaderTestCase):
         assert attributes1["compare"] == "sim_size"
         assert attributes1["lines_diff"] == 4
 
+    def test_xrefs(self):
+        xrefs = self._tool_source.parse_xrefs()
+        assert xrefs[0] == "bwa"
+
     def test_sanitize(self):
         assert self._tool_source.parse_sanitize() is True
 

From b76eb61c81bbebde1ec3776929067ced8d79d780 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 26 Jun 2019 16:41:56 -0400
Subject: [PATCH 08/31] Bring more directories under packages/ export.

Add quota to data/ (should be refactored to not use trans but is straight forward and the imports are fine for now), and add three new packages.

- auth
- authnz
- app

A lot more needs to be added to app but we need to de-tangle the circular imports between app and web stuff and webapp stuff. It is messier than I thought.
---
 packages/app/HISTORY.rst                      |  12 ++
 packages/app/LICENSE                          |   1 +
 packages/app/MANIFEST.in                      |   1 +
 packages/app/Makefile                         |   1 +
 packages/app/README.rst                       |  14 +++
 packages/app/dev-requirements.txt             |   1 +
 packages/app/galaxy/__init__.py               |   1 +
 packages/app/galaxy/actions                   |   1 +
 packages/app/galaxy/dependencies              |   1 +
 packages/app/galaxy/eggs                      |   1 +
 packages/app/galaxy/forms                     |   1 +
 packages/app/galaxy/project_galaxy_app.py     |  13 +++
 packages/app/galaxy/tours                     |   1 +
 packages/app/galaxy/webhooks                  |   1 +
 packages/app/requirements.txt                 |   3 +
 packages/app/scripts                          |   1 +
 packages/app/setup.cfg                        |   1 +
 packages/app/setup.py                         | 105 ++++++++++++++++++
 packages/auth/HISTORY.rst                     |  12 ++
 packages/auth/LICENSE                         |   1 +
 packages/auth/MANIFEST.in                     |   1 +
 packages/auth/Makefile                        |   1 +
 packages/auth/README.rst                      |  14 +++
 packages/auth/dev-requirements.txt            |   1 +
 packages/auth/galaxy/__init__.py              |   1 +
 packages/auth/galaxy/auth                     |   1 +
 packages/auth/galaxy/project_galaxy_auth.py   |  13 +++
 packages/auth/requirements.txt                |   1 +
 packages/auth/scripts                         |   1 +
 packages/auth/setup.cfg                       |   1 +
 packages/auth/setup.py                        | 101 +++++++++++++++++
 packages/authnz/HISTORY.rst                   |  12 ++
 packages/authnz/LICENSE                       |   1 +
 packages/authnz/MANIFEST.in                   |   1 +
 packages/authnz/Makefile                      |   1 +
 packages/authnz/README.rst                    |  14 +++
 packages/authnz/dev-requirements.txt          |   1 +
 packages/authnz/galaxy/__init__.py            |   1 +
 packages/authnz/galaxy/authnz                 |   1 +
 .../authnz/galaxy/project_galaxy_authnz.py    |  13 +++
 packages/authnz/requirements.txt              |   7 ++
 packages/authnz/scripts                       |   1 +
 packages/authnz/setup.cfg                     |   1 +
 packages/authnz/setup.py                      | 100 +++++++++++++++++
 packages/authnz/tests/test_custos_authnz.py   |   1 +
 packages/data/galaxy/quota                    |   1 +
 packages/data/setup.py                        |   1 +
 packages/test.sh                              |   5 +-
 48 files changed, 470 insertions(+), 1 deletion(-)
 create mode 100644 packages/app/HISTORY.rst
 create mode 120000 packages/app/LICENSE
 create mode 100644 packages/app/MANIFEST.in
 create mode 120000 packages/app/Makefile
 create mode 100644 packages/app/README.rst
 create mode 120000 packages/app/dev-requirements.txt
 create mode 100644 packages/app/galaxy/__init__.py
 create mode 120000 packages/app/galaxy/actions
 create mode 120000 packages/app/galaxy/dependencies
 create mode 120000 packages/app/galaxy/eggs
 create mode 120000 packages/app/galaxy/forms
 create mode 100644 packages/app/galaxy/project_galaxy_app.py
 create mode 120000 packages/app/galaxy/tours
 create mode 120000 packages/app/galaxy/webhooks
 create mode 100644 packages/app/requirements.txt
 create mode 120000 packages/app/scripts
 create mode 120000 packages/app/setup.cfg
 create mode 100644 packages/app/setup.py
 create mode 100644 packages/auth/HISTORY.rst
 create mode 120000 packages/auth/LICENSE
 create mode 100644 packages/auth/MANIFEST.in
 create mode 120000 packages/auth/Makefile
 create mode 100644 packages/auth/README.rst
 create mode 120000 packages/auth/dev-requirements.txt
 create mode 100644 packages/auth/galaxy/__init__.py
 create mode 120000 packages/auth/galaxy/auth
 create mode 100644 packages/auth/galaxy/project_galaxy_auth.py
 create mode 100644 packages/auth/requirements.txt
 create mode 120000 packages/auth/scripts
 create mode 120000 packages/auth/setup.cfg
 create mode 100644 packages/auth/setup.py
 create mode 100644 packages/authnz/HISTORY.rst
 create mode 120000 packages/authnz/LICENSE
 create mode 100644 packages/authnz/MANIFEST.in
 create mode 120000 packages/authnz/Makefile
 create mode 100644 packages/authnz/README.rst
 create mode 120000 packages/authnz/dev-requirements.txt
 create mode 100644 packages/authnz/galaxy/__init__.py
 create mode 120000 packages/authnz/galaxy/authnz
 create mode 100644 packages/authnz/galaxy/project_galaxy_authnz.py
 create mode 100644 packages/authnz/requirements.txt
 create mode 120000 packages/authnz/scripts
 create mode 120000 packages/authnz/setup.cfg
 create mode 100644 packages/authnz/setup.py
 create mode 120000 packages/authnz/tests/test_custos_authnz.py
 create mode 120000 packages/data/galaxy/quota

diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
new file mode 100644
index 00000000000..ec2f0e746e9
--- /dev/null
+++ b/packages/app/HISTORY.rst
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.9.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/app/LICENSE b/packages/app/LICENSE
new file mode 120000
index 00000000000..1ef648f64b3
--- /dev/null
+++ b/packages/app/LICENSE
@@ -0,0 +1 @@
+../../LICENSE.txt
\ No newline at end of file
diff --git a/packages/app/MANIFEST.in b/packages/app/MANIFEST.in
new file mode 100644
index 00000000000..c74cefe0942
--- /dev/null
+++ b/packages/app/MANIFEST.in
@@ -0,0 +1 @@
+include *.rst LICENSE
diff --git a/packages/app/Makefile b/packages/app/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/app/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/app/README.rst b/packages/app/README.rst
new file mode 100644
index 00000000000..0f4e347dd92
--- /dev/null
+++ b/packages/app/README.rst
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-job-metrics.svg
+   :target: https://pypi.python.org/pypi/galaxy-job-metrics/
+
+
+Overview
+--------
+
+The Galaxy_ application logic (backend).
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
diff --git a/packages/app/dev-requirements.txt b/packages/app/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/app/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/app/galaxy/__init__.py b/packages/app/galaxy/__init__.py
new file mode 100644
index 00000000000..69e3be50dac
--- /dev/null
+++ b/packages/app/galaxy/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/packages/app/galaxy/actions b/packages/app/galaxy/actions
new file mode 120000
index 00000000000..0a3660ca78f
--- /dev/null
+++ b/packages/app/galaxy/actions
@@ -0,0 +1 @@
+../../../lib/galaxy/actions
\ No newline at end of file
diff --git a/packages/app/galaxy/dependencies b/packages/app/galaxy/dependencies
new file mode 120000
index 00000000000..abd12a041aa
--- /dev/null
+++ b/packages/app/galaxy/dependencies
@@ -0,0 +1 @@
+../../../lib/galaxy/dependencies
\ No newline at end of file
diff --git a/packages/app/galaxy/eggs b/packages/app/galaxy/eggs
new file mode 120000
index 00000000000..eb181a74790
--- /dev/null
+++ b/packages/app/galaxy/eggs
@@ -0,0 +1 @@
+../../../lib/galaxy/eggs
\ No newline at end of file
diff --git a/packages/app/galaxy/forms b/packages/app/galaxy/forms
new file mode 120000
index 00000000000..b15f3ec2fa6
--- /dev/null
+++ b/packages/app/galaxy/forms
@@ -0,0 +1 @@
+../../../lib/galaxy/forms
\ No newline at end of file
diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py
new file mode 100644
index 00000000000..d6992f8a9b4
--- /dev/null
+++ b/packages/app/galaxy/project_galaxy_app.py
@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev0'
+
+PROJECT_NAME = "galaxy-app"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Application (backend)'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
diff --git a/packages/app/galaxy/tours b/packages/app/galaxy/tours
new file mode 120000
index 00000000000..4cb21b13e3a
--- /dev/null
+++ b/packages/app/galaxy/tours
@@ -0,0 +1 @@
+../../../lib/galaxy/tours
\ No newline at end of file
diff --git a/packages/app/galaxy/webhooks b/packages/app/galaxy/webhooks
new file mode 120000
index 00000000000..4f76d9fd9ea
--- /dev/null
+++ b/packages/app/galaxy/webhooks
@@ -0,0 +1 @@
+../../../lib/galaxy/webhooks
\ No newline at end of file
diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt
new file mode 100644
index 00000000000..9c87be95eff
--- /dev/null
+++ b/packages/app/requirements.txt
@@ -0,0 +1,3 @@
+galaxy-auth
+galaxy-job-execution
+
diff --git a/packages/app/scripts b/packages/app/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/app/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
new file mode 120000
index 00000000000..eb7cf09393f
--- /dev/null
+++ b/packages/app/setup.cfg
@@ -0,0 +1 @@
+../../setup.cfg
\ No newline at end of file
diff --git a/packages/app/setup.py b/packages/app/setup.py
new file mode 100644
index 00000000000..2debd87be4b
--- /dev/null
+++ b/packages/app/setup.py
@@ -0,0 +1,105 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import ast
+import os
+import re
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+SOURCE_DIR = "galaxy"
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__)))
+with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f:
+    init_contents = f.read().decode('utf-8')
+
+    def get_var(var_name):
+        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        match = pattern.search(init_contents).group(1)
+        return str(ast.literal_eval(match))
+
+    version = get_var("__version__")
+    PROJECT_NAME = get_var("PROJECT_NAME")
+    PROJECT_URL = get_var("PROJECT_URL")
+    PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
+    PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.actions',
+    'galaxy.dependencies',
+    'galaxy.eggs',
+    'galaxy.forms',
+    'galaxy.tours',
+    'galaxy.webhooks',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+    ],
+}
+PACKAGE_DIR = {
+    SOURCE_DIR: SOURCE_DIR,
+}
+
+readme = open('README.rst').read()
+history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+
+if os.path.exists("requirements.txt"):
+    requirements = open("requirements.txt").read().split("\n")
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+
+
+test_requirements = [
+    # TODO: put package test requirements here
+]
+
+
+setup(
+    name=PROJECT_NAME,
+    version=version,
+    description=PROJECT_DESCRIPTION,
+    long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
+    author=PROJECT_AUTHOR,
+    author_email=PROJECT_EMAIL,
+    url=PROJECT_URL,
+    packages=PACKAGES,
+    entry_points=ENTRY_POINTS,
+    package_data=PACKAGE_DATA,
+    package_dir=PACKAGE_DIR,
+    include_package_data=True,
+    install_requires=requirements,
+    license="AFL",
+    zip_safe=False,
+    keywords='galaxy',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'Environment :: Console',
+        'License :: OSI Approved :: Academic Free License (AFL)',
+        'Operating System :: POSIX',
+        'Topic :: Software Development',
+        'Topic :: Software Development :: Code Generators',
+        'Topic :: Software Development :: Testing',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)
diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
new file mode 100644
index 00000000000..ec2f0e746e9
--- /dev/null
+++ b/packages/auth/HISTORY.rst
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.9.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/auth/LICENSE b/packages/auth/LICENSE
new file mode 120000
index 00000000000..1ef648f64b3
--- /dev/null
+++ b/packages/auth/LICENSE
@@ -0,0 +1 @@
+../../LICENSE.txt
\ No newline at end of file
diff --git a/packages/auth/MANIFEST.in b/packages/auth/MANIFEST.in
new file mode 100644
index 00000000000..c74cefe0942
--- /dev/null
+++ b/packages/auth/MANIFEST.in
@@ -0,0 +1 @@
+include *.rst LICENSE
diff --git a/packages/auth/Makefile b/packages/auth/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/auth/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/auth/README.rst b/packages/auth/README.rst
new file mode 100644
index 00000000000..3d7d85c9ed7
--- /dev/null
+++ b/packages/auth/README.rst
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-job-metrics.svg
+   :target: https://pypi.python.org/pypi/galaxy-job-metrics/
+
+
+Overview
+--------
+
+The Galaxy_ auth framework and default plugins.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
diff --git a/packages/auth/dev-requirements.txt b/packages/auth/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/auth/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/auth/galaxy/__init__.py b/packages/auth/galaxy/__init__.py
new file mode 100644
index 00000000000..69e3be50dac
--- /dev/null
+++ b/packages/auth/galaxy/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/packages/auth/galaxy/auth b/packages/auth/galaxy/auth
new file mode 120000
index 00000000000..9c9b6bf2e30
--- /dev/null
+++ b/packages/auth/galaxy/auth
@@ -0,0 +1 @@
+../../../lib/galaxy/auth
\ No newline at end of file
diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py
new file mode 100644
index 00000000000..ade44591c93
--- /dev/null
+++ b/packages/auth/galaxy/project_galaxy_auth.py
@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev0'
+
+PROJECT_NAME = "galaxy-auth"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Auth Framework and Implementations'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
diff --git a/packages/auth/requirements.txt b/packages/auth/requirements.txt
new file mode 100644
index 00000000000..7dcf8f4def7
--- /dev/null
+++ b/packages/auth/requirements.txt
@@ -0,0 +1 @@
+galaxy-data
diff --git a/packages/auth/scripts b/packages/auth/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/auth/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg
new file mode 120000
index 00000000000..eb7cf09393f
--- /dev/null
+++ b/packages/auth/setup.cfg
@@ -0,0 +1 @@
+../../setup.cfg
\ No newline at end of file
diff --git a/packages/auth/setup.py b/packages/auth/setup.py
new file mode 100644
index 00000000000..63367f57581
--- /dev/null
+++ b/packages/auth/setup.py
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import ast
+import os
+import re
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+SOURCE_DIR = "galaxy"
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__)))
+with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f:
+    init_contents = f.read().decode('utf-8')
+
+    def get_var(var_name):
+        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        match = pattern.search(init_contents).group(1)
+        return str(ast.literal_eval(match))
+
+    version = get_var("__version__")
+    PROJECT_NAME = get_var("PROJECT_NAME")
+    PROJECT_URL = get_var("PROJECT_URL")
+    PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
+    PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.auth',
+    'galaxy.auth.providers',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+    ],
+}
+PACKAGE_DIR = {
+    SOURCE_DIR: SOURCE_DIR,
+}
+
+readme = open('README.rst').read()
+history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+
+if os.path.exists("requirements.txt"):
+    requirements = open("requirements.txt").read().split("\n")
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+
+
+test_requirements = [
+    # TODO: put package test requirements here
+]
+
+
+setup(
+    name=PROJECT_NAME,
+    version=version,
+    description=PROJECT_DESCRIPTION,
+    long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
+    author=PROJECT_AUTHOR,
+    author_email=PROJECT_EMAIL,
+    url=PROJECT_URL,
+    packages=PACKAGES,
+    entry_points=ENTRY_POINTS,
+    package_data=PACKAGE_DATA,
+    package_dir=PACKAGE_DIR,
+    include_package_data=True,
+    install_requires=requirements,
+    license="AFL",
+    zip_safe=False,
+    keywords='galaxy',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'Environment :: Console',
+        'License :: OSI Approved :: Academic Free License (AFL)',
+        'Operating System :: POSIX',
+        'Topic :: Software Development',
+        'Topic :: Software Development :: Code Generators',
+        'Topic :: Software Development :: Testing',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)
diff --git a/packages/authnz/HISTORY.rst b/packages/authnz/HISTORY.rst
new file mode 100644
index 00000000000..ec2f0e746e9
--- /dev/null
+++ b/packages/authnz/HISTORY.rst
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.9.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/authnz/LICENSE b/packages/authnz/LICENSE
new file mode 120000
index 00000000000..1ef648f64b3
--- /dev/null
+++ b/packages/authnz/LICENSE
@@ -0,0 +1 @@
+../../LICENSE.txt
\ No newline at end of file
diff --git a/packages/authnz/MANIFEST.in b/packages/authnz/MANIFEST.in
new file mode 100644
index 00000000000..c74cefe0942
--- /dev/null
+++ b/packages/authnz/MANIFEST.in
@@ -0,0 +1 @@
+include *.rst LICENSE
diff --git a/packages/authnz/Makefile b/packages/authnz/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/authnz/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/authnz/README.rst b/packages/authnz/README.rst
new file mode 100644
index 00000000000..070b598d46a
--- /dev/null
+++ b/packages/authnz/README.rst
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-job-metrics.svg
+   :target: https://pypi.python.org/pypi/galaxy-job-metrics/
+
+
+Overview
+--------
+
+The Galaxy_ authnz module.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
diff --git a/packages/authnz/dev-requirements.txt b/packages/authnz/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/authnz/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/authnz/galaxy/__init__.py b/packages/authnz/galaxy/__init__.py
new file mode 100644
index 00000000000..69e3be50dac
--- /dev/null
+++ b/packages/authnz/galaxy/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/packages/authnz/galaxy/authnz b/packages/authnz/galaxy/authnz
new file mode 120000
index 00000000000..801410c14dc
--- /dev/null
+++ b/packages/authnz/galaxy/authnz
@@ -0,0 +1 @@
+../../../lib/galaxy/authnz
\ No newline at end of file
diff --git a/packages/authnz/galaxy/project_galaxy_authnz.py b/packages/authnz/galaxy/project_galaxy_authnz.py
new file mode 100644
index 00000000000..c4bf5b7ffc9
--- /dev/null
+++ b/packages/authnz/galaxy/project_galaxy_authnz.py
@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev0'
+
+PROJECT_NAME = "galaxy-auth"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy AuthNZ'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
diff --git a/packages/authnz/requirements.txt b/packages/authnz/requirements.txt
new file mode 100644
index 00000000000..353d6bbd324
--- /dev/null
+++ b/packages/authnz/requirements.txt
@@ -0,0 +1,7 @@
+galaxy-data
+pyjwt
+cloudauthz
+# Following three shouldn't be needed, cloudauthz should be updated to require them
+google-api-python-client
+httplib2
+oauth2client
diff --git a/packages/authnz/scripts b/packages/authnz/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/authnz/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/authnz/setup.cfg b/packages/authnz/setup.cfg
new file mode 120000
index 00000000000..eb7cf09393f
--- /dev/null
+++ b/packages/authnz/setup.cfg
@@ -0,0 +1 @@
+../../setup.cfg
\ No newline at end of file
diff --git a/packages/authnz/setup.py b/packages/authnz/setup.py
new file mode 100644
index 00000000000..8c8f3053e79
--- /dev/null
+++ b/packages/authnz/setup.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import ast
+import os
+import re
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+SOURCE_DIR = "galaxy"
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__)))
+with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f:
+    init_contents = f.read().decode('utf-8')
+
+    def get_var(var_name):
+        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        match = pattern.search(init_contents).group(1)
+        return str(ast.literal_eval(match))
+
+    version = get_var("__version__")
+    PROJECT_NAME = get_var("PROJECT_NAME")
+    PROJECT_URL = get_var("PROJECT_URL")
+    PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
+    PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.authnz',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+    ],
+}
+PACKAGE_DIR = {
+    SOURCE_DIR: SOURCE_DIR,
+}
+
+readme = open('README.rst').read()
+history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+
+if os.path.exists("requirements.txt"):
+    requirements = open("requirements.txt").read().split("\n")
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+
+
+test_requirements = [
+    # TODO: put package test requirements here
+]
+
+
+setup(
+    name=PROJECT_NAME,
+    version=version,
+    description=PROJECT_DESCRIPTION,
+    long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
+    author=PROJECT_AUTHOR,
+    author_email=PROJECT_EMAIL,
+    url=PROJECT_URL,
+    packages=PACKAGES,
+    entry_points=ENTRY_POINTS,
+    package_data=PACKAGE_DATA,
+    package_dir=PACKAGE_DIR,
+    include_package_data=True,
+    install_requires=requirements,
+    license="AFL",
+    zip_safe=False,
+    keywords='galaxy',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'Environment :: Console',
+        'License :: OSI Approved :: Academic Free License (AFL)',
+        'Operating System :: POSIX',
+        'Topic :: Software Development',
+        'Topic :: Software Development :: Code Generators',
+        'Topic :: Software Development :: Testing',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)
diff --git a/packages/authnz/tests/test_custos_authnz.py b/packages/authnz/tests/test_custos_authnz.py
new file mode 120000
index 00000000000..d41840c35c6
--- /dev/null
+++ b/packages/authnz/tests/test_custos_authnz.py
@@ -0,0 +1 @@
+../../../test/unit/authnz/test_custos_authnz.py
\ No newline at end of file
diff --git a/packages/data/galaxy/quota b/packages/data/galaxy/quota
new file mode 120000
index 00000000000..a16f2ec8773
--- /dev/null
+++ b/packages/data/galaxy/quota
@@ -0,0 +1 @@
+../../../lib/galaxy/quota
\ No newline at end of file
diff --git a/packages/data/setup.py b/packages/data/setup.py
index 38ec5a74e13..12556d60ed4 100644
--- a/packages/data/setup.py
+++ b/packages/data/setup.py
@@ -42,6 +42,7 @@ PACKAGES = [
     'galaxy.model.orm',
     'galaxy.model.store',
     'galaxy.model.tool_shed_install',
+    'galaxy.quota',
     'galaxy.security',
 ]
 ENTRY_POINTS = '''
diff --git a/packages/test.sh b/packages/test.sh
index aacfab67a3e..ae6c0d33704 100755
--- a/packages/test.sh
+++ b/packages/test.sh
@@ -22,10 +22,13 @@ PACKAGE_DIRS=(
     tool_util
     data
     job_execution
+    auth
+    authnz
+    app
 )
 # containers has no tests, tool_util not yet working 100%,
 # data has many problems quota, tool shed install database, etc..
-RUN_TESTS=(1 1 1 0 0 0 0 1)
+RUN_TESTS=(1 1 1 0 0 0 0 0 1 0)
 
 for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
     package_dir=${PACKAGE_DIRS[$i]}

From 6a6ade54fa897a5913b5ec9c8a6cb8475a0aebd8 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Thu, 27 Jun 2019 15:39:07 +0200
Subject: [PATCH 09/31] xrefs yaml parser

---
 lib/galaxy/tool_util/parser/yaml.py | 10 ++++++++--
 test/unit/tools/test_parsing.py     |  3 +++
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 76bbdc1e133..1f594655c6a 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -41,7 +41,14 @@ class YamlToolSource(ToolSource):
         return self.root_dict.get("edam_topics", [])
 
     def parse_xrefs(self):
-        return self.root_dict.get("xrefs", [])
+        xrefs = []
+        rval = dict(
+            xrefs=xrefs
+        )
+        for i, xref_dict in enumerate(self.root_dict.get("xrefs", [])):
+            if xref_dict["type"] == "bio.tools"
+                xrefs.append(xref_dict["value"])
+        return rval
 
     def parse_is_multi_byte(self):
         return self.root_dict.get("is_multi_byte", self.default_is_multi_byte)
@@ -173,7 +180,6 @@ class YamlToolSource(ToolSource):
             python_template_version = packaging.version.parse(python_template_version)
         return python_template_version
 
-
 def _parse_test(i, test_dict):
     inputs = test_dict["inputs"]
     if is_dict(inputs):
diff --git a/test/unit/tools/test_parsing.py b/test/unit/tools/test_parsing.py
index ca04095367b..ddd51373703 100644
--- a/test/unit/tools/test_parsing.py
+++ b/test/unit/tools/test_parsing.py
@@ -87,6 +87,9 @@ class: GalaxyTool
 id: bowtie
 version: 1.0.2
 description: "The Bowtie Mapper"
+xrefs:
+  - type: bio.tools
+    value: bwa
 command: "bowtie_wrapper.pl --map-the-stuff"
 interpreter: "perl"
 runtime_version:

From 8957463a512e2bc1ecd182b36726958da1c15711 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Thu, 27 Jun 2019 16:03:09 +0200
Subject: [PATCH 10/31] xrefs yaml parser

---
 lib/galaxy/tool_util/parser/yaml.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 1f594655c6a..352d9581be3 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -46,7 +46,7 @@ class YamlToolSource(ToolSource):
             xrefs=xrefs
         )
         for i, xref_dict in enumerate(self.root_dict.get("xrefs", [])):
-            if xref_dict["type"] == "bio.tools"
+            if xref_dict["type"] == "bio.tools":
                 xrefs.append(xref_dict["value"])
         return rval
 

From e86fe68e76bd19ea2ec4499729bf9589d8f43d6e Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Thu, 27 Jun 2019 16:34:08 +0200
Subject: [PATCH 11/31] xrefs yaml parser

---
 lib/galaxy/tool_util/parser/yaml.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 352d9581be3..bb4c62cd1d6 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -42,13 +42,10 @@ class YamlToolSource(ToolSource):
 
     def parse_xrefs(self):
         xrefs = []
-        rval = dict(
-            xrefs=xrefs
-        )
         for i, xref_dict in enumerate(self.root_dict.get("xrefs", [])):
             if xref_dict["type"] == "bio.tools":
                 xrefs.append(xref_dict["value"])
-        return rval
+        return xrefs
 
     def parse_is_multi_byte(self):
         return self.root_dict.get("is_multi_byte", self.default_is_multi_byte)

From 5748861fdfbe33534ad1ec8018859877ab760f16 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Thu, 27 Jun 2019 17:10:51 +0200
Subject: [PATCH 12/31] xrefs yaml parser

---
 lib/galaxy/tool_util/parser/yaml.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index bb4c62cd1d6..272d49edc71 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -177,6 +177,7 @@ class YamlToolSource(ToolSource):
             python_template_version = packaging.version.parse(python_template_version)
         return python_template_version
 
+
 def _parse_test(i, test_dict):
     inputs = test_dict["inputs"]
     if is_dict(inputs):

From f71324451f2df2d8e54b9443e24d4a27dae01963 Mon Sep 17 00:00:00 2001
From: Valentin Marcon <v.marcon@outlook.fr>
Date: Thu, 27 Jun 2019 17:50:31 +0200
Subject: [PATCH 13/31] Update lib/galaxy/tool_util/parser/yaml.py

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tool_util/parser/yaml.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 272d49edc71..731e6452cbd 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -42,7 +42,7 @@ class YamlToolSource(ToolSource):
 
     def parse_xrefs(self):
         xrefs = []
-        for i, xref_dict in enumerate(self.root_dict.get("xrefs", [])):
+        for xref_dict in self.root_dict.get("xrefs", []):
             if xref_dict["type"] == "bio.tools":
                 xrefs.append(xref_dict["value"])
         return xrefs

From 03ba7a3c01775c42c1692d3c3e874e19ce01c442 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Fri, 28 Jun 2019 11:02:57 +0200
Subject: [PATCH 14/31] standardization of 'reftype' & 'value'

---
 client/galaxy/scripts/components/xrefs.vue | 14 +++++++-------
 lib/galaxy/tool_util/parser/xml.py         |  2 +-
 lib/galaxy/tool_util/parser/yaml.py        |  9 ++++-----
 lib/galaxy/tools/__init__.py               | 18 ------------------
 lib/galaxy/webapps/galaxy/api/tools.py     |  3 ++-
 test/unit/tools/test_parsing.py            |  4 ++--
 6 files changed, 16 insertions(+), 34 deletions(-)

diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue
index a6f925d6eb8..fc9d3969f39 100644
--- a/client/galaxy/scripts/components/xrefs.vue
+++ b/client/galaxy/scripts/components/xrefs.vue
@@ -20,7 +20,7 @@ export default {
             type: String,
             required: true
         },
-        type: {
+        reftype: {
             type: String,
             required: true
         },
@@ -44,21 +44,21 @@ export default {
         axios
             .get(`${getAppRoot()}api/${this.source}/${this.id}/xrefs`)
             .then(response => {
-                this.type = "";
+                this.reftype = "";
                 this.content = "<table>";
                 for (var raw_xref of response.data) {
                     try {
-                        this.type = raw_xref.reftype;
+                        this.reftype = raw_xref.reftype;
                         this.content += "<tr>";
                         this.content += "<th> - ";
-                        this.content += this.type;
+                        this.content += this.reftype;
                         this.content += "</th>";
                         this.content += "<td> : ";
-                        if (this.type == "bio.tools") {
-                            this.content += "<a href=\"https://bio.tools/" + raw_xref.content + "\" target=\"_blank\">" + raw_xref.content + "</a>";
+                        if (this.reftype == "bio.tools") {
+                            this.content += "<a href=\"https://bio.tools/" + raw_xref.value + "\" target=\"_blank\">" + raw_xref.value + "</a>";
                         }
                         else {
-                            this.content += raw_xref.content;
+                            this.content += raw_xref.value;
                         }
                         this.content += "</td>";
                         this.content += "</tr>";
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index f65280298c9..fed101560ba 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -99,7 +99,7 @@ class XmlToolSource(ToolSource):
         xrefs = self.root.find("xrefs")
         if xrefs is None:
             return []
-        return [xref.text for xref in xrefs.findall("xref") if xref.get("type") in {'bio.tools'}]
+        return [dict(value=xref.text.strip(), reftype=xref.attrib['type']) for xref in xrefs.findall("xref") if xref.get("type")]
 
     def parse_description(self):
         return xml_text(self.root, "description")
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 731e6452cbd..ac31a349de4 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -41,11 +41,10 @@ class YamlToolSource(ToolSource):
         return self.root_dict.get("edam_topics", [])
 
     def parse_xrefs(self):
-        xrefs = []
-        for xref_dict in self.root_dict.get("xrefs", []):
-            if xref_dict["type"] == "bio.tools":
-                xrefs.append(xref_dict["value"])
-        return xrefs
+        xrefs = self.root_dict.get("xrefs", [])
+        if xrefs is None:
+            return []
+        return [dict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]]
 
     def parse_is_multi_byte(self):
         return self.root_dict.get("is_multi_byte", self.default_is_multi_byte)
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 59ca8c21c17..540f658af9b 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1080,24 +1080,6 @@ class Tool(Dictifiable):
                     citations.append(citation)
         return citations
 
-    def _parse_xrefs(self, tool_source):
-        if not hasattr(tool_source, 'root'):
-            return []
-        root = tool_source.root
-        xrefs = []
-        xrefs_elem = root.find("xrefs")
-        if xrefs_elem is None:
-            return xrefs
-        for xref_elem in xrefs_elem:
-            if xref_elem.tag != "xref":
-                pass
-            xref = dict(
-                reftype=xref_elem.attrib.get('type', None),
-                content=xref_elem.text.strip()
-            )
-            xrefs.append(xref)
-        return xrefs
-
     def parse_input_elem(self, page_source, enctypes, context=None):
         """
         Parse a parent element whose children are inputs -- these could be
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index f62fc1bb619..7df930f36f2 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -406,7 +406,8 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
     @expose_api_anonymous_and_sessionless
     def xrefs(self, trans, id, **kwds):
         tool = self._get_tool(id, user=trans.user)
-        return [_.to_dict() for _ in tool.xrefs]
+        #return [_.to_dict() for _ in tool.xrefs]
+        return [_ for _ in tool.xrefs]
 
     @web.legacy_expose_api_raw
     @web.require_admin
diff --git a/test/unit/tools/test_parsing.py b/test/unit/tools/test_parsing.py
index ddd51373703..dcce2145c94 100644
--- a/test/unit/tools/test_parsing.py
+++ b/test/unit/tools/test_parsing.py
@@ -319,7 +319,7 @@ class XmlLoaderTestCase(BaseLoaderTestCase):
 
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
-        assert xrefs[0] == "bwa"
+        assert xrefs == [{'value': 'bwa', 'reftype': 'bio.tools'}]
 
     def test_exit_code(self):
         tool_source = self._get_tool_source(source_contents="""<tool id="bwa" name="bwa">
@@ -480,7 +480,7 @@ class YamlLoaderTestCase(BaseLoaderTestCase):
 
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
-        assert xrefs[0] == "bwa"
+        assert xrefs == [{'value': 'bwa', 'reftype': 'bio.tools'}]
 
     def test_sanitize(self):
         assert self._tool_source.parse_sanitize() is True

From 6db58f56e53376125b21e127822f753477d847d8 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Fri, 28 Jun 2019 11:10:32 +0200
Subject: [PATCH 15/31] lint failed

---
 lib/galaxy/webapps/galaxy/api/tools.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 7df930f36f2..2aef7a037c7 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -406,7 +406,6 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
     @expose_api_anonymous_and_sessionless
     def xrefs(self, trans, id, **kwds):
         tool = self._get_tool(id, user=trans.user)
-        #return [_.to_dict() for _ in tool.xrefs]
         return [_ for _ in tool.xrefs]
 
     @web.legacy_expose_api_raw

From fb825b10fbd482f328b4c40e88bf3f4ec43b2f9e Mon Sep 17 00:00:00 2001
From: Valentin Marcon <v.marcon@outlook.fr>
Date: Fri, 28 Jun 2019 13:35:09 +0200
Subject: [PATCH 16/31] Update lib/galaxy/webapps/galaxy/api/tools.py

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/webapps/galaxy/api/tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 2aef7a037c7..cee0fc78524 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -406,7 +406,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
     @expose_api_anonymous_and_sessionless
     def xrefs(self, trans, id, **kwds):
         tool = self._get_tool(id, user=trans.user)
-        return [_ for _ in tool.xrefs]
+        return tool.xrefs
 
     @web.legacy_expose_api_raw
     @web.require_admin

From 647b82c29ae546600469de0af120c39852bed6d3 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Fri, 28 Jun 2019 13:44:24 +0200
Subject: [PATCH 17/31] Update lib/galaxy/tool_util/parser/yaml.py

---
 lib/galaxy/tool_util/parser/yaml.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index ac31a349de4..8790c0419ea 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -42,8 +42,6 @@ class YamlToolSource(ToolSource):
 
     def parse_xrefs(self):
         xrefs = self.root_dict.get("xrefs", [])
-        if xrefs is None:
-            return []
         return [dict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]]
 
     def parse_is_multi_byte(self):

From fb507bfe8c1bbd57a1c76a32a69ef446080e1790 Mon Sep 17 00:00:00 2001
From: ValentinMarcon <v.marcon@outlook.fr>
Date: Fri, 28 Jun 2019 18:01:52 +0200
Subject: [PATCH 18/31] Update lib/galaxy/tools/__init__.py

---
 lib/galaxy/tools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 540f658af9b..41e245c3ab0 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1877,6 +1877,7 @@ class Tool(Dictifiable):
 
         tool_dict["edam_operations"] = self.edam_operations
         tool_dict["edam_topics"] = self.edam_topics
+        tool_dict["xrefs"] = self.xrefs
 
         # Fill in ToolShedRepository info
         if hasattr(self, 'tool_shed') and self.tool_shed:
@@ -1990,7 +1991,6 @@ class Tool(Dictifiable):
             'id'            : self.id,
             'help'          : tool_help,
             'citations'     : bool(self.citations),
-            'xrefs'         : bool(self.xrefs),
             'sharable_url'  : self.sharable_url,
             'message'       : tool_message,
             'warnings'      : tool_warnings,

From 3c4ed6aa999719e648a0290c455290d4b20944c4 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 4 Jul 2019 09:44:52 -0400
Subject: [PATCH 19/31] Render in vue template instead of composed html
 injection

---
 client/galaxy/scripts/components/xrefs.vue | 38 ++++++++--------------
 1 file changed, 14 insertions(+), 24 deletions(-)

diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue
index fc9d3969f39..ca79bc99ce2 100644
--- a/client/galaxy/scripts/components/xrefs.vue
+++ b/client/galaxy/scripts/components/xrefs.vue
@@ -3,7 +3,19 @@
         <h4 slot="header" class="mb-0">
             References
         </h4>
-        <span v-html="content"></span>
+        <table>
+            <tr v-for="(xref, index) in xrefs" v-bind:key="index">
+                <th> - {{xref.reftype}}: </th>
+                <td>
+                    <template v-if="xref.reftype == 'bio.tools'">
+                        <a :href="`https://bio.tools/${xref.value}/`" target="_blank">{{xref.value}}</a>
+                    </template>
+                    <template v-else>
+                        {{ xref.value }}
+                    </template>
+                </td>
+            </tr>
+        </table>
     </b-card>
 </template>
 <script>
@@ -44,29 +56,7 @@ export default {
         axios
             .get(`${getAppRoot()}api/${this.source}/${this.id}/xrefs`)
             .then(response => {
-                this.reftype = "";
-                this.content = "<table>";
-                for (var raw_xref of response.data) {
-                    try {
-                        this.reftype = raw_xref.reftype;
-                        this.content += "<tr>";
-                        this.content += "<th> - ";
-                        this.content += this.reftype;
-                        this.content += "</th>";
-                        this.content += "<td> : ";
-                        if (this.reftype == "bio.tools") {
-                            this.content += "<a href=\"https://bio.tools/" + raw_xref.value + "\" target=\"_blank\">" + raw_xref.value + "</a>";
-                        }
-                        else {
-                            this.content += raw_xref.value;
-                        }
-                        this.content += "</td>";
-                        this.content += "</tr>";
-                    } catch (err) {
-                        console.warn("Error parsing xref: " + err);
-                    }
-                }
-                this.content += "</table>";
+                this.xrefs = response.data;
             })
             .catch(e => {
                 console.error(e);

From 6070cca8ec6669f009d474a0380b651976e51fcb Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 4 Jul 2019 09:45:08 -0400
Subject: [PATCH 20/31] Drop unused props.

---
 client/galaxy/scripts/components/xrefs.vue | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue
index ca79bc99ce2..1b5a3efe2ab 100644
--- a/client/galaxy/scripts/components/xrefs.vue
+++ b/client/galaxy/scripts/components/xrefs.vue
@@ -31,19 +31,6 @@ export default {
         id: {
             type: String,
             required: true
-        },
-        reftype: {
-            type: String,
-            required: true
-        },
-        content: {
-            type: String,
-            required: true
-        },
-        viewRender: {
-            type: Boolean,
-            requried: false,
-            default: true
         }
     },
     data() {

From def12f2e0caaa9002faa4f27d207d023391dcb87 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 4 Jul 2019 09:50:54 -0400
Subject: [PATCH 21/31] Drop trailing slash on bio.tools urls (fixes 404)

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

diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue
index 1b5a3efe2ab..13c005243ba 100644
--- a/client/galaxy/scripts/components/xrefs.vue
+++ b/client/galaxy/scripts/components/xrefs.vue
@@ -8,7 +8,7 @@
                 <th> - {{xref.reftype}}: </th>
                 <td>
                     <template v-if="xref.reftype == 'bio.tools'">
-                        <a :href="`https://bio.tools/${xref.value}/`" target="_blank">{{xref.value}}</a>
+                        <a :href="`https://bio.tools/${xref.value}`" target="_blank">{{xref.value}}</a>
                     </template>
                     <template v-else>
                         {{ xref.value }}

From 3114408017b62740e48178fad8eb095eee316d88 Mon Sep 17 00:00:00 2001
From: Yo Yehudi <yochannah@gmail.com>
Date: Fri, 5 Jul 2019 16:16:56 +0200
Subject: [PATCH 22/31] typo fix comunity -> community

---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 84fe45dc6e3..4c9fb28c3a2 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -112,5 +112,5 @@ If no existing Galaxy issue seems appropriate, a new issue can be opened using
   this repository - please checkout the
   [tools-iuc](https://github.com/galaxyproject/tools-iuc) repository on GitHub.
 
-  More information about tool development can be found [on the comunity
+  More information about tool development can be found [on the community
   hub](https://galaxyproject.org/develop).

From 94201a9e81c4ee37ed217cec56857e8580dc31c7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 5 Jul 2019 13:56:22 +0200
Subject: [PATCH 23/31] Update packages/ per review

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 packages/app/README.rst                         | 4 ++--
 packages/app/galaxy/project_galaxy_app.py       | 2 +-
 packages/auth/README.rst                        | 4 ++--
 packages/auth/galaxy/project_galaxy_auth.py     | 2 +-
 packages/authnz/README.rst                      | 4 ++--
 packages/authnz/galaxy/project_galaxy_authnz.py | 4 ++--
 6 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/packages/app/README.rst b/packages/app/README.rst
index 0f4e347dd92..898b0262617 100644
--- a/packages/app/README.rst
+++ b/packages/app/README.rst
@@ -1,6 +1,6 @@
 
-.. image:: https://badge.fury.io/py/galaxy-job-metrics.svg
-   :target: https://pypi.python.org/pypi/galaxy-job-metrics/
+.. image:: https://badge.fury.io/py/galaxy-app.svg
+   :target: https://pypi.org/project/galaxy-app/
 
 
 Overview
diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py
index d6992f8a9b4..95cac65f339 100644
--- a/packages/app/galaxy/project_galaxy_app.py
+++ b/packages/app/galaxy/project_galaxy_app.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Application (backend)'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )
diff --git a/packages/auth/README.rst b/packages/auth/README.rst
index 3d7d85c9ed7..b493770764f 100644
--- a/packages/auth/README.rst
+++ b/packages/auth/README.rst
@@ -1,6 +1,6 @@
 
-.. image:: https://badge.fury.io/py/galaxy-job-metrics.svg
-   :target: https://pypi.python.org/pypi/galaxy-job-metrics/
+.. image:: https://badge.fury.io/py/galaxy-auth.svg
+   :target: https://pypi.org/project/galaxy-auth/
 
 
 Overview
diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py
index ade44591c93..dbd94f1ced5 100644
--- a/packages/auth/galaxy/project_galaxy_auth.py
+++ b/packages/auth/galaxy/project_galaxy_auth.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Auth Framework and Implementations'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )
diff --git a/packages/authnz/README.rst b/packages/authnz/README.rst
index 070b598d46a..5f94cd6f231 100644
--- a/packages/authnz/README.rst
+++ b/packages/authnz/README.rst
@@ -1,6 +1,6 @@
 
-.. image:: https://badge.fury.io/py/galaxy-job-metrics.svg
-   :target: https://pypi.python.org/pypi/galaxy-job-metrics/
+.. image:: https://badge.fury.io/py/galaxy-authnz.svg
+   :target: https://pypi.org/project/galaxy-authnz/
 
 
 Overview
diff --git a/packages/authnz/galaxy/project_galaxy_authnz.py b/packages/authnz/galaxy/project_galaxy_authnz.py
index c4bf5b7ffc9..bf401824d4f 100644
--- a/packages/authnz/galaxy/project_galaxy_authnz.py
+++ b/packages/authnz/galaxy/project_galaxy_authnz.py
@@ -2,12 +2,12 @@
 
 __version__ = '19.9.0.dev0'
 
-PROJECT_NAME = "galaxy-auth"
+PROJECT_NAME = "galaxy-authnz"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy AuthNZ'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )

From 64516cb92fe54b8c91a67e05f6763a65b607be42 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 5 Jul 2019 15:11:51 +0200
Subject: [PATCH 24/31] Remove unnecessary symlinks

---
 packages/app/galaxy/dependencies | 1 -
 packages/app/galaxy/eggs         | 1 -
 packages/app/setup.py            | 2 --
 3 files changed, 4 deletions(-)
 delete mode 120000 packages/app/galaxy/dependencies
 delete mode 120000 packages/app/galaxy/eggs

diff --git a/packages/app/galaxy/dependencies b/packages/app/galaxy/dependencies
deleted file mode 120000
index abd12a041aa..00000000000
--- a/packages/app/galaxy/dependencies
+++ /dev/null
@@ -1 +0,0 @@
-../../../lib/galaxy/dependencies
\ No newline at end of file
diff --git a/packages/app/galaxy/eggs b/packages/app/galaxy/eggs
deleted file mode 120000
index eb181a74790..00000000000
--- a/packages/app/galaxy/eggs
+++ /dev/null
@@ -1 +0,0 @@
-../../../lib/galaxy/eggs
\ No newline at end of file
diff --git a/packages/app/setup.py b/packages/app/setup.py
index 2debd87be4b..73e771657f8 100644
--- a/packages/app/setup.py
+++ b/packages/app/setup.py
@@ -33,8 +33,6 @@ TEST_DIR = 'tests'
 PACKAGES = [
     'galaxy',
     'galaxy.actions',
-    'galaxy.dependencies',
-    'galaxy.eggs',
     'galaxy.forms',
     'galaxy.tours',
     'galaxy.webhooks',

From 1c292702ca9eb0cc058c5447a5c74f04aaeadc0e Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 5 Jul 2019 16:27:36 +0200
Subject: [PATCH 25/31] Update PROJECT_EMAIL and PyPI URL for old packages

---
 packages/containers/README.rst                                | 2 +-
 packages/containers/galaxy/project_galaxy_containers.py       | 2 +-
 packages/data/README.rst                                      | 2 +-
 packages/data/galaxy/project_galaxy_data.py                   | 2 +-
 packages/job_execution/README.rst                             | 2 +-
 packages/job_execution/galaxy/project_galaxy_job_execution.py | 2 +-
 packages/job_metrics/README.rst                               | 2 +-
 packages/job_metrics/galaxy/project_galaxy_job_metrics.py     | 2 +-
 packages/objectstore/README.rst                               | 2 +-
 packages/objectstore/galaxy/project_galaxy_objectstore.py     | 2 +-
 packages/tool_util/README.rst                                 | 2 +-
 packages/tool_util/galaxy/project_galaxy_tool_util.py         | 2 +-
 packages/util/README.rst                                      | 2 +-
 packages/util/galaxy/project_galaxy_util.py                   | 2 +-
 14 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/packages/containers/README.rst b/packages/containers/README.rst
index ed360aeef60..90be9b0a80a 100644
--- a/packages/containers/README.rst
+++ b/packages/containers/README.rst
@@ -1,6 +1,6 @@
 
 .. image:: https://badge.fury.io/py/galaxy-containers.svg
-   :target: https://pypi.python.org/pypi/galaxy-containers/
+   :target: https://pypi.org/project/galaxy-containers/
 
 
 Overview
diff --git a/packages/containers/galaxy/project_galaxy_containers.py b/packages/containers/galaxy/project_galaxy_containers.py
index 6442c8261bb..aaa2331fcce 100644
--- a/packages/containers/galaxy/project_galaxy_containers.py
+++ b/packages/containers/galaxy/project_galaxy_containers.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Container Modeling and Interaction Abstractions'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )
diff --git a/packages/data/README.rst b/packages/data/README.rst
index 4deccf230e9..daf960bc982 100644
--- a/packages/data/README.rst
+++ b/packages/data/README.rst
@@ -1,6 +1,6 @@
 
 .. image:: https://badge.fury.io/py/galaxy-data.svg
-   :target: https://pypi.python.org/pypi/galaxy-data/
+   :target: https://pypi.org/project/galaxy-data/
 
 
 Overview
diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py
index b7c780d82ab..1a2efe784b6 100644
--- a/packages/data/galaxy/project_galaxy_data.py
+++ b/packages/data/galaxy/project_galaxy_data.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )
diff --git a/packages/job_execution/README.rst b/packages/job_execution/README.rst
index 3a7574eab70..8ec9c6f91cf 100644
--- a/packages/job_execution/README.rst
+++ b/packages/job_execution/README.rst
@@ -1,6 +1,6 @@
 
 .. image:: https://badge.fury.io/py/galaxy-job-execution.svg
-   :target: https://pypi.python.org/pypi/galaxy-job-execution/
+   :target: https://pypi.org/project/galaxy-job-execution/
 
 
 Overview
diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py
index a30f915133d..f2c11c58e0e 100644
--- a/packages/job_execution/galaxy/project_galaxy_job_execution.py
+++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Job Execution Runtime Utilities'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )
diff --git a/packages/job_metrics/README.rst b/packages/job_metrics/README.rst
index 65a810c4c24..f584e6b993d 100644
--- a/packages/job_metrics/README.rst
+++ b/packages/job_metrics/README.rst
@@ -1,6 +1,6 @@
 
 .. image:: https://badge.fury.io/py/galaxy-job-metrics.svg
-   :target: https://pypi.python.org/pypi/galaxy-job-metrics/
+   :target: https://pypi.org/project/galaxy-job-metrics/
 
 
 Overview
diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
index 5c5c5411ab8..a14ffc17c67 100644
--- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
+++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Job Metrics'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )
diff --git a/packages/objectstore/README.rst b/packages/objectstore/README.rst
index fa243ffe29b..ceaa2466eaf 100644
--- a/packages/objectstore/README.rst
+++ b/packages/objectstore/README.rst
@@ -1,6 +1,6 @@
 
 .. image:: https://badge.fury.io/py/galaxy-objectstore.svg
-   :target: https://pypi.python.org/pypi/galaxy-objectstore/
+   :target: https://pypi.org/project/galaxy-objectstore/
 
 
 Overview
diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py
index 825abc23062..be0292f59e7 100644
--- a/packages/objectstore/galaxy/project_galaxy_objectstore.py
+++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Objectstore Framework and Plugins'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )
diff --git a/packages/tool_util/README.rst b/packages/tool_util/README.rst
index 74c8c0f1f31..badd671d78a 100644
--- a/packages/tool_util/README.rst
+++ b/packages/tool_util/README.rst
@@ -1,6 +1,6 @@
 
 .. image:: https://badge.fury.io/py/galaxy-tool-util.svg
-   :target: https://pypi.python.org/pypi/galaxy-tool-util/
+   :target: https://pypi.org/project/galaxy-tool-util/
 
 
 Overview
diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
index 4f526958884..f9518421336 100644
--- a/packages/tool_util/galaxy/project_galaxy_tool_util.py
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Tool and Tool Dependency Utilities'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )
diff --git a/packages/util/README.rst b/packages/util/README.rst
index 778c380a853..378cb991e37 100644
--- a/packages/util/README.rst
+++ b/packages/util/README.rst
@@ -1,6 +1,6 @@
 
 .. image:: https://badge.fury.io/py/galaxy-util.svg
-   :target: https://pypi.python.org/pypi/galaxy-util/
+   :target: https://pypi.org/project/galaxy-util/
 
 
 Overview
diff --git a/packages/util/galaxy/project_galaxy_util.py b/packages/util/galaxy/project_galaxy_util.py
index c5a4d0ce99a..f8d1291d92b 100644
--- a/packages/util/galaxy/project_galaxy_util.py
+++ b/packages/util/galaxy/project_galaxy_util.py
@@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
 PROJECT_DESCRIPTION = 'Galaxy Generic Utilities'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
 )

From 291597f4d113b172e17f981d7f7e4e4397ecd026 Mon Sep 17 00:00:00 2001
From: Ashok Varadharajan <ashvark@gmail.com>
Date: Fri, 5 Jul 2019 16:45:49 +0200
Subject: [PATCH 26/31] Ignore files in database/shed_tools directory

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 9fbaa7c97f3..e52c67610a4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,6 +18,7 @@ database/files
 database/jobs_directory
 database/job_working_directory
 database/pbs
+database/shed_tools
 database/test_errors
 database/tmp
 database/*.sqlite

From 58ef19e1bf233cf58120fb772e63b18218abb122 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 5 Jul 2019 13:33:08 +0200
Subject: [PATCH 27/31] Move loader_directory from tools to tool_util [WIP]

This is WIP: this move (obviously) breaks many things, whick are
currently being fixed.
---
 lib/galaxy/{tools => tool_util}/loader_directory.py | 0
 lib/galaxy/tools/toolbox/base.py                    | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename lib/galaxy/{tools => tool_util}/loader_directory.py (100%)

diff --git a/lib/galaxy/tools/loader_directory.py b/lib/galaxy/tool_util/loader_directory.py
similarity index 100%
rename from lib/galaxy/tools/loader_directory.py
rename to lib/galaxy/tool_util/loader_directory.py
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index df38375939d..ae9757bb1d3 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -12,7 +12,7 @@ from six.moves.urllib.parse import urlparse
 
 from galaxy.exceptions import MessageException, ObjectNotFound
 from galaxy.tool_util.deps import build_dependency_manager
-from galaxy.tools.loader_directory import looks_like_a_tool
+from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.util import (
     ExecutionTimer,
     listify,

From 1694b79185f2f59c508487c9d7b611aa7ea90bfa Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 5 Jul 2019 14:34:13 +0200
Subject: [PATCH 28/31] Update import paths for loader_directory

---
 lib/galaxy/tool_util/deps/dockerfiles.py     | 2 +-
 lib/tool_shed/metadata/metadata_generator.py | 2 +-
 scripts/tool_shed/build_ts_whoosh_index.py   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tool_util/deps/dockerfiles.py b/lib/galaxy/tool_util/deps/dockerfiles.py
index 67944dcbc04..be97bd2dc11 100644
--- a/lib/galaxy/tool_util/deps/dockerfiles.py
+++ b/lib/galaxy/tool_util/deps/dockerfiles.py
@@ -5,7 +5,7 @@ from ..deps import commands
 from ..deps import docker_util
 from ..deps.container_classes import docker_cache_path
 from ..deps.requirements import parse_requirements_from_xml
-from ...tools import loader_directory
+from .. import loader_directory
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py
index 7aa5b0007f6..37231ff618a 100644
--- a/lib/tool_shed/metadata/metadata_generator.py
+++ b/lib/tool_shed/metadata/metadata_generator.py
@@ -8,7 +8,7 @@ from sqlalchemy import and_
 from galaxy import util
 from galaxy.tool_util.parser.interface import TestCollectionDef
 from galaxy.tools.data_manager.manager import DataManager
-from galaxy.tools.loader_directory import looks_like_a_tool
+from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.tools.repositories import ValidationContext
 from galaxy.web import url_for
 from tool_shed.repository_types import util as rt_util
diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py
index 41ce98e83ce..541b199965f 100644
--- a/scripts/tool_shed/build_ts_whoosh_index.py
+++ b/scripts/tool_shed/build_ts_whoosh_index.py
@@ -24,7 +24,7 @@ from whoosh.filedb.filestore import FileStorage
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
 
 import galaxy.webapps.tool_shed.model.mapping
-from galaxy.tools.loader_directory import load_tool_elements_from_path
+from galaxy.tool_util.loader_directory import load_tool_elements_from_path
 from galaxy.util import (
     directory_hash_id,
     pretty_print_time_interval,

From b51ca225a928bffb2b17d12e43659045db5a35fe Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 5 Jul 2019 15:45:48 +0200
Subject: [PATCH 29/31] Fix import order; change relative import to global

Relative to global import: doesn't make much difference, so just for the
sake of (a) consistency with many other files in same dir; and (b)
easier grepping for import paths.
---
 lib/galaxy/tool_util/deps/dockerfiles.py     | 12 ++++++------
 lib/tool_shed/metadata/metadata_generator.py |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/tool_util/deps/dockerfiles.py b/lib/galaxy/tool_util/deps/dockerfiles.py
index be97bd2dc11..72a44e9a2c7 100644
--- a/lib/galaxy/tool_util/deps/dockerfiles.py
+++ b/lib/galaxy/tool_util/deps/dockerfiles.py
@@ -1,11 +1,11 @@
 import logging
 import os
 
-from ..deps import commands
-from ..deps import docker_util
-from ..deps.container_classes import docker_cache_path
-from ..deps.requirements import parse_requirements_from_xml
-from .. import loader_directory
+from galaxy.tool_util.deps import commands
+from galaxy.tool_util.deps import docker_util
+from galaxy.tool_util.deps.container_classes import docker_cache_path
+from galaxy.tool_util.deps.requirements import parse_requirements_from_xml
+from galaxy.tool_util.loader_directory import load_tool_elements_from_path
 
 log = logging.getLogger(__name__)
 
@@ -22,7 +22,7 @@ def docker_host_args(**kwds):
 def dockerfile_build(path, dockerfile=None, error=log.error, **kwds):
     expected_container_names = set()
     tool_directories = set()
-    for (tool_path, tool_xml) in loader_directory.load_tool_elements_from_path(path):
+    for (tool_path, tool_xml) in load_tool_elements_from_path(path):
         requirements, containers = parse_requirements_from_xml(tool_xml)
         for container in containers:
             if container.type == "docker":
diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py
index 37231ff618a..a37ddac7b0c 100644
--- a/lib/tool_shed/metadata/metadata_generator.py
+++ b/lib/tool_shed/metadata/metadata_generator.py
@@ -6,9 +6,9 @@ import tempfile
 from sqlalchemy import and_
 
 from galaxy import util
+from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.tool_util.parser.interface import TestCollectionDef
 from galaxy.tools.data_manager.manager import DataManager
-from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.tools.repositories import ValidationContext
 from galaxy.web import url_for
 from tool_shed.repository_types import util as rt_util

From 92fde4fbfa8521a18e67d754445fb05fe5a7880d Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 5 Jul 2019 16:09:44 +0200
Subject: [PATCH 30/31] Move ParallelismInfo out of jobs into tool_util

This is part of #8240
(Figure out why packages/tool_util isn't being tested and fix the problems.)

This PR does not include updated documentation rst files. These will be
submitted as a separate PR due to a just discovered (potential) issue
with sphinx v. 1.8.5. (period is no longer escaped: foo.bar becomes
foo.bar)
---
 lib/galaxy/jobs/__init__.py        | 19 -------------------
 lib/galaxy/tool_util/parser/xml.py | 20 +++++++++++++++++++-
 2 files changed, 19 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 7ec38255bb9..4d1582a936c 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -2394,22 +2394,3 @@ class NoopQueue(object):
 
     def shutdown(self):
         return
-
-
-class ParallelismInfo(object):
-    """
-    Stores the information (if any) for running multiple instances of the tool in parallel
-    on the same set of inputs.
-    """
-
-    def __init__(self, tag):
-        self.method = tag.get('method')
-        if isinstance(tag, dict):
-            items = tag.items()
-        else:
-            items = tag.attrib.items()
-        self.attributes = dict([item for item in items if item[0] != 'method'])
-        if len(self.attributes) == 0:
-            # legacy basic mode - provide compatible defaults
-            self.attributes['split_size'] = 20
-            self.attributes['split_mode'] = 'number_of_parts'
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index fed101560ba..1182fac116c 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -197,7 +197,6 @@ class XmlToolSource(ToolSource):
         parallelism = self.root.find("parallelism")
         parallelism_info = None
         if parallelism is not None and parallelism.get("method"):
-            from galaxy.jobs import ParallelismInfo
             return ParallelismInfo(parallelism)
         return parallelism_info
 
@@ -1098,3 +1097,22 @@ class XmlInputSource(InputSource):
             case_page_source = XmlPageSource(case_elem)
             sources.append((value, case_page_source))
         return sources
+
+
+class ParallelismInfo(object):
+    """
+    Stores the information (if any) for running multiple instances of the tool in parallel
+    on the same set of inputs.
+    """
+
+    def __init__(self, tag):
+        self.method = tag.get('method')
+        if isinstance(tag, dict):
+            items = tag.items()
+        else:
+            items = tag.attrib.items()
+        self.attributes = dict([item for item in items if item[0] != 'method'])
+        if len(self.attributes) == 0:
+            # legacy basic mode - provide compatible defaults
+            self.attributes['split_size'] = 20
+            self.attributes['split_mode'] = 'number_of_parts'

From 2e1c3ee1c7a1eea9c83c7cf9a461f2a1dfdce8f5 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 6 Jul 2019 00:54:08 +0200
Subject: [PATCH 31/31] Run tests for galaxy-tool-util package

---
 packages/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/test.sh b/packages/test.sh
index ae6c0d33704..d05f3cc5dbb 100755
--- a/packages/test.sh
+++ b/packages/test.sh
@@ -28,7 +28,7 @@ PACKAGE_DIRS=(
 )
 # containers has no tests, tool_util not yet working 100%,
 # data has many problems quota, tool shed install database, etc..
-RUN_TESTS=(1 1 1 0 0 0 0 0 1 0)
+RUN_TESTS=(1 1 1 0 1 0 0 0 1 0)
 
 for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
     package_dir=${PACKAGE_DIRS[$i]}