From a625e334721df9002ef2150e2808f508e1bb4c5a Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 31 Oct 2019 15:35:12 -0400
Subject: [PATCH 001/101] Initial addition of vue-fa

---
 client/package.json | 1 +
 client/yarn.lock    | 5 +++++
 2 files changed, 6 insertions(+)

diff --git a/client/package.json b/client/package.json
index 9161e57aca2..d16be42bdeb 100644
--- a/client/package.json
+++ b/client/package.json
@@ -12,6 +12,7 @@
   "license": "AFL-3.0",
   "dependencies": {
     "@babel/polyfill": "^7.4.0",
+    "@fortawesome/vue-fontawesome": "^0.1.7",
     "@handsontable/vue": "^2.0.0-beta1",
     "@johmun/vue-tags-input": "^2.0.1",
     "@vue/test-utils": "1.0.0-beta.29",
diff --git a/client/yarn.lock b/client/yarn.lock
index eb875cefffd..6df98942090 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -826,6 +826,11 @@
     lodash "^4.17.13"
     to-fast-properties "^2.0.0"
 
+"@fortawesome/vue-fontawesome@^0.1.7":
+  version "0.1.7"
+  resolved "https://registry.yarnpkg.com/@fortawesome/vue-fontawesome/-/vue-fontawesome-0.1.7.tgz#121867297cafd141af78c67d92ab9f1ad4b7328b"
+  integrity sha512-YCw2Q2m4fxzyFsPOH3uDYMoJztTD+pT+AAyse4LFpbdrBg+r8ueaVT8BFnXEjrGwMDJJeXrwJ5AOC6q/JWBI4w==
+
 "@handsontable/vue@^2.0.0-beta1":
   version "2.0.0"
   resolved "https://registry.yarnpkg.com/@handsontable/vue/-/vue-2.0.0.tgz#28ae7d247a89738088abc32584562925dde18db0"

From 8d776a69e5108b8feeb4ed224b06f69e4b2a74dd Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 31 Oct 2019 15:36:49 -0400
Subject: [PATCH 002/101] Add core fa icon libs

---
 client/package.json |  2 ++
 client/yarn.lock    | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+)

diff --git a/client/package.json b/client/package.json
index d16be42bdeb..0b585f0161d 100644
--- a/client/package.json
+++ b/client/package.json
@@ -12,6 +12,8 @@
   "license": "AFL-3.0",
   "dependencies": {
     "@babel/polyfill": "^7.4.0",
+    "@fortawesome/fontawesome-svg-core": "^1.2.25",
+    "@fortawesome/free-solid-svg-icons": "^5.11.2",
     "@fortawesome/vue-fontawesome": "^0.1.7",
     "@handsontable/vue": "^2.0.0-beta1",
     "@johmun/vue-tags-input": "^2.0.1",
diff --git a/client/yarn.lock b/client/yarn.lock
index 6df98942090..71267f5b1c2 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -826,6 +826,25 @@
     lodash "^4.17.13"
     to-fast-properties "^2.0.0"
 
+"@fortawesome/fontawesome-common-types@^0.2.25":
+  version "0.2.25"
+  resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-0.2.25.tgz#6df015905081f2762e5cfddeb7a20d2e9b16c786"
+  integrity sha512-3RuZPDuuPELd7RXtUqTCfed14fcny9UiPOkdr2i+cYxBoTOfQgxcDoq77fHiiHcgWuo1LoBUpvGxFF1H/y7s3Q==
+
+"@fortawesome/fontawesome-svg-core@^1.2.25":
+  version "1.2.25"
+  resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-svg-core/-/fontawesome-svg-core-1.2.25.tgz#24b03391d14f0c6171e8cad7057c687b74049790"
+  integrity sha512-MotKnn53JKqbkLQiwcZSBJVYtTgIKFbh7B8+kd05TSnfKYPFmjKKI59o2fpz5t0Hzl35vVGU6+N4twoOpZUrqA==
+  dependencies:
+    "@fortawesome/fontawesome-common-types" "^0.2.25"
+
+"@fortawesome/free-solid-svg-icons@^5.11.2":
+  version "5.11.2"
+  resolved "https://registry.yarnpkg.com/@fortawesome/free-solid-svg-icons/-/free-solid-svg-icons-5.11.2.tgz#2f2f1459743a27902b76655a0d0bc5ec4d945631"
+  integrity sha512-zBue4i0PAZJUXOmLBBvM7L0O7wmsDC8dFv9IhpW5QL4kT9xhhVUsYg/LX1+5KaukWq4/cbDcKT+RT1aRe543sg==
+  dependencies:
+    "@fortawesome/fontawesome-common-types" "^0.2.25"
+
 "@fortawesome/vue-fontawesome@^0.1.7":
   version "0.1.7"
   resolved "https://registry.yarnpkg.com/@fortawesome/vue-fontawesome/-/vue-fontawesome-0.1.7.tgz#121867297cafd141af78c67d92ab9f1ad4b7328b"

From b2221cacb10d2a86d0acf8f0de384599d9a12af5 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 6 Nov 2019 13:57:54 -0500
Subject: [PATCH 003/101] Minor version bump after rebase, inclusion of
 fontawesome-free

---
 client/package.json |  4 ++--
 client/yarn.lock    | 18 +++++++++---------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/client/package.json b/client/package.json
index 0b585f0161d..8354b5dca64 100644
--- a/client/package.json
+++ b/client/package.json
@@ -12,9 +12,10 @@
   "license": "AFL-3.0",
   "dependencies": {
     "@babel/polyfill": "^7.4.0",
+    "@fortawesome/fontawesome-free": "^5.11.2",
     "@fortawesome/fontawesome-svg-core": "^1.2.25",
     "@fortawesome/free-solid-svg-icons": "^5.11.2",
-    "@fortawesome/vue-fontawesome": "^0.1.7",
+    "@fortawesome/vue-fontawesome": "^0.1.8",
     "@handsontable/vue": "^2.0.0-beta1",
     "@johmun/vue-tags-input": "^2.0.1",
     "@vue/test-utils": "1.0.0-beta.29",
@@ -27,7 +28,6 @@
     "d3": "3",
     "decode-uri-component": "^0.2.0",
     "flush-promises": "^1.0.2",
-    "font-awesome": "^4.7.0",
     "glob": "^7.1.4",
     "handsontable": "^2.0.0",
     "imask": "^4.1.5",
diff --git a/client/yarn.lock b/client/yarn.lock
index 71267f5b1c2..1c1a9065ba2 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -831,6 +831,11 @@
   resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-0.2.25.tgz#6df015905081f2762e5cfddeb7a20d2e9b16c786"
   integrity sha512-3RuZPDuuPELd7RXtUqTCfed14fcny9UiPOkdr2i+cYxBoTOfQgxcDoq77fHiiHcgWuo1LoBUpvGxFF1H/y7s3Q==
 
+"@fortawesome/fontawesome-free@^5.11.2":
+  version "5.11.2"
+  resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-free/-/fontawesome-free-5.11.2.tgz#8644bc25b19475779a7b7c1fc104bc0a794f4465"
+  integrity sha512-XiUPoS79r1G7PcpnNtq85TJ7inJWe0v+b5oZJZKb0pGHNIV6+UiNeQWiFGmuQ0aj7GEhnD/v9iqxIsjuRKtEnQ==
+
 "@fortawesome/fontawesome-svg-core@^1.2.25":
   version "1.2.25"
   resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-svg-core/-/fontawesome-svg-core-1.2.25.tgz#24b03391d14f0c6171e8cad7057c687b74049790"
@@ -845,10 +850,10 @@
   dependencies:
     "@fortawesome/fontawesome-common-types" "^0.2.25"
 
-"@fortawesome/vue-fontawesome@^0.1.7":
-  version "0.1.7"
-  resolved "https://registry.yarnpkg.com/@fortawesome/vue-fontawesome/-/vue-fontawesome-0.1.7.tgz#121867297cafd141af78c67d92ab9f1ad4b7328b"
-  integrity sha512-YCw2Q2m4fxzyFsPOH3uDYMoJztTD+pT+AAyse4LFpbdrBg+r8ueaVT8BFnXEjrGwMDJJeXrwJ5AOC6q/JWBI4w==
+"@fortawesome/vue-fontawesome@^0.1.8":
+  version "0.1.8"
+  resolved "https://registry.yarnpkg.com/@fortawesome/vue-fontawesome/-/vue-fontawesome-0.1.8.tgz#615347c56d285eb634315f59fe4f4156e4eee8b4"
+  integrity sha512-SdFiUD+vFDA/xKuEbnQTVrK8FDxoV0eyQaiHxmCcjAc0+vQe0Kf6oGm28opNPIt8MTgKWR3+Yg3xXP455Ae4tQ==
 
 "@handsontable/vue@^2.0.0-beta1":
   version "2.0.0"
@@ -5941,11 +5946,6 @@ follow-redirects@^1.0.0:
   dependencies:
     debug "=3.1.0"
 
-font-awesome@^4.7.0:
-  version "4.7.0"
-  resolved "https://registry.yarnpkg.com/font-awesome/-/font-awesome-4.7.0.tgz#8fa8cf0411a1a31afd07b06d2902bb9fc815a133"
-  integrity sha1-j6jPBBGhoxr9B7BtKQK7n8gVoTM=
-
 for-in@^0.1.3:
   version "0.1.8"
   resolved "https://registry.yarnpkg.com/for-in/-/for-in-0.1.8.tgz#d8773908e31256109952b1fdb9b3fa867d2775e1"

From cc85a701b76a5582d46cecc7bda29a79386168a4 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 26 Nov 2019 18:43:18 -0500
Subject: [PATCH 004/101] Incremental work getting fa5 working.

---
 client/galaxy/style/scss/base.scss    | 12 ++++++++++--
 client/galaxy/style/scss/dataset.scss |  7 ++++---
 client/galaxy/style/scss/mixins.scss  |  9 ++++++---
 3 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index f9ac0766b5e..e35d739d64b 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -8,8 +8,16 @@
 @import "overrides.scss";
 
 // Fontawesome configuration.
-$fa-font-path: "../../../node_modules/font-awesome/fonts/";
-@import "../../../node_modules/font-awesome/scss/font-awesome.scss";
+//$fa-font-path: "../../../node_modules/font-awesome/fonts/";
+//@import "../../../node_modules/font-awesome/scss/font-awesome.scss";
+
+$fa-font-path: "../../../node_modules/@fortawesome/fontawesome-free/webfonts/";
+@import "../../../node_modules/@fortawesome/fontawesome-free/scss/fontawesome";
+@import "../../../node_modules/@fortawesome/fontawesome-free/scss/brands";
+@import "../../../node_modules/@fortawesome/fontawesome-free/scss/regular";
+@import "../../../node_modules/@fortawesome/fontawesome-free/scss/solid";
+@import "../../../node_modules/@fortawesome/fontawesome-free/scss/v4-shims";
+@import "../../../node_modules/@fortawesome/fontawesome-free/scss/_variables";
 
 @import "select2.scss";
 @import "jquery.rating.scss";
diff --git a/client/galaxy/style/scss/dataset.scss b/client/galaxy/style/scss/dataset.scss
index 1c57cbe23a9..8ddfe473c5e 100644
--- a/client/galaxy/style/scss/dataset.scss
+++ b/client/galaxy/style/scss/dataset.scss
@@ -1,5 +1,6 @@
 @import "sprite-history-states.scss";
 @import "sprite-history-buttons.scss";
+@import "~@fortawesome/fontawesome-free/scss/_variables";
 
 // ---------------------------------------------------------------------------- dataset states
 //.dataset .state-icon {
@@ -117,7 +118,7 @@
         background: $state-default-bg;
         .state-icon {
             &:before {
-                content: $fa-var-clock-o;
+                content: $fa-var-clock;
             }
         }
     }
@@ -143,7 +144,7 @@
         background: $state-default-bg;
         .state-icon {
             &:before {
-                content: $fa-var-trash-o;
+                content: $fa-var-trash;
             }
         }
     }
@@ -165,7 +166,7 @@
         background: $state-default-bg;
         .state-icon {
             &:before {
-                content: $fa-var-clock-o;
+                content: $fa-var-clock;
             }
         }
     }
diff --git a/client/galaxy/style/scss/mixins.scss b/client/galaxy/style/scss/mixins.scss
index 81f7b907670..233c938d394 100644
--- a/client/galaxy/style/scss/mixins.scss
+++ b/client/galaxy/style/scss/mixins.scss
@@ -1,6 +1,9 @@
-$fa-font-path: "~font-awesome/fonts/";
-@import "~font-awesome/scss/font-awesome.scss";
-@import "~font-awesome/scss/_mixins";
+//$fa-font-path: "~font-awesome/fonts/";
+//@import "~font-awesome/scss/font-awesome.scss";
+//@import "~font-awesome/scss/_mixins";
+$fa-font-path: "../../../node_modules/@fortawesome/fontawesome-free/webfonts/";
+@import "~@fortawesome/fontawesome-free/scss/fontawesome";
+@import "~@fortawesome/fontawesome-free/scss/_variables";
 
 // Utility mixin expands to container edges
 @mixin fill() {

From a4f01d0c413eda8eae7c7352dbffe8af60625f91 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 Dec 2019 15:54:06 -0500
Subject: [PATCH 005/101] Test two svg-based fontawesome-vue icons in the
 workflow list

---
 .../scripts/components/Workflow/WorkflowList.vue  | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/WorkflowList.vue b/client/galaxy/scripts/components/Workflow/WorkflowList.vue
index 5015e2a3f1d..ec8ee95faa8 100644
--- a/client/galaxy/scripts/components/Workflow/WorkflowList.vue
+++ b/client/galaxy/scripts/components/Workflow/WorkflowList.vue
@@ -23,11 +23,11 @@
                     <b-col>
                         <span class="float-right">
                             <b-button id="workflow-create" class="m-1" @click="createWorkflow">
-                                <span class="fa fa-plus" />
+                                <font-awesome-icon icon="plus"/>
                                 Create
                             </b-button>
                             <b-button id="workflow-import" class="m-1" @click="importWorkflow">
-                                <span class="fa fa-upload" />
+                                <font-awesome-icon icon="upload"/>
                                 Import
                             </b-button>
                         </span>
@@ -80,6 +80,14 @@
     </div>
 </template>
 <script>
+import { library } from '@fortawesome/fontawesome-svg-core'
+import { FontAwesomeIcon } from '@fortawesome/vue-fontawesome'
+import { faPlus } from "@fortawesome/free-solid-svg-icons";
+import { faUpload } from "@fortawesome/free-solid-svg-icons";
+
+library.add(faPlus)
+library.add(faUpload)
+
 import { getAppRoot } from "onload/loadConfig";
 import { Services } from "./services.js";
 import WorkflowTags from "./WorkflowTags.vue";
@@ -88,7 +96,8 @@ import WorkflowDropdown from "./WorkflowDropdown.vue";
 export default {
     components: {
         workflowtags: WorkflowTags,
-        workflowdropdown: WorkflowDropdown
+        workflowdropdown: WorkflowDropdown,
+        FontAwesomeIcon
     },
     data() {
         return {

From 7d34b4f720f2a7490702bb2deefcc638223f1111 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 Dec 2019 15:54:18 -0500
Subject: [PATCH 006/101] Minor code formatting.

---
 .../scripts/components/Workflow/WorkflowList.vue     | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/WorkflowList.vue b/client/galaxy/scripts/components/Workflow/WorkflowList.vue
index ec8ee95faa8..dfa41453803 100644
--- a/client/galaxy/scripts/components/Workflow/WorkflowList.vue
+++ b/client/galaxy/scripts/components/Workflow/WorkflowList.vue
@@ -23,11 +23,11 @@
                     <b-col>
                         <span class="float-right">
                             <b-button id="workflow-create" class="m-1" @click="createWorkflow">
-                                <font-awesome-icon icon="plus"/>
+                                <font-awesome-icon icon="plus" />
                                 Create
                             </b-button>
                             <b-button id="workflow-import" class="m-1" @click="importWorkflow">
-                                <font-awesome-icon icon="upload"/>
+                                <font-awesome-icon icon="upload" />
                                 Import
                             </b-button>
                         </span>
@@ -80,13 +80,13 @@
     </div>
 </template>
 <script>
-import { library } from '@fortawesome/fontawesome-svg-core'
-import { FontAwesomeIcon } from '@fortawesome/vue-fontawesome'
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { faPlus } from "@fortawesome/free-solid-svg-icons";
 import { faUpload } from "@fortawesome/free-solid-svg-icons";
 
-library.add(faPlus)
-library.add(faUpload)
+library.add(faPlus);
+library.add(faUpload);
 
 import { getAppRoot } from "onload/loadConfig";
 import { Services } from "./services.js";

From 2308925f63caab3622be1876ae33356bd9c57ab7 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 Dec 2019 16:29:14 -0500
Subject: [PATCH 007/101] Test spinner -- works great, swap for svg in
 workflowlist.

---
 .../scripts/components/Workflow/WorkflowList.vue     | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/components/Workflow/WorkflowList.vue b/client/galaxy/scripts/components/Workflow/WorkflowList.vue
index dfa41453803..898f3f7aca1 100644
--- a/client/galaxy/scripts/components/Workflow/WorkflowList.vue
+++ b/client/galaxy/scripts/components/Workflow/WorkflowList.vue
@@ -3,7 +3,7 @@
         <div v-if="error" class="alert alert-danger" show>{{ error }}</div>
         <div v-else>
             <span v-if="loading">
-                <span class="fa fa-spinner fa-spin" />
+                <font-awesome-icon icon="spinner" spin />
                 Loading workflows...
             </span>
             <div v-else>
@@ -80,19 +80,21 @@
     </div>
 </template>
 <script>
-import { library } from "@fortawesome/fontawesome-svg-core";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
 import { faPlus } from "@fortawesome/free-solid-svg-icons";
+import { faSpinner } from "@fortawesome/free-solid-svg-icons";
 import { faUpload } from "@fortawesome/free-solid-svg-icons";
 
-library.add(faPlus);
-library.add(faUpload);
-
 import { getAppRoot } from "onload/loadConfig";
 import { Services } from "./services.js";
 import WorkflowTags from "./WorkflowTags.vue";
 import WorkflowDropdown from "./WorkflowDropdown.vue";
 
+library.add(faPlus);
+library.add(faUpload);
+library.add(faSpinner);
+
 export default {
     components: {
         workflowtags: WorkflowTags,

From dab2fba64cd3d83b1ab64a907c6577de475e5577 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 Dec 2019 17:33:54 -0500
Subject: [PATCH 008/101] Fix access to fa-content via vars

---
 client/galaxy/style/scss/dataset.scss | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/client/galaxy/style/scss/dataset.scss b/client/galaxy/style/scss/dataset.scss
index 8ddfe473c5e..1f27021246f 100644
--- a/client/galaxy/style/scss/dataset.scss
+++ b/client/galaxy/style/scss/dataset.scss
@@ -73,7 +73,7 @@
                 transform: translate(0px, -16px);
             }
         }
-        content: $fa-var-arrow-up;
+        content: fa-content($fa-var-arrow-up);
     }
 }
 
@@ -84,7 +84,7 @@
         font-size: 20px;
         line-height: 16px;
         color: red;
-        content: $fa-var-times-circle;
+        content: fa-content($fa-var-times-circle);
     }
 }
 
@@ -118,7 +118,7 @@
         background: $state-default-bg;
         .state-icon {
             &:before {
-                content: $fa-var-clock;
+                content: fa-content($fa-var-clock);
             }
         }
     }
@@ -135,7 +135,7 @@
         background: $state-paused-bg;
         .state-icon {
             &:before {
-                content: $fa-var-pause;
+                content: fa-content($fa-var-pause);
             }
         }
     }
@@ -144,7 +144,7 @@
         background: $state-default-bg;
         .state-icon {
             &:before {
-                content: $fa-var-trash;
+                content: fa-content($fa-var-trash);
             }
         }
     }
@@ -157,7 +157,7 @@
         .state-icon {
             font-size: 20px;
             &:before {
-                content: $fa-var-lock;
+                content: fa-content($fa-var-lock);
             }
         }
     }
@@ -166,7 +166,7 @@
         background: $state-default-bg;
         .state-icon {
             &:before {
-                content: $fa-var-clock;
+                content: fa-content($fa-var-clock);
             }
         }
     }

From d88beec0d5795da2b002ca01ed39e78c076e6191 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 Dec 2019 18:21:04 -0500
Subject: [PATCH 009/101] Add fontawesome regular svgs (in addition to solid)

---
 client/package.json |  1 +
 client/yarn.lock    | 12 ++++++++++++
 2 files changed, 13 insertions(+)

diff --git a/client/package.json b/client/package.json
index 8354b5dca64..757bf64c9aa 100644
--- a/client/package.json
+++ b/client/package.json
@@ -14,6 +14,7 @@
     "@babel/polyfill": "^7.4.0",
     "@fortawesome/fontawesome-free": "^5.11.2",
     "@fortawesome/fontawesome-svg-core": "^1.2.25",
+    "@fortawesome/free-regular-svg-icons": "^5.12.0",
     "@fortawesome/free-solid-svg-icons": "^5.11.2",
     "@fortawesome/vue-fontawesome": "^0.1.8",
     "@handsontable/vue": "^2.0.0-beta1",
diff --git a/client/yarn.lock b/client/yarn.lock
index 1c1a9065ba2..50ad9b7ff3f 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -831,6 +831,11 @@
   resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-0.2.25.tgz#6df015905081f2762e5cfddeb7a20d2e9b16c786"
   integrity sha512-3RuZPDuuPELd7RXtUqTCfed14fcny9UiPOkdr2i+cYxBoTOfQgxcDoq77fHiiHcgWuo1LoBUpvGxFF1H/y7s3Q==
 
+"@fortawesome/fontawesome-common-types@^0.2.26":
+  version "0.2.26"
+  resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-0.2.26.tgz#6e0b13a752676036f8196f8a1500d53a27b4adc1"
+  integrity sha512-CcM/fIFwZlRdiWG/25xE/wHbtyUuCtqoCTrr6BsWw7hH072fR++n4L56KPydAr3ANgMJMjT8v83ZFIsDc7kE+A==
+
 "@fortawesome/fontawesome-free@^5.11.2":
   version "5.11.2"
   resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-free/-/fontawesome-free-5.11.2.tgz#8644bc25b19475779a7b7c1fc104bc0a794f4465"
@@ -843,6 +848,13 @@
   dependencies:
     "@fortawesome/fontawesome-common-types" "^0.2.25"
 
+"@fortawesome/free-regular-svg-icons@^5.12.0":
+  version "5.12.0"
+  resolved "https://registry.yarnpkg.com/@fortawesome/free-regular-svg-icons/-/free-regular-svg-icons-5.12.0.tgz#9b7ed5dbd7581aab47960802cc116fdc8b6c8b7d"
+  integrity sha512-FAvpmylTs0PosHwHrWPQX6/7ODc9M11kCE6AOAujFufDYzqTj2cPHT4yJO7zTEkKdAbbusJzbWpnOboMuyjeQA==
+  dependencies:
+    "@fortawesome/fontawesome-common-types" "^0.2.26"
+
 "@fortawesome/free-solid-svg-icons@^5.11.2":
   version "5.11.2"
   resolved "https://registry.yarnpkg.com/@fortawesome/free-solid-svg-icons/-/free-solid-svg-icons-5.11.2.tgz#2f2f1459743a27902b76655a0d0bc5ec4d945631"

From 1f772365a63407043ba2bf8474db38e02b95344a Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 Dec 2019 18:33:12 -0500
Subject: [PATCH 010/101] Convert fa usage in toolbox to vue+svg-based.;

---
 .../scripts/components/FavoritesButton.vue    |  7 +++++-
 .../galaxy/scripts/components/ToolSearch.vue  | 22 ++++++++++++++-----
 .../scripts/components/UploadButton.vue       |  8 ++++++-
 3 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/client/galaxy/scripts/components/FavoritesButton.vue b/client/galaxy/scripts/components/FavoritesButton.vue
index fefffc206ac..e3a3b695f92 100644
--- a/client/galaxy/scripts/components/FavoritesButton.vue
+++ b/client/galaxy/scripts/components/FavoritesButton.vue
@@ -8,15 +8,20 @@
         role="button"
         aria-label="Show favorite tools"
     >
-        <span class="fa fa-star-o"></span>
+        <font-awesome-icon :icon="['far', 'star']" />
     </a>
 </template>
 
 <script>
 import { VBTooltip } from "bootstrap-vue";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faStar } from "@fortawesome/free-regular-svg-icons";
+library.add(faStar);
 
 export default {
     name: "FavoritesButton",
+    components: { FontAwesomeIcon },
     data() {
         return {
             tooltipText: "Show favorites"
diff --git a/client/galaxy/scripts/components/ToolSearch.vue b/client/galaxy/scripts/components/ToolSearch.vue
index 5a8c1583295..c8c5ecc3732 100644
--- a/client/galaxy/scripts/components/ToolSearch.vue
+++ b/client/galaxy/scripts/components/ToolSearch.vue
@@ -11,14 +11,15 @@
             autocomplete="off"
             type="text"
         />
-        <span
-            class="search-clear fa fa-times-circle"
+        <font-awesome-icon
+            class="search-clear"
+            v-if="showClear"
+            icon="times-circle"
             v-b-tooltip.hover
             title="clear search (esc)"
-            v-if="showClear"
             @click="clear"
-        ></span>
-        <span class="search-loading fa fa-spinner fa-spin" v-if="showSpinner"></span>
+        />
+        <font-awesome-icon class="search-loading" v-if="showSpinner" icon="spinner" spin />
     </div>
 </template>
 
@@ -27,12 +28,23 @@ import { VBTooltip } from "bootstrap-vue";
 import _ from "underscore";
 import axios from "axios";
 
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faTimesCircle } from "@fortawesome/free-solid-svg-icons";
+import { faSpinner } from "@fortawesome/free-solid-svg-icons";
+
 import { getAppRoot } from "onload/loadConfig";
 import { getGalaxyInstance } from "app"; // FIXME: may be we can move it to the ToolBox?
 /* global ga */
 
+library.add(faSpinner);
+library.add(faTimesCircle);
+
 export default {
     name: "ToolSearch",
+    components: {
+        FontAwesomeIcon
+    },
     directives: {
         "v-b-tooltip": VBTooltip
     },
diff --git a/client/galaxy/scripts/components/UploadButton.vue b/client/galaxy/scripts/components/UploadButton.vue
index 57d310a9b9d..75a8983f5ac 100644
--- a/client/galaxy/scripts/components/UploadButton.vue
+++ b/client/galaxy/scripts/components/UploadButton.vue
@@ -18,7 +18,7 @@
                 aria-label="Download from URL or upload files from disk"
                 title="Download from URL or upload files from disk"
             >
-                <span class="fa fa-upload"></span>
+                <font-awesome-icon icon="upload" />
             </a>
         </div>
     </div>
@@ -28,8 +28,14 @@
 import { VBTooltip } from "bootstrap-vue";
 import { getGalaxyInstance } from "app"; // FIXME:
 
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faUpload } from "@fortawesome/free-solid-svg-icons";
+library.add(faUpload);
+
 export default {
     name: "UploadButton",
+    components: { FontAwesomeIcon },
     directives: {
         "v-b-tooltip": VBTooltip
     },

From c54a6c4c5b557635b34c43fc93c1eaeece18827c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 Dec 2019 21:39:29 -0500
Subject: [PATCH 011/101] Adjust icon-btn glyph size to account for changes in
 fa5.

---
 client/galaxy/style/scss/ui/icon-btn.scss | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/galaxy/style/scss/ui/icon-btn.scss b/client/galaxy/style/scss/ui/icon-btn.scss
index 0bafffa2bd0..c3e3e7355fd 100644
--- a/client/galaxy/style/scss/ui/icon-btn.scss
+++ b/client/galaxy/style/scss/ui/icon-btn.scss
@@ -8,7 +8,6 @@ $icon-btn-border: $btn-default-border;
     display: inline-block;
     height: $icon-btn-size;
     width: $icon-btn-size;
-    font-size: 125%;
 
     // center the icon
     text-align: center;

From 982e13fd82da1d16debcefb1944c6474a23eb349 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 8 Nov 2019 17:35:30 -0500
Subject: [PATCH 012/101] Migrate job stop logic to API.

---
 .../galaxy/scripts/components/admin/Jobs.vue  | 21 +++++++------
 lib/galaxy/managers/jobs.py                   |  9 ++++++
 lib/galaxy/webapps/galaxy/api/jobs.py         | 12 +++----
 .../webapps/galaxy/controllers/admin.py       | 31 ++-----------------
 4 files changed, 28 insertions(+), 45 deletions(-)

diff --git a/client/galaxy/scripts/components/admin/Jobs.vue b/client/galaxy/scripts/components/admin/Jobs.vue
index 85f02a14a6b..c0563512f18 100644
--- a/client/galaxy/scripts/components/admin/Jobs.vue
+++ b/client/galaxy/scripts/components/admin/Jobs.vue
@@ -126,7 +126,7 @@
                         v-model="selectedStopJobIds"
                         :checked="allSelected"
                         :key="data.index"
-                        :value="data.item['job_info']['id']"
+                        :value="data.item['id']"
                     ></b-form-checkbox>
                 </template>
                 <template v-slot:cell(job_info)="data">
@@ -187,6 +187,11 @@ import { getAppRoot } from "onload/loadConfig";
 import UtcDate from "components/UtcDate";
 import axios from "axios";
 
+function cancelJob(jobId, message) {
+    const url = `${getAppRoot()}api/jobs/${jobId}`;
+    return axios.delete(url, { data: { message: message } });
+}
+
 export default {
     components: { UtcDate },
     data() {
@@ -249,8 +254,6 @@ export default {
             this.busy = true;
             let params = [];
             params.push(`cutoff=${this.cutoff}`);
-            params.push(`stop_msg=${this.stopMessage}`);
-            params.push(`stop=${this.selectedStopJobIds.join()}`);
             params = params.join("&");
             axios
                 .get(`${getAppRoot()}admin/jobs_list?${params}`)
@@ -275,9 +278,11 @@ export default {
             this.update();
         },
         onStopJobs() {
-            this.update();
-            this.selectedStopJobIds = [];
-            this.stopMessage = "";
+            axios.all(this.selectedStopJobIds.map(jobId => cancelJob(jobId, this.stopMessage))).then(res => {
+                this.update();
+                this.selectedStopJobIds = [];
+                this.stopMessage = "";
+            });
         },
         showRowDetails(row, index, e) {
             if (e.target.nodeName != "A") {
@@ -315,9 +320,7 @@ export default {
             return f;
         },
         toggleAll(checked) {
-            this.selectedStopJobIds = checked
-                ? this.jobsItemsModel.reduce((acc, j) => [...acc, j["job_info"]["id"]], [])
-                : [];
+            this.selectedStopJobIds = checked ? this.jobsItemsModel.reduce((acc, j) => [...acc, j["id"]], []) : [];
         },
         galaxyKwdToBootstrap(status) {
             let variant = "info";
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 152ad89ea1d..c2c4abcabfd 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -65,6 +65,15 @@ class JobManager(object):
         trans.sa_session.refresh(job)
         return job
 
+    def stop(self, job, message=None):
+        if not job.finished:
+            job.mark_deleted(self.app.config.track_jobs_in_database)
+            self.app.model.context.current.flush()
+            self.app.job_manager.stop(job, message=message)
+            return True
+        else:
+            return False
+
 
 class JobSearch(object):
     """Search for jobs using tool inputs or other jobs"""
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index bd6b948f73b..369d2c5d036 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -237,15 +237,13 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
 
         :type   id: string
         :param  id: Encoded job id
+        :type   message: string
+        :param  message: Stop message.
         """
+        payload = kwd.get("payload") or {}
         job = self.__get_job(trans, id)
-        if not job.finished:
-            job.mark_deleted(self.app.config.track_jobs_in_database)
-            trans.sa_session.flush()
-            self.app.job_manager.stop(job)
-            return True
-        else:
-            return False
+        message = payload.get("message", None)
+        return self.job_manager.stop(job, message=message)
 
     @expose_api
     def resume(self, trans, id, **kwd):
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index b4b50564b65..7181cb45200 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -3,7 +3,6 @@ import logging
 import os
 from collections import OrderedDict
 from datetime import datetime, timedelta
-from string import punctuation as PUNCTUATION
 
 import six
 from sqlalchemy import and_, false, or_
@@ -1531,36 +1530,9 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
     @web.expose
     @web.json
     @web.require_admin
-    def jobs_list(self, trans, stop=[], stop_msg=None, cutoff=180, **kwd):
-        deleted = []
+    def jobs_list(self, trans, cutoff=180, **kwd):
         message = kwd.get('message', '')
         status = kwd.get('status', 'info')
-        job_ids = util.listify(stop)
-        if job_ids and stop_msg in [None, '']:
-            message = 'Please enter an error message to display to the user describing why the job was terminated'
-            return self.message_exception(trans, message)
-        elif job_ids:
-            if stop_msg[-1] not in PUNCTUATION:
-                stop_msg += '.'
-            for job_id in job_ids:
-                error_msg = "This job was stopped by an administrator: %s  <a href='%s' target='_blank'>Contact support</a> for additional help." \
-                    % (stop_msg, self.app.config.get("support_url", "https://galaxyproject.org/support/"))
-                if trans.app.config.track_jobs_in_database:
-                    job = trans.sa_session.query(trans.app.model.Job).get(job_id)
-                    job.job_stderr = error_msg
-                    job.set_state(trans.app.model.Job.states.DELETED_NEW)
-                    trans.sa_session.add(job)
-                else:
-                    trans.app.job_manager.stop(job, message=error_msg)
-                deleted.append(str(job_id))
-        if deleted:
-            message = 'Queued job'
-            if len(deleted) > 1:
-                message += 's'
-            message += ' for deletion: '
-            message += ', '.join(deleted)
-            status = 'done'
-            trans.sa_session.flush()
         job_lock = trans.app.job_manager.job_lock
         cutoff_time = datetime.utcnow() - timedelta(seconds=int(cutoff))
         jobs = trans.sa_session.query(trans.app.model.Job) \
@@ -1589,6 +1561,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                         'id': job.id,
                         'info_url': "{}?jobid={}".format(web.url_for(controller="admin", action="job_info"), job.id)
                     },
+                    'id': trans.security.encode_id(job.id),
                     'user': job.history.user.email if job.history and job.history.user else 'anonymous',
                     'update_time': job.update_time.isoformat(),
                     'tool_id': job.tool_id,

From cc8e776e79e6b28273f440347c769aab77d99a7c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 10 Dec 2019 23:24:56 -0500
Subject: [PATCH 013/101] Jobs grid - replace job_lock with real API calls.

---
 .../galaxy/scripts/components/admin/Jobs.vue  | 26 +++++++++++--------
 lib/galaxy/webapps/galaxy/api/jobs.py         | 21 +++++++++++++++
 lib/galaxy/webapps/galaxy/buildapp.py         |  2 ++
 .../webapps/galaxy/controllers/admin.py       | 14 +---------
 4 files changed, 39 insertions(+), 24 deletions(-)

diff --git a/client/galaxy/scripts/components/admin/Jobs.vue b/client/galaxy/scripts/components/admin/Jobs.vue
index c0563512f18..2d75872fd3b 100644
--- a/client/galaxy/scripts/components/admin/Jobs.vue
+++ b/client/galaxy/scripts/components/admin/Jobs.vue
@@ -226,15 +226,7 @@ export default {
     },
     watch: {
         jobLock(newVal) {
-            axios
-                .get(`${getAppRoot()}admin/jobs_control?job_lock=${this.jobLock}`)
-                .then(response => {
-                    this.jobLock = response.data.job_lock;
-                    this.jobLockDisplay = response.data.job_lock;
-                })
-                .catch(error => {
-                    console.error(error);
-                });
+            this.handleJobLock(axios.put(`${getAppRoot()}api/job_lock`, { active: this.jobLock }));
         },
         selectedStopJobIds(newVal) {
             if (newVal.length === 0) {
@@ -250,6 +242,19 @@ export default {
         }
     },
     methods: {
+        initJobLock() {
+            this.handleJobLock(axios.get(`${getAppRoot()}api/job_lock`));
+        },
+        handleJobLock(axiosPromise) {
+            axiosPromise
+                .then(response => {
+                    this.jobLock = response.data.active;
+                    this.jobLockDisplay = response.data.active;
+                })
+                .catch(error => {
+                    console.error(error);
+                });
+        },
         update() {
             this.busy = true;
             let params = [];
@@ -263,8 +268,6 @@ export default {
                     this.cutoffDisplay = response.data.cutoff;
                     this.message = response.data.message;
                     this.status = response.data.status;
-                    this.jobLock = response.data.job_lock;
-                    this.jobLockDisplay = response.data.job_lock;
                     this.loading = false;
                     this.busy = false;
                 })
@@ -360,6 +363,7 @@ export default {
         }
     },
     created() {
+        this.initJobLock();
         this.update();
     }
 };
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 369d2c5d036..8da05d4979d 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -16,6 +16,7 @@ from galaxy.managers.jobs import JobManager, JobSearch
 from galaxy.web import (
     expose_api,
     expose_api_anonymous,
+    require_admin,
 )
 from galaxy.webapps.base.controller import (
     BaseAPIController,
@@ -567,3 +568,23 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         )
 
         return {'messages': messages}
+
+    @require_admin
+    @expose_api
+    def show_job_lock(self, trans, **kwd):
+        """
+        * GET /api/job_lock
+            return boolean indicating if job lock active.
+        """
+        return {"active": self.app.job_manager.job_lock}
+
+    @require_admin
+    @expose_api
+    def update_job_lock(self, trans, payload, **kwd):
+        """
+        * PUT /api/job_lock
+            return boolean indicating if job lock active.
+        """
+        job_lock = payload.get("active")
+        self.app.queue_worker.send_control_task('admin_job_lock', kwargs={'job_lock': job_lock}, get_response=True)
+        return {"active": self.app.job_manager.job_lock}
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index bf004dcd673..3cef442dfcd 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -928,6 +928,8 @@ def populate_api_routes(webapp, app):
     webapp.mapper.connect('common_problems', '/api/jobs/{id}/common_problems', controller='jobs', action='common_problems', conditions=dict(method=['GET']))
     # Job metrics and parameters by job id or dataset id (for slightly different accessibility checking)
     webapp.mapper.connect('metrics', '/api/jobs/{job_id}/metrics', controller='jobs', action='metrics', conditions=dict(method=['GET']))
+    webapp.mapper.connect('show_job_lock', '/api/job_lock', controller='jobs', action='show_job_lock', conditions=dict(method=['GET']))
+    webapp.mapper.connect('update_job_lock', '/api/job_lock', controller='jobs', action='update_job_lock', conditions=dict(method=['PUT']))
     webapp.mapper.connect('dataset_metrics', '/api/datasets/{dataset_id}/metrics', controller='jobs', action='metrics', conditions=dict(method=['GET']))
     webapp.mapper.connect('parameters_display', '/api/jobs/{job_id}/parameters_display', controller='jobs', action='parameters_display', conditions=dict(method=['GET']))
     webapp.mapper.connect('dataset_parameters_display', '/api/datasets/{dataset_id}/parameters_display', controller='jobs', action='parameters_display', conditions=dict(method=['GET']))
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 7181cb45200..fa729690c64 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -1517,23 +1517,12 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
             trans.sa_session.refresh(user)
             return {'message' : 'User \'%s\' has been updated with %d associated roles and %d associated groups (private roles are not displayed).' % (user.email, len(in_roles) - 1, len(in_groups))}
 
-    @web.expose
-    @web.json
-    @web.require_admin
-    def jobs_control(self, trans, job_lock=None, **kwd):
-        if job_lock is not None:
-            job_lock = True if job_lock == 'true' else False
-            trans.app.queue_worker.send_control_task('admin_job_lock', kwargs={'job_lock': job_lock}, get_response=True)
-        job_lock = trans.app.job_manager.job_lock
-        return {'job_lock': job_lock}
-
     @web.expose
     @web.json
     @web.require_admin
     def jobs_list(self, trans, cutoff=180, **kwd):
         message = kwd.get('message', '')
         status = kwd.get('status', 'info')
-        job_lock = trans.app.job_manager.job_lock
         cutoff_time = datetime.utcnow() - timedelta(seconds=int(cutoff))
         jobs = trans.sa_session.query(trans.app.model.Job) \
                                .filter(and_(trans.app.model.Job.table.c.update_time < cutoff_time,
@@ -1576,8 +1565,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                 'recent_jobs': prepare_jobs_list(recent_jobs),
                 'cutoff': cutoff,
                 'message': message,
-                'status': status,
-                'job_lock': job_lock}
+                'status': status}
 
     @web.expose
     @web.require_admin

From 0af53803159884aa5287b3221a2e7826c30c7f28 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 18 Dec 2019 17:20:02 -0500
Subject: [PATCH 014/101] Enable manual user activation

Re #3208

Assumptions: confirmation not needed; single user activation only.

Refactoring: move user activation into user manager; update user
controller.

TODO: selenium test
---
 lib/galaxy/managers/users.py                   |  5 +++++
 lib/galaxy/webapps/galaxy/controllers/admin.py | 14 ++++++++++++++
 lib/galaxy/webapps/galaxy/controllers/user.py  |  4 +---
 3 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 5d1b5ae9283..3025834596f 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -522,6 +522,11 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
                 log.exception('Subscribing to the mailing list has failed.')
                 return "Subscribing to the mailing list has failed."
 
+    def activate(self, trans, user):
+        user.active = True
+        trans.sa_session.add(user)
+        trans.sa_session.flush()
+
 
 class UserSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin):
     model_manager_class = UserManager
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 70472e83322..fffb90efb5f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -152,6 +152,10 @@ class UserListGrid(grids.Grid):
                             condition=(lambda item: not item.deleted),
                             allow_multiple=False),
         grids.GridOperation("Generate New API Key",
+                            allow_multiple=False,
+                            async_compatible=True),
+        grids.GridOperation("Activate User",
+                            condition=(lambda item: not item.active),
                             allow_multiple=False,
                             async_compatible=True)
     ]
@@ -614,6 +618,9 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                 message, status = self._recalculate_user(trans, id)
             elif operation == 'generate new api key':
                 message, status = self._new_user_apikey(trans, id)
+            elif operation == 'activate user':
+                message, status = self._activate_user(trans, id)
+
         if trans.app.config.allow_user_deletion:
             if self.delete_operation not in self.user_list_grid.operations:
                 self.user_list_grid.operations.append(self.delete_operation)
@@ -1457,6 +1464,13 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         trans.sa_session.flush()
         return ("New key '%s' generated for requested user '%s'." % (new_key.key, user.email), "done")
 
+    def _activate_user(self, trans, user_id):
+        user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
+        if not user:
+            return ('User not found for id (%s)' % sanitize_text(str(user_id)), 'error')
+        self.user_manager.activate(trans, user)
+        return ('Activated user: %s.' % user.email, 'done')
+
     @web.legacy_expose_api
     @web.require_admin
     def manage_roles_and_groups_for_user(self, trans, payload=None, **kwd):
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 56394bcf968..bc0244265a3 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -273,9 +273,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
                 return trans.show_ok_message("Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>") % web.url_for(controller='root', action='index')
             if user.activation_token == activation_token:
                 user.activation_token = None
-                user.active = True
-                trans.sa_session.add(user)
-                trans.sa_session.flush()
+                self.user_manager.activate(trans, user)
                 return trans.show_ok_message("Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>") % web.url_for(controller='root', action='index')
             else:
                 #  Tokens don't match. Activation is denied.

From 3a914e4ed04b49dc6a20e7e2a8943ec7f4f6f33e Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 19 Dec 2019 13:52:14 +0000
Subject: [PATCH 015/101] Add implementation of `parse_interactivetool` to
 `CwlToolSource` class

In https://github.com/galaxyproject/galaxy/pull/7494 and
https://github.com/galaxyproject/galaxy/pull/8574 , the abstract
`parse_interactivetool()` method was added to the `ToolSource` class
without a corresponding implementation in its `CwlToolSource` subclass,
leading to the following error:

```
In [4]: from galaxy.tool_util.parser.cwl import CwlToolSource
In [5]: cts = CwlToolSource('path')
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-6-2f94370fb293> in <module>()
----> 1 cts = CwlToolSource('path')

TypeError: Can't instantiate abstract class CwlToolSource with abstract methods parse_interactivetool
```
---
 lib/galaxy/tool_util/parser/cwl.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/galaxy/tool_util/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
index f08b48ec0d9..6e729ec9c28 100644
--- a/lib/galaxy/tool_util/parser/cwl.py
+++ b/lib/galaxy/tool_util/parser/cwl.py
@@ -100,6 +100,9 @@ class CwlToolSource(ToolSource):
     def parse_description(self):
         return self.tool_proxy.description()
 
+    def parse_interactivetool(self):
+        return []
+
     def parse_input_pages(self):
         page_source = CwlPageSource(self.tool_proxy)
         return PagesSource([page_source])

From d12f21d62e5e370ad5d8b29cb674e0e26b2e9578 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 19 Dec 2019 17:53:53 +0100
Subject: [PATCH 016/101] Add test for unset optional parameters

---
 test/unit/tools/test_wrappers.py | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/test/unit/tools/test_wrappers.py b/test/unit/tools/test_wrappers.py
index 9bb9bb53a18..b1567be682c 100644
--- a/test/unit/tools/test_wrappers.py
+++ b/test/unit/tools/test_wrappers.py
@@ -108,15 +108,19 @@ def test_raw_object_wrapper():
     assert not false_wrapper
 
 
-def valuewrapper(tool, value, paramtype):
+def valuewrapper(tool, value, paramtype, optional=False):
     if paramtype == "integer":
-        parameter = IntegerToolParameter(tool, XML('<param name="blah" type="integer" value="10" min="0" />'))
+        optional = 'optional="true"' if optional else 'value="10"'
+        parameter = IntegerToolParameter(tool, XML('<param name="blah" type="integer" %s min="0" />' % optional))
     elif paramtype == "text":
-        parameter = TextToolParameter(tool, XML('<param name="blah" type="text" value="foo"/>'))
+        optional = 'optional="true"' if optional else 'value="foo"'
+        parameter = TextToolParameter(tool, XML('<param name="blah" type="text" %s/>' % optional))
     elif paramtype == "float":
-        parameter = FloatToolParameter(tool, XML('<param name="blah" type="float" value="10.0"/>'))
+        optional = 'optional="true"' if optional else 'value="10.0"'
+        parameter = FloatToolParameter(tool, XML('<param name="blah" type="float" %s/>' % optional))
     elif paramtype == "boolean":
-        parameter = BooleanToolParameter(tool, XML('<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue"/>'))
+        optional = 'optional="true"' if optional else 'value=""'
+        parameter = BooleanToolParameter(tool, XML('<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue" %s/>' % optional))
     return InputValueWrapper(parameter, value)
 
 
@@ -143,19 +147,23 @@ def test_input_value_wrapper_comparison(tool):
 
 @with_mock_tool
 def test_input_value_wrapper_comparison_optional(tool):
-    parameter = IntegerToolParameter(tool, XML('<param name="blah" type="integer" min="0" optional="true"/>'))
-    wrapper = InputValueWrapper(parameter, None)
+    wrapper = valuewrapper(tool, None, 'integer', optional=True)
     assert not wrapper
     with pytest.raises(ValueError):
         int(wrapper)
     assert str(wrapper) == ""
     assert wrapper == ""  # for backward-compatibility
-    parameter = IntegerToolParameter(tool, XML('<param name="blah" type="integer" min="0" optional="true"/>'))
-    wrapper = InputValueWrapper(parameter, 0)
+    wrapper = valuewrapper(tool, 0, 'integer', optional=True)
     assert wrapper == 0
     assert int(wrapper) == 0
     assert str(wrapper)
     assert wrapper != ""  # for backward-compatibility, the correct way to check if an optional integer param is not empty is to use str(wrapper)
+    wrapper = valuewrapper(tool, None, 'integer', optional=True)
+    assert wrapper != 1
+    assert str(wrapper) == ""
+    wrapper = valuewrapper(tool, None, "boolean")
+    assert bool(wrapper) is False, wrapper
+    assert str(wrapper) == 'falsevalue'
 
 
 @with_mock_tool

From 18fb12b6f0b85049802f67aa1f2a67206531a796 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 19 Dec 2019 17:52:01 +0100
Subject: [PATCH 017/101] Fix optional integer/float comparisons

Neither of them can be cast to int/float respectively.
Fixes test 3 in bowtie2, which errors with:
```
2019-12-19 17:11:34,022 ERROR [galaxy.jobs.runners] (12) Failure preparing job
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/lib/galaxy/util/__init__.py", line 1039, in unicodify
    value = text_type(value)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.6/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1576771894_0091798_17143.py", line 680, in respond
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/wrappers.py", line 94, in __ne__
    return not self == other
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/wrappers.py", line 91, in __eq__
    return self._get_cast_value(other) == other
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/wrappers.py", line 88, in _get_cast_value
    return cast.get(self.input.type, str)(self)
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/wrappers.py", line 117, in __int__
    return int(float(self))
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/wrappers.py", line 120, in __float__
    return float(str(self))
ValueError: could not convert string to float:
```
---
 lib/galaxy/tools/wrappers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index a7425d50472..89776480080 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -83,7 +83,7 @@ class InputValueWrapper(ToolParameterValueWrapper):
         if self.input.type == 'boolean' and isinstance(other, string_types):
             return str(self)
         # For backward compatibility, allow `$wrapper != ""` for optional non-text param
-        if self.input.optional and self.value is None and isinstance(other, string_types):
+        if self.input.optional and self.value is None and self.input.type != 'boolean':
             return str(self)
         cast = {
             'text': str,

From c5d7dc0765fefbaf794b40f8d5ffb7bd028b1447 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 19 Dec 2019 13:39:05 -0500
Subject: [PATCH 018/101] Fix icons for oidc idps without defined fancy ones.

---
 client/galaxy/scripts/components/login/Login.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/login/Login.vue b/client/galaxy/scripts/components/login/Login.vue
index 396a97de72b..c88e6f34caa 100644
--- a/client/galaxy/scripts/components/login/Login.vue
+++ b/client/galaxy/scripts/components/login/Login.vue
@@ -40,11 +40,11 @@
                 </b-form>
                 <div v-for="idp in oidc_idps" :key="idp" style="margin:0.5em">
                     <span v-if="oidc_idps_icons[idp]">
-                        <img v-bind:src="oidc_idps_icons[idp]" height="45" v-bind:alt="idp" />
+                        <img v-bind:src="oidc_idps[idp]" height="45" v-bind:alt="idp" />
                     </span>
                     <span v-else>
                         <b-button class="d-block mt-3" @click="submitOIDCLogin(idp)">
-                            <i v-bind:class="oidc_idps_icons[idp]" /> Sign in with
+                            <i v-bind:class="oidc_idps[idp]" /> Sign in with
                             {{ idp.charAt(0).toUpperCase() + idp.slice(1) }}
                         </b-button>
                     </span>

From 9091727668d227ec3726b727731d8c391a16b22d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 19 Dec 2019 14:21:03 -0500
Subject: [PATCH 019/101] Simplification of oidc icon presentation.

---
 client/galaxy/scripts/components/login/Login.vue | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/client/galaxy/scripts/components/login/Login.vue b/client/galaxy/scripts/components/login/Login.vue
index c88e6f34caa..7246b45555e 100644
--- a/client/galaxy/scripts/components/login/Login.vue
+++ b/client/galaxy/scripts/components/login/Login.vue
@@ -40,7 +40,9 @@
                 </b-form>
                 <div v-for="idp in oidc_idps" :key="idp" style="margin:0.5em">
                     <span v-if="oidc_idps_icons[idp]">
-                        <img v-bind:src="oidc_idps[idp]" height="45" v-bind:alt="idp" />
+                        <b-button variant="link"  class="d-block mt-3" @click="submitOIDCLogin(idp)">
+                            <img v-bind:src="oidc_idps_icons[idp]" height="45" v-bind:alt="idp" />
+                        </b-button>
                     </span>
                     <span v-else>
                         <b-button class="d-block mt-3" @click="submitOIDCLogin(idp)">
@@ -78,20 +80,11 @@ export default {
     },
     data() {
         const galaxy = getGalaxyInstance();
-        const oidc_idps = galaxy.config.oidc;
         // Icons to use for each IdP
         const oidc_idps_icons = {
             google: "https://developers.google.com/identity/images/btn_google_signin_light_normal_web.png",
             elixir: "https://elixir-europe.org/sites/default/files/images/login-button-orange.png"
         };
-        // Add default icons to IdPs without icons
-        oidc_idps
-            .filter(function(key) {
-                return oidc_idps_icons[key] === undefined;
-            })
-            .forEach(function(idp) {
-                oidc_idps_icons[idp] = "fa fa-id-card";
-            });
         return {
             login: null,
             password: null,
@@ -103,7 +96,7 @@ export default {
             redirect: galaxy.params.redirect,
             session_csrf_token: galaxy.session_csrf_token,
             enable_oidc: galaxy.config.enable_oidc,
-            oidc_idps: oidc_idps,
+            oidc_idps: galaxy.config.oidc,
             oidc_idps_icons: oidc_idps_icons
         };
     },

From 96c33a196dda0cf8afa6dc60fac28c32a7337c59 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 19 Dec 2019 15:06:40 -0500
Subject: [PATCH 020/101] Don't just silently ignore a misconfigured
 oidc_backends_config provider.

---
 lib/galaxy/authnz/managers.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index 1238a4ce203..b2bcbd94953 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -104,6 +104,8 @@ class AuthnzManager(object):
                     self.oidc_backends_config[idp] = self._parse_custos_config(child)
                     self.oidc_backends_implementation[idp] = 'custos'
                     self.app.config.oidc.append(idp)
+                else:
+                    raise ParseError("Unknown provider specified")
             if len(self.oidc_backends_config) == 0:
                 raise ParseError("No valid provider configuration parsed.")
         except ImportError:

From 0bfeda6726a8a1d48512b9779560799e1a9e5953 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 19 Dec 2019 16:05:19 -0500
Subject: [PATCH 021/101] Fix logout/login redirect loop.  We changed logout to
 go home in a workaround for the loop, but this is a more robust solution
 that'll also work with require_login

---
 client/galaxy/scripts/layout/menu.js          | 2 +-
 lib/galaxy/webapps/galaxy/controllers/root.py | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index abca17e0562..2e4e39502f2 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -18,7 +18,7 @@ function logoutClick() {
         if (galaxy.user) {
             galaxy.user.clearSessionStorage();
         }
-        window.top.location.href = galaxy.root;
+        window.top.location.href = `${galaxy.root}login?logout=true`
     });
 }
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py
index 49fa09f4921..6140289596b 100644
--- a/lib/galaxy/webapps/galaxy/controllers/root.py
+++ b/lib/galaxy/webapps/galaxy/controllers/root.py
@@ -87,7 +87,8 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         # there is only one oidc provider, 3) auth_conf.xml has no authenticators
         if (trans.app.config.enable_oidc and
                 len(trans.app.config.oidc) == 1 and
-                len(trans.app.auth_manager.authenticators) == 0):
+                len(trans.app.auth_manager.authenticators) == 0
+                and not kwd.get('logout', False)):
 
             provider = trans.app.config.oidc[0]
             success, message, redirect_uri = trans.app.authnz_manager.authenticate(provider, trans)

From 5b0e30834e2c3fbdf41b04a86be0b893e3e980f0 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 19 Dec 2019 16:09:25 -0500
Subject: [PATCH 022/101] Client formatting.

---
 client/galaxy/scripts/components/login/Login.vue | 2 +-
 client/galaxy/scripts/layout/menu.js             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/components/login/Login.vue b/client/galaxy/scripts/components/login/Login.vue
index 7246b45555e..f2410c9cddf 100644
--- a/client/galaxy/scripts/components/login/Login.vue
+++ b/client/galaxy/scripts/components/login/Login.vue
@@ -40,7 +40,7 @@
                 </b-form>
                 <div v-for="idp in oidc_idps" :key="idp" style="margin:0.5em">
                     <span v-if="oidc_idps_icons[idp]">
-                        <b-button variant="link"  class="d-block mt-3" @click="submitOIDCLogin(idp)">
+                        <b-button variant="link" class="d-block mt-3" @click="submitOIDCLogin(idp)">
                             <img v-bind:src="oidc_idps_icons[idp]" height="45" v-bind:alt="idp" />
                         </b-button>
                     </span>
diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index 2e4e39502f2..b287065292c 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -18,7 +18,7 @@ function logoutClick() {
         if (galaxy.user) {
             galaxy.user.clearSessionStorage();
         }
-        window.top.location.href = `${galaxy.root}login?logout=true`
+        window.top.location.href = `${galaxy.root}login?logout=true`;
     });
 }
 

From 83d1c6e121dbfa8b200ef72e0e8a9a9ecc2143d3 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 15 Nov 2019 12:18:35 -0500
Subject: [PATCH 023/101] New outputs/ directory needs to be mounted rw
 obviously.

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

diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
index 9970334fdea..aaab9a05650 100644
--- a/lib/galaxy/tool_util/deps/container_classes.py
+++ b/lib/galaxy/tool_util/deps/container_classes.py
@@ -179,7 +179,7 @@ class HasDockerLikeVolumes(object):
             if self.job_info.tool_directory:
                 defaults += ",$tool_directory:default_ro"
             if self.job_info.job_directory:
-                defaults += ",$job_directory:default_ro"
+                defaults += ",$job_directory:default_ro,$job_directory/outputs:rw"
             if self.job_info.tmp_directory is not None:
                 defaults += ",$tmp_directory:rw"
             if self.job_info.home_directory is not None:

From 738ea0c50692e04ede8b50dc5fbecaa1f74cb4f7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 15 Nov 2019 12:23:21 -0500
Subject: [PATCH 024/101] Re-locate version path to a writable directory in
 containers.

---
 lib/galaxy/jobs/__init__.py        | 6 +++---
 test/unit/jobs/test_job_wrapper.py | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index ef942469d48..9bb04908efd 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1034,11 +1034,11 @@ class JobWrapper(HasResourceParameters):
         return False
 
     def get_version_string_path(self):
-        return os.path.abspath(os.path.join(self.working_directory, COMMAND_VERSION_FILENAME))
+        return os.path.abspath(os.path.join(self.working_directory, "outputs", COMMAND_VERSION_FILENAME))
 
-    # TODO: Remove in Galaxy 20.XX, for running jobs at GX upgrade
+    # TODO: Remove in Galaxy 21.XX, for running jobs at GX upgrade
     def get_version_string_path_legacy(self):
-        return os.path.abspath(os.path.join(self.app.config.new_file_path, "GALAXY_VERSION_STRING_%s" % self.job_id))
+        return os.path.abspath(os.path.join(self.working_directory, COMMAND_VERSION_FILENAME))
 
     def __prepare_upload_paramfile(self, tool_evaluator):
         """Special case paramfile handling for the upload tool. Moves the paramfile to the working directory
diff --git a/test/unit/jobs/test_job_wrapper.py b/test/unit/jobs/test_job_wrapper.py
index 50389f204ef..30289b74118 100644
--- a/test/unit/jobs/test_job_wrapper.py
+++ b/test/unit/jobs/test_job_wrapper.py
@@ -53,7 +53,7 @@ class BaseWrapperTestCase(UsesApp):
     def test_version_path(self):
         wrapper = self._wrapper()
         version_path = wrapper.get_version_string_path_legacy()
-        expected_path = os.path.join(self.test_directory, "new_files", "GALAXY_VERSION_STRING_345")
+        expected_path = os.path.join(self.test_directory, "working", "COMMAND_VERSION")
         self.assertEqual(version_path, expected_path)
 
     def test_prepare_sets_command_line(self):

From a2d14be11f2304d77158f51b6fb4bfc7d8e1c377 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 15 Nov 2019 12:57:15 -0500
Subject: [PATCH 025/101] Allow testing command versions in tools - tests, XSD.

---
 lib/galaxy/model/__init__.py              |  8 +++++++-
 lib/galaxy/tool_util/parser/xml.py        |  1 +
 lib/galaxy/tool_util/verify/interactor.py |  3 +++
 lib/galaxy/tool_util/xsd/galaxy.xsd       |  9 +++++++++
 lib/galaxy/tools/test.py                  |  1 +
 test/functional/tools/job_properties.xml  |  4 ++++
 test/unit/tool_util/test_parsing.py       | 12 ++++++++++++
 7 files changed, 37 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index e687b521df0..e77c9de7920 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -659,7 +659,7 @@ class TaskMetricNumeric(BaseJobMetric, RepresentById):
 
 class Job(JobLike, UsesCreateAndUpdateTime, Dictifiable, RepresentById):
     dict_collection_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version']
-    dict_element_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version']
+    dict_element_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version', 'command_version']
 
     """
     A job represents a request to run a tool given input datasets, tool
@@ -1132,6 +1132,12 @@ class Job(JobLike, UsesCreateAndUpdateTime, Dictifiable, RepresentById):
             config_value = default
         return config_value
 
+    @property
+    def command_version(self):
+        # TODO: make actual database property and track properly - we should be recording this on the job and not on the datasets
+        for dataset_assoc in self.output_datasets:
+            return dataset_assoc.dataset.tool_version
+
 
 class Task(JobLike, RepresentById):
     """
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 9aaddfa09ee..f38301762e0 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -531,6 +531,7 @@ def _test_elem_to_dict(test_elem, i):
         inputs=__parse_input_elems(test_elem, i),
         expect_num_outputs=test_elem.get("expect_num_outputs"),
         command=__parse_assert_list_from_elem(test_elem.find("assert_command")),
+        command_version=__parse_assert_list_from_elem(test_elem.find("assert_command_version")),
         stdout=__parse_assert_list_from_elem(test_elem.find("assert_stdout")),
         stderr=__parse_assert_list_from_elem(test_elem.find("assert_stderr")),
         expect_exit_code=test_elem.get("expect_exit_code"),
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index fc404959ee0..cac93ddd30d 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -901,6 +901,7 @@ def _verify_outputs(testdef, history, jobs, tool_id, data_list, data_collection_
 
     other_checks = {
         "command_line": "Command produced by the job",
+        "command_version": "Tool version indicated during job execution",
         "stdout": "Standard output of the job",
         "stderr": "Standard error of the job",
     }
@@ -1064,6 +1065,7 @@ class ToolTestDescription(object):
 
         self.output_collections = map(TestCollectionOutputDef.from_dict, processed_test_dict.get("output_collections", []))
         self.command_line = processed_test_dict.get("command_line", None)
+        self.command_version = processed_test_dict.get("command_version", None)
         self.stdout = processed_test_dict.get("stdout", None)
         self.stderr = processed_test_dict.get("stderr", None)
         self.expect_exit_code = processed_test_dict.get("expect_exit_code", None)
@@ -1089,6 +1091,7 @@ class ToolTestDescription(object):
             "output_collections": map(lambda o: o.to_dict(), self.output_collections),
             "num_outputs": self.num_outputs,
             "command_line": self.command_line,
+            "command_version": self.command_version,
             "stdout": self.stdout,
             "stderr": self.stderr,
             "expect_exit_code": self.expect_exit_code,
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 05f7355b97b..57dfedab140 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -851,6 +851,15 @@ $assertions
           <xs:documentation xml:lang="en">Describe assertions about the job's
 standard error.
 
+$assertions
+</xs:documentation>
+        </xs:annotation>
+      </xs:element>
+      <xs:element name="assert_command_version" type="TestAssertions">
+        <xs:annotation>
+          <xs:documentation xml:lang="en">Describe assertions about the job's
+command version.
+
 $assertions
 </xs:documentation>
         </xs:annotation>
diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index 8dc6e5d41fc..8313832d494 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -50,6 +50,7 @@ def description_from_tool_object(tool, test_index, raw_test_dict):
             "output_collections": raw_test_dict["output_collections"],
             "num_outputs": num_outputs,
             "command_line": raw_test_dict.get("command", None),
+            "command_version": raw_test_dict.get("command_version", None),
             "stdout": raw_test_dict.get("stdout", None),
             "stderr": raw_test_dict.get("stderr", None),
             "expect_exit_code": raw_test_dict.get("expect_exit_code", None),
diff --git a/test/functional/tools/job_properties.xml b/test/functional/tools/job_properties.xml
index 1bad9a7f4e2..753aa026a25 100644
--- a/test/functional/tools/job_properties.xml
+++ b/test/functional/tools/job_properties.xml
@@ -2,6 +2,7 @@
     <stdio>
         <exit_code range="127" level="fatal" description="Failing exit code." />
     </stdio>
+    <version_command>echo 'v1.1'</version_command>
     <command><![CDATA[
         #if $thebool
             echo "The bool is true" &&
@@ -44,6 +45,9 @@
             <assert_stderr>
                 <has_line line="The bool is really true" />
             </assert_stderr>
+            <assert_command_version>
+                <has_text text="v1.1" />
+            </assert_command_version>
         </test>
         <test expect_exit_code="2">
             <param name="thebool" value="false" />
diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py
index da646d19894..27047fe46a2 100644
--- a/test/unit/tool_util/test_parsing.py
+++ b/test/unit/tool_util/test_parsing.py
@@ -641,6 +641,18 @@ class ExpectationsTestCase(BaseLoaderTestCase):
         assert len(test_0["stdout"]) == 2
 
 
+class ExpectationsCommandVersionTestCase(BaseLoaderTestCase):
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/job_properties.xml")
+    source_contents = None
+
+    def test_tests(self):
+        tests_dict = self._tool_source.parse_tests_to_dict()
+        tests = tests_dict["tests"]
+        assert len(tests) > 0
+        test_0 = tests[0]
+        assert len(test_0["command_version"]) == 1
+
+
 class QcStdioTestCase(BaseLoaderTestCase):
     source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/qc_stdout.xml")
     source_contents = None

From 4e92e6eb26f72e425e86b269e068bf7032f8df54 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 19 Dec 2019 20:51:49 -0500
Subject: [PATCH 026/101] Undo previous commit; simplify call to activate()

As per code review (more in follow-up)
---
 lib/galaxy/managers/users.py                   | 6 +++---
 lib/galaxy/webapps/galaxy/controllers/admin.py | 2 +-
 lib/galaxy/webapps/galaxy/controllers/user.py  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 3025834596f..70d40fa904f 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -522,10 +522,10 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
                 log.exception('Subscribing to the mailing list has failed.')
                 return "Subscribing to the mailing list has failed."
 
-    def activate(self, trans, user):
+    def activate(self, user):
         user.active = True
-        trans.sa_session.add(user)
-        trans.sa_session.flush()
+        self.session().add(user)
+        self.session().flush()
 
 
 class UserSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin):
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index fffb90efb5f..2f5f66773e7 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -1468,7 +1468,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
         if not user:
             return ('User not found for id (%s)' % sanitize_text(str(user_id)), 'error')
-        self.user_manager.activate(trans, user)
+        self.user_manager.activate(user)
         return ('Activated user: %s.' % user.email, 'done')
 
     @web.legacy_expose_api
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index bc0244265a3..2284daae3d6 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -273,7 +273,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
                 return trans.show_ok_message("Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>") % web.url_for(controller='root', action='index')
             if user.activation_token == activation_token:
                 user.activation_token = None
-                self.user_manager.activate(trans, user)
+                self.user_manager.activate(user)
                 return trans.show_ok_message("Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>") % web.url_for(controller='root', action='index')
             else:
                 #  Tokens don't match. Activation is denied.

From 1d62d73480548cb78b213a4edafb56e66a216f8c Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 19 Dec 2019 21:44:59 -0500
Subject: [PATCH 027/101] Change implementation based on code review

---
 lib/galaxy/webapps/galaxy/controllers/admin.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 2f5f66773e7..6ba07304f0a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -152,10 +152,6 @@ class UserListGrid(grids.Grid):
                             condition=(lambda item: not item.deleted),
                             allow_multiple=False),
         grids.GridOperation("Generate New API Key",
-                            allow_multiple=False,
-                            async_compatible=True),
-        grids.GridOperation("Activate User",
-                            condition=(lambda item: not item.active),
                             allow_multiple=False,
                             async_compatible=True)
     ]
@@ -535,6 +531,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         condition=(lambda item: not item.deleted and not item.purged),
         allow_multiple=False
     )
+    activate_operation = grids.GridOperation("Activate User", condition=(lambda item: not item.active), allow_multiple=False)
 
     @web.expose
     @web.require_admin
@@ -631,6 +628,9 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         if trans.app.config.allow_user_impersonation:
             if self.impersonate_operation not in self.user_list_grid.operations:
                 self.user_list_grid.operations.append(self.impersonate_operation)
+        if trans.app.config.user_activation_on:
+            if self.activate_operation not in self.user_list_grid.operations:
+                self.user_list_grid.operations.append(self.activate_operation)
         if message and status:
             kwd['message'] = util.sanitize_text(message)
             kwd['status'] = status

From e1a1584799bee61726466f5c979a7ce2f07070ce Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Dec 2019 11:56:28 +0100
Subject: [PATCH 028/101] Fix cool & mcool sniffing on python3

h5py returns bytestrings, so this worked on python 2 but not python 3.
Fixes hicexplorer tests on python 3.
---
 lib/galaxy/datatypes/binary.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 5016ee313f0..1ba208f2c6f 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1102,8 +1102,8 @@ class Cool(H5):
         if super(Cool, self).sniff(filename):
             keys = ['chroms', 'bins', 'pixels', 'indexes']
             with h5py.File(filename, 'r') as handle:
-                fmt = handle.attrs.get('format')
-                url = handle.attrs.get('format-url')
+                fmt = util.unicodify(handle.attrs.get('format'))
+                url = util.unicodify(handle.attrs.get('format-url'))
                 if fmt == MAGIC or url == URL:
                     if not all(name in handle.keys() for name in keys):
                         return False
@@ -1162,8 +1162,8 @@ class MCool(H5):
                     return False
                 res0 = list(handle['resolutions'].keys())[0]
                 keys = ['chroms', 'bins', 'pixels', 'indexes']
-                fmt = handle['resolutions'][res0].attrs.get('format')
-                url = handle['resolutions'][res0].attrs.get('format-url')
+                fmt = util.unicodify(handle['resolutions'][res0].attrs.get('format'))
+                url = util.unicodify(handle['resolutions'][res0].attrs.get('format-url'))
                 if fmt == MAGIC or url == URL:
                     if not all(name in handle['resolutions'][res0].keys() for name in keys):
                         return False

From ee9a0e977b7f55264c1de2569275fd01c3e5a93c Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 20 Dec 2019 10:56:35 -0500
Subject: [PATCH 029/101] Enable admin resend activation email

---
 .../webapps/galaxy/controllers/admin.py       | 20 +++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 6ba07304f0a..00243f054bb 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -532,6 +532,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         allow_multiple=False
     )
     activate_operation = grids.GridOperation("Activate User", condition=(lambda item: not item.active), allow_multiple=False)
+    resend_activation_email = grids.GridOperation("Resend Activation Email", condition=(lambda item: not item.active), allow_multiple=False)
 
     @web.expose
     @web.require_admin
@@ -617,7 +618,11 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                 message, status = self._new_user_apikey(trans, id)
             elif operation == 'activate user':
                 message, status = self._activate_user(trans, id)
-
+            elif operation == 'resend activation email':
+                message, status = self._resend_activation_email(trans, id)
+        if message and status:
+            kwd['message'] = util.sanitize_text(message)
+            kwd['status'] = status
         if trans.app.config.allow_user_deletion:
             if self.delete_operation not in self.user_list_grid.operations:
                 self.user_list_grid.operations.append(self.delete_operation)
@@ -631,9 +636,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         if trans.app.config.user_activation_on:
             if self.activate_operation not in self.user_list_grid.operations:
                 self.user_list_grid.operations.append(self.activate_operation)
-        if message and status:
-            kwd['message'] = util.sanitize_text(message)
-            kwd['status'] = status
+                self.user_list_grid.operations.append(self.resend_activation_email)
         return self.user_list_grid(trans, **kwd)
 
     @web.legacy_expose_api
@@ -1471,6 +1474,15 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         self.user_manager.activate(user)
         return ('Activated user: %s.' % user.email, 'done')
 
+    def _resend_activation_email(self, trans, user_id):
+        user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
+        if not user:
+            return ('User not found for id (%s)' % sanitize_text(str(user_id)), 'error')
+        if self.user_manager.send_activation_email(trans, user.email, user.username):
+            return ('Activation email has been sent to user: %s.' % user.email, 'done')
+        else:
+            return ('Unable to send activation email to user: %s.' % user.email, 'error')
+
     @web.legacy_expose_api
     @web.require_admin
     def manage_roles_and_groups_for_user(self, trans, payload=None, **kwd):

From b1561b504dcc8b440ec6db9af36904c0f221a179 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 20 Dec 2019 14:42:23 -0500
Subject: [PATCH 030/101] Add markdown to pinned requirements.

---
 .../dependencies/pipfiles/default/pinned-dev-requirements.txt   | 2 +-
 .../dependencies/pipfiles/default/pinned-requirements.txt       | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 02c01a9bc06..d5784c22828 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -20,7 +20,7 @@ imagesize==1.1.0
 importlib-metadata==1.2.0 ; python_version < '3.8'
 jinja2==2.10.3
 lxml==4.4.2
-markdown==3.0.1
+markdown==3.1.1
 markupsafe==1.1.1
 mirakuru==1.1.0
 mock==3.0.5
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 4214b7cec27..b7ff526367a 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -82,6 +82,7 @@ kombu==4.6.6
 lockfile==0.12.2
 lxml==4.4.2
 mako==1.1.0
+markdown==3.1.1
 markupsafe==1.1.1
 mercurial==5.2
 mistune==0.8.4

From 32df08a48c877ae0bc506f0461c0b2912070be7e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 20 Dec 2019 14:57:03 -0500
Subject: [PATCH 031/101] Rebuild config to include new options related to
 markdown.

---
 doc/source/admin/galaxy_options.rst        | 114 +++++++++++++++++++++
 lib/galaxy/config/sample/galaxy.yml.sample |  43 ++++++++
 2 files changed, 157 insertions(+)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index e244b0a8480..337c64051bc 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -3622,6 +3622,120 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_beta_markdown_export``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Enable export of Galaxy Markdown documents (pages and workflow
+    reports) to PDF. Requires manual installation and setup of
+    weasyprint (latest version available for Python 2.7 is 0.42).
+:Default: ``false``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_css``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    CSS file to apply to all Markdown exports to PDF - currently used
+    by WeasyPrint during rendering an HTML export of the document to
+    PDF.
+:Default: ``markdown_export.css``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_css_pages``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    CSS file to apply to "Galaxy Page" exports to PDF. Generally
+    prefer  markdown_export_css, but this is here for deployments that
+    would like to tailor different kinds of exports.
+:Default: ``markdown_export_pages.css``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_css_invocation_reports``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    CSS file to apply to invocation report exports to PDF. Generally
+    prefer  markdown_export_css, but this is here for deployments that
+    would like to tailor different kinds of exports.
+:Default: ``markdown_export_invocation_reports.css``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_prologue``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Prologue Markdown/HTML to apply to markdown exports to PDF.
+    Allowing branded headers.
+:Default: ````
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_epilogue``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Prologue Markdown/HTML to apply to markdown exports to PDF.
+    Allowing branded footers.
+:Default: ````
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_prologue_pages``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Alternative to markdown_export_prologue that applies just to page
+    exports.
+:Default: ````
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_prologue_invocation_reports``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Alternative to markdown_export_prologue that applies just to
+    invocation report exports.
+:Default: ````
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_epilogue_pages``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Alternative to markdown_export_epilogue that applies just to page
+    exports.
+:Default: ````
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``markdown_export_epilogue_invocation_reports``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Alternative to markdown_export_epilogue that applies just to
+    invocation report exports.
+:Default: ````
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``job_resource_params_file``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 05a7666e407..eccf4c67895 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1785,6 +1785,49 @@ galaxy:
   # environment individually.
   #environment_setup_file: null
 
+  # Enable export of Galaxy Markdown documents (pages and workflow
+  # reports) to PDF. Requires manual installation and setup of
+  # weasyprint (latest version available for Python 2.7 is 0.42).
+  #enable_beta_markdown_export: false
+
+  # CSS file to apply to all Markdown exports to PDF - currently used by
+  # WeasyPrint during rendering an HTML export of the document to PDF.
+  #markdown_export_css: markdown_export.css
+
+  # CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer
+  # markdown_export_css, but this is here for deployments that would
+  # like to tailor different kinds of exports.
+  #markdown_export_css_pages: markdown_export_pages.css
+
+  # CSS file to apply to invocation report exports to PDF. Generally
+  # prefer  markdown_export_css, but this is here for deployments that
+  # would like to tailor different kinds of exports.
+  #markdown_export_css_invocation_reports: markdown_export_invocation_reports.css
+
+  # Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing
+  # branded headers.
+  #markdown_export_prologue: ''
+
+  # Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing
+  # branded footers.
+  #markdown_export_epilogue: ''
+
+  # Alternative to markdown_export_prologue that applies just to page
+  # exports.
+  #markdown_export_prologue_pages: ''
+
+  # Alternative to markdown_export_prologue that applies just to
+  # invocation report exports.
+  #markdown_export_prologue_invocation_reports: ''
+
+  # Alternative to markdown_export_epilogue that applies just to page
+  # exports.
+  #markdown_export_epilogue_pages: ''
+
+  # Alternative to markdown_export_epilogue that applies just to
+  # invocation report exports.
+  #markdown_export_epilogue_invocation_reports: ''
+
   # Optional file containing job resource data entry fields definition.
   # These fields will be presented to users in the tool forms and allow
   # them to overwrite default job resources such as number of

From 79aaff92d0bec1f6be43a1d8e5857a54bf637b62 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 18 Dec 2019 16:11:53 +0100
Subject: [PATCH 032/101] make more tool parsing errors contain id

---
 lib/galaxy/tools/__init__.py | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 726617d8f2e..8a939f850ac 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -922,7 +922,7 @@ class Tool(Dictifiable):
                     self.__tests = parse_tests(self, tests_source)
                 except Exception:
                     self.__tests = None
-                    log.exception("Failed to parse tool tests")
+                    log.exception("Failed to parse tool tests for tool '%s'", self.id)
             else:
                 self.__tests = None
             self.__tests_populated = True
@@ -939,7 +939,7 @@ class Tool(Dictifiable):
                 if repo_dir.stem == self.repository_name:
                     return str(repo_dir)
             else:
-                log.error("Problem finding repository dir for tool [%s]" % self.id)
+                log.error("Problem finding repository dir for tool '%s'" % self.id)
 
         return repository_base_dir
 
@@ -1128,8 +1128,7 @@ class Tool(Dictifiable):
                 group.min = int(input_source.get("min", 0))
                 # Use float instead of int so that 'inf' can be used for no max
                 group.max = float(input_source.get("max", "inf"))
-                assert group.min <= group.max, \
-                    ValueError("Min repeat count must be less-than-or-equal to the max.")
+                assert group.min <= group.max, ValueError("Tool with id '%s': min repeat count must be less-than-or-equal to the max." % self.id)
                 # Force default to be within min-max range
                 group.default = min(max(group.default, group.min), group.max)
                 rval[group.name] = group
@@ -1160,7 +1159,7 @@ class Tool(Dictifiable):
                     test_param_input_source = input_source.parse_test_input_source()
                     group.test_param = self.parse_param_elem(test_param_input_source, enctypes, context)
                     if group.test_param.optional:
-                        log.debug("Tool with id %s declares a conditional test parameter as optional, this is invalid and will be ignored." % self.id)
+                        log.debug("Tool with id '%s': declares a conditional test parameter as optional, this is invalid and will be ignored." % self.id)
                         group.test_param.optional = False
                     possible_cases = list(group.test_param.legal_values)  # store possible cases, undefined whens will have no inputs
                     # Must refresh when test_param changes
@@ -1174,10 +1173,10 @@ class Tool(Dictifiable):
                         try:
                             possible_cases.remove(case.value)
                         except Exception:
-                            log.debug("Tool %s: a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." %
+                            log.debug("Tool with id '%s': a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." %
                                       (self.id, group.name, group.test_param.name, case.value))
                     for unspecified_case in possible_cases:
-                        log.warning("Tool %s: a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." %
+                        log.warning("Tool with id '%s': a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." %
                                     (self.id, group.name, group.test_param.name, unspecified_case))
                         case = ConditionalWhen()
                         case.value = unspecified_case
@@ -1231,7 +1230,7 @@ class Tool(Dictifiable):
         for name in param.get_dependencies():
             # Let it throw exception, but give some hint what the problem might be
             if name not in context:
-                log.error("Could not find dependency '%s' of parameter '%s' in tool %s" % (name, param.name, self.name))
+                log.error("Tool with id '%s': Could not find dependency '%s' of parameter '%s'" % (self.id, name, param.name))
             context[name].refresh_on_change = True
         return param
 
@@ -1294,7 +1293,7 @@ class Tool(Dictifiable):
                         self.app, help_text, encoded_repository_id=self.repository_id, tool_shed_repository=self.tool_shed_repository, tool_id=self.old_id, tool_version=self.version
                     )
             except Exception:
-                log.exception("Exception in parse_help, so images may not be properly displayed")
+                log.exception("Exception in parse_help, so images may not be properly displayed for tool with id '%s'", self.id)
             try:
                 self.__help = Template(rst_to_html(help_text), input_encoding='utf-8',
                                        default_filters=['decode.utf8'],
@@ -1409,7 +1408,7 @@ class Tool(Dictifiable):
                 rerun_remap_job_id = trans.app.security.decode_id(incoming['rerun_remap_job_id'])
             except Exception as exception:
                 log.error(str(exception))
-                raise exceptions.MessageException('Failure executing tool (attempting to rerun invalid job).')
+                raise exceptions.MessageException("Failure executing tool with id '%s' (attempting to rerun invalid job).", self.id)
 
         set_dataset_matcher_factory(request_context, self)
 
@@ -1421,7 +1420,7 @@ class Tool(Dictifiable):
         # remap if multi-runs of tools are being used.
         if rerun_remap_job_id and len(expanded_incomings) > 1:
             raise exceptions.MessageException(
-                'Failure executing tool (cannot create multiple jobs when remapping existing job).')
+                "Failure executing tool with id '%s' (cannot create multiple jobs when remapping existing job).", self.id)
 
         # Process incoming data
         validation_timer = self.app.execution_timer_factory.get_timer(
@@ -1522,8 +1521,8 @@ class Tool(Dictifiable):
         except ToolInputsNotReadyException as e:
             return False, e
         except Exception as e:
-            log.exception('Exception caught while attempting tool execution:')
-            message = 'Error executing tool: %s' % unicodify(e)
+            log.exception("Exception caught while attempting to execute tool with id '%s':", self.id)
+            message = "Error executing tool with id '%s': %s" % (self.id, unicodify(e))
             return False, message
         if isinstance(out_data, OrderedDict):
             return job, list(out_data.items())
@@ -1531,7 +1530,7 @@ class Tool(Dictifiable):
             if isinstance(out_data, string_types):
                 message = out_data
             else:
-                message = 'Failure executing tool (invalid data returned from tool execution)'
+                message = "Failure executing tool with id '%s' (invalid data returned from tool execution)" % self.id
             return False, message
 
     def find_fieldstorage(self, x):

From 9d1cccd14d409f1464abe345ce8601c08c6a092a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 20 Dec 2019 12:17:46 +0100
Subject: [PATCH 033/101] Cast to None for optional params if not comparing
 strings

Proposed by @nsroanzo in https://github.com/galaxyproject/galaxy/pull/9149#discussion_r360225247
---
 lib/galaxy/tools/wrappers.py     | 7 +++++--
 test/unit/tools/test_wrappers.py | 1 +
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index 89776480080..c49702fe307 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -83,8 +83,11 @@ class InputValueWrapper(ToolParameterValueWrapper):
         if self.input.type == 'boolean' and isinstance(other, string_types):
             return str(self)
         # For backward compatibility, allow `$wrapper != ""` for optional non-text param
-        if self.input.optional and self.value is None and self.input.type != 'boolean':
-            return str(self)
+        if self.input.optional and self.value is None:
+            if isinstance(other, string_types):
+                return str(self)
+            else:
+                return None
         cast = {
             'text': str,
             'integer': int,
diff --git a/test/unit/tools/test_wrappers.py b/test/unit/tools/test_wrappers.py
index b1567be682c..5acea546dbd 100644
--- a/test/unit/tools/test_wrappers.py
+++ b/test/unit/tools/test_wrappers.py
@@ -161,6 +161,7 @@ def test_input_value_wrapper_comparison_optional(tool):
     wrapper = valuewrapper(tool, None, 'integer', optional=True)
     assert wrapper != 1
     assert str(wrapper) == ""
+    assert wrapper == None  # noqa: E711
     wrapper = valuewrapper(tool, None, "boolean")
     assert bool(wrapper) is False, wrapper
     assert str(wrapper) == 'falsevalue'

From dfb9e2cd3a3b89347e3fd59b86cb883bf5298aed Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 21 Dec 2019 11:39:52 -0500
Subject: [PATCH 034/101] Remove unused variable passed out of admin job
 controller.

---
 lib/galaxy/webapps/galaxy/controllers/admin.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 840149ece27..192ca3e5d64 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -1549,7 +1549,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                 res.append({
                     'job_info': {
                         'id': job.id,
-                        'info_url': "{}?jobid={}".format(web.url_for(controller="admin", action="job_info"), job.id)
                     },
                     'id': trans.security.encode_id(job.id),
                     'user': job.history.user.email if job.history and job.history.user else 'anonymous',

From 948a3f60e4a0af71c1c7221011273d147a131c4c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 21 Dec 2019 11:50:20 -0500
Subject: [PATCH 035/101] Jobs vue: eliminate show command line button.

No reason to put it in the table - it looks a lot better in expanded view detail.
---
 client/galaxy/scripts/components/admin/Jobs.vue | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/client/galaxy/scripts/components/admin/Jobs.vue b/client/galaxy/scripts/components/admin/Jobs.vue
index 196b6b20937..9fea9b53a7d 100644
--- a/client/galaxy/scripts/components/admin/Jobs.vue
+++ b/client/galaxy/scripts/components/admin/Jobs.vue
@@ -68,9 +68,6 @@
                                 </b-input-group-append>
                             </b-input-group>
                         </b-form-group>
-                        <b-button :pressed.sync="showCommandLine" variant="outline-secondary">
-                            {{ showCommandLine ? "Hide" : "Show" }} Command Line
-                        </b-button>
                     </b-col>
                     <b-col>
                         <b-card v-if="jobsItemsComputed.length" header="Stop Selected Jobs">
@@ -213,7 +210,6 @@ export default {
                 { key: "job_runner_name", label: "Job Runner" },
                 { key: "job_runner_external_id", label: "PID/Cluster ID", sortable: true }
             ],
-            showCommandLine: false,
             cutoff: 180,
             cutoffDisplay: 180,
             jobLock: false,
@@ -327,12 +323,6 @@ export default {
         },
         computeFields(fields) {
             const f = Array.from(fields).slice(0);
-            if (this.showCommandLine) {
-                f.splice(6, 0, {
-                    key: "command_line",
-                    tdClass: ["text-white", "bg-dark", "break-word"]
-                });
-            }
             return f;
         },
         toggleAll(checked) {

From 8318f41ea42bd691ee3335c028294a6fa7ff5221 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 21 Dec 2019 12:06:03 -0500
Subject: [PATCH 036/101] Eliminate custom job inputs handling in job list
 controller.

---
 .../scripts/components/admin/JobDetails.vue   | 39 +++++++++++++++++++
 .../galaxy/scripts/components/admin/Jobs.vue  | 18 ++-------
 .../webapps/galaxy/controllers/admin.py       |  6 ---
 3 files changed, 43 insertions(+), 20 deletions(-)
 create mode 100644 client/galaxy/scripts/components/admin/JobDetails.vue

diff --git a/client/galaxy/scripts/components/admin/JobDetails.vue b/client/galaxy/scripts/components/admin/JobDetails.vue
new file mode 100644
index 00000000000..2c1ebd3c67a
--- /dev/null
+++ b/client/galaxy/scripts/components/admin/JobDetails.vue
@@ -0,0 +1,39 @@
+<template>
+    <b-card>
+        <h5>Command Line</h5>
+        <pre class="text-white bg-dark"><code class="break-word">{{ commandLine }}</code></pre>
+        <h5>Job Parameters</h5>
+        <job-parameters :jobId="jobId" :includeTitle="false" />
+        <h5>Job Metrics</h5>
+        <job-metrics :jobId="jobId" :includeTitle="false" />
+    </b-card>
+</template>
+
+<script>
+import { JobMetrics } from "components/JobMetrics";
+import { JobParameters } from "components/JobParameters";
+
+export default {
+    components: {
+        JobMetrics,
+        JobParameters
+    },
+    props: {
+        commandLine: {
+            type: String,
+            required: true
+        },
+        jobId: {
+            type: String,
+            required: true
+        }
+    }
+};
+</script>
+
+<style scoped>
+.break-word {
+    white-space: pre-wrap;
+    word-break: break-word;
+}
+</style>
diff --git a/client/galaxy/scripts/components/admin/Jobs.vue b/client/galaxy/scripts/components/admin/Jobs.vue
index 9fea9b53a7d..ce60f9909a7 100644
--- a/client/galaxy/scripts/components/admin/Jobs.vue
+++ b/client/galaxy/scripts/components/admin/Jobs.vue
@@ -132,12 +132,7 @@
                     </b-link>
                 </template>
                 <template v-slot:row-details="row">
-                    <b-card>
-                        <h5>Command Line</h5>
-                        <pre
-                            class="text-white bg-dark"
-                        ><code class="break-word">{{ row.item.command_line }}</code></pre>
-                    </b-card>
+                    <job-details :commandLine="row.item.command_line" :jobId="row.item.jobId" />
                 </template>
             </b-table>
             <b-alert v-if="!recentJobsItemsComputed.length" variant="secondary" show>
@@ -167,12 +162,7 @@
                     <utc-date :date="data.value" mode="elapsed" />
                 </template>
                 <template v-slot:row-details="row">
-                    <b-card>
-                        <h5>Command Line</h5>
-                        <pre
-                            class="text-white bg-dark"
-                        ><code class="break-word">{{ row.item.command_line }}</code></pre>
-                    </b-card>
+                    <job-details :commandLine="row.item.command_line" :jobId="row.item.id" />
                 </template>
             </b-table>
             <b-modal ref="job-info-modal" scrollable hide-header ok-only @hidden="resetModalContents">
@@ -188,6 +178,7 @@
 import { getAppRoot } from "onload/loadConfig";
 import UtcDate from "components/UtcDate";
 import axios from "axios";
+import JobDetails from "./JobDetails";
 
 function cancelJob(jobId, message) {
     const url = `${getAppRoot()}api/jobs/${jobId}`;
@@ -195,7 +186,7 @@ function cancelJob(jobId, message) {
 }
 
 export default {
-    components: { UtcDate },
+    components: { UtcDate, JobDetails },
     data() {
         return {
             jobsItems: [],
@@ -206,7 +197,6 @@ export default {
                 { key: "user" },
                 { key: "tool_id", label: "Tool", tdClass: ["break-word"] },
                 { key: "state" },
-                { key: "input_dataset", label: "Inputs" },
                 { key: "job_runner_name", label: "Job Runner" },
                 { key: "job_runner_external_id", label: "PID/Cluster ID", sortable: true }
             ],
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 192ca3e5d64..1fb22973525 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -1541,11 +1541,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         def prepare_jobs_list(jobs):
             res = []
             for job in jobs:
-                inputs = ""
-                try:
-                    inputs = ", ".join(['{} {}'.format(da.dataset.id, da.dataset.state) for da in job.input_datasets])
-                except Exception:
-                    inputs = 'Unable to determine inputs'
                 res.append({
                     'job_info': {
                         'id': job.id,
@@ -1555,7 +1550,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                     'update_time': job.update_time.isoformat(),
                     'tool_id': job.tool_id,
                     'state': job.state,
-                    'input_dataset': inputs,
                     'command_line': job.command_line,
                     'job_runner_name': job.job_runner_name,
                     'job_runner_external_id': job.job_runner_external_id

From c66969a7d867fbe20c630d43ee6d1daa8f201a08 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Sat, 21 Dec 2019 15:59:55 -0500
Subject: [PATCH 037/101] Correct typos, update location of api tests

---
 doc/source/api/guidelines.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/source/api/guidelines.rst b/doc/source/api/guidelines.rst
index c49f94f8ce1..4260144da2f 100644
--- a/doc/source/api/guidelines.rst
+++ b/doc/source/api/guidelines.rst
@@ -14,14 +14,14 @@ these guidelines.
       should properly set the status code according to the result - in particular
       2XX responses should be used for successful requests, 4XX for various
       kinds of client errors, and 5XX for the errors on the server side.
-    - If there is an error processing some part of request (one item in a list
+    - If there is an error processing some part of the request (one item in a list
       for instance), the status code should be set to reflect the error and the
       partial result may or may not be returned depending on the controller -
       this behavior should be documented.
     - API methods should throw a finite number of exceptions 
       (defined in :mod:`galaxy.exceptions`) and these should subclass 
       `MessageException` and not paste/wsgi HTTP exceptions. When possible, 
-      the framework itself should be responsible catching these exceptions, 
+      the framework itself should be responsible for catching these exceptions, 
       setting the status code, and building an error response.
     - Error responses should not consist of plain text strings - they should be
       dictionaries describing the error and containing the following::
@@ -53,7 +53,7 @@ consider them when modifying the API.
       changes and so a second opinion on API changes should be sought.
     - New API functionality should include functional tests. These functional
       tests should be implemented in Python and placed in
-      `test/functional/api`.
+      `lib/galaxy_test/api`.
     - Changes to reflect modifications to the API should be pushed upstream to
       the BioBlend project if possible.
 

From 0419350a1b94b2fda38f660b85e7b8e82e20bea8 Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Sun, 22 Dec 2019 11:56:41 +0530
Subject: [PATCH 038/101] Fix incorrect reference to app

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

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index c9364c43485..a48f0509369 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -137,7 +137,7 @@ class ToolShedRepository(object):
                 self.shed_config_filename = shed_tool_conf_dict['config_filename']
                 return shed_tool_conf_dict
         # Very last resort, get default shed_tool_config file for this instance
-        shed_tool_conf_dict = self.app.toolbox.default_shed_tool_conf_dict()
+        shed_tool_conf_dict = app.toolbox.default_shed_tool_conf_dict()
         self.shed_config_filename = shed_tool_conf_dict['config_filename']
         return shed_tool_conf_dict
 

From 4a89e8220a7bd89ae0c72bc0c66bc515df7f710f Mon Sep 17 00:00:00 2001
From: Marcel Bargull <marcel.bargull@udo.edu>
Date: Mon, 23 Dec 2019 19:27:32 +0100
Subject: [PATCH 039/101] mulled: use threading.Event in PrintProgress to avoid
 unnecessary waiting

---
 lib/galaxy/tool_util/deps/mulled/util.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py
index d005d89ffd6..57e76127180 100644
--- a/lib/galaxy/tool_util/deps/mulled/util.py
+++ b/lib/galaxy/tool_util/deps/mulled/util.py
@@ -8,7 +8,6 @@ import re
 import sys
 import tarfile
 import threading
-import time
 from io import BytesIO
 
 import packaging.version
@@ -293,13 +292,13 @@ def split_container_name(name):
 class PrintProgress(object):
     def __init__(self):
         self.thread = threading.Thread(target=self.progress)
-        self.stop = False
+        self.stop = threading.Event()
 
     def progress(self):
-        while not self.stop:
+        while not self.stop.is_set():
             print(".", end="")
             sys.stdout.flush()
-            time.sleep(60)
+            self.stop.wait(60)
         print("")
 
     def __enter__(self):
@@ -307,7 +306,7 @@ class PrintProgress(object):
         return self
 
     def __exit__(self, exc_type, exc_val, exc_tb):
-        self.stop = True
+        self.stop.set()
         self.thread.join()
 
 

From 6b4f0b4a50472dcf1b7c8aeeac15e9467c32d5e4 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 27 Dec 2019 13:40:34 -0500
Subject: [PATCH 040/101] Ensure that the user has a private role before login

---
 lib/galaxy/web/framework/webapp.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index c8c4811aaaa..e4f35a8cf41 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -712,6 +712,9 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
            - add the disk usage of the current session to the user's total disk usage
         """
         self.user_checks(user)
+        # Make sure that user has a private role
+        if not self.app.security_agent.get_private_user_role(user):
+            self.app.security_agent.create_private_user_role(user)
         # Set the previous session
         prev_galaxy_session = self.galaxy_session
         prev_galaxy_session.is_valid = False

From 10c23226626809576efb9d243f3ccb3900940619 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 27 Dec 2019 14:55:29 -0500
Subject: [PATCH 041/101] Move user creation helper from user manager to
 security model

---
 lib/galaxy/managers/users.py       |  7 +------
 lib/galaxy/model/security.py       | 12 ++++++++++++
 lib/galaxy/web/framework/webapp.py |  4 +---
 3 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 7ca6d1d1aaa..5ef93c7e7d3 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -102,12 +102,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
             # TODO:?? flush needed for permissions below? If not, make optional
         except exc.IntegrityError as db_err:
             raise exceptions.Conflict(str(db_err))
-        # can throw an sqlalx.IntegrityError if username not unique
-        self.app.security_agent.create_private_user_role(user)
-        # We set default user permissions, before we log in and set the default history permissions
-        if hasattr(self.app.config, "new_user_dataset_access_role_default_private"):
-            permissions = self.app.config.new_user_dataset_access_role_default_private
-            self.app.security_agent.user_set_default_permissions(user, default_access_private=permissions)
+        self.app.security_agent.create_user_role(user, self.app)
         return user
 
     def delete(self, user, flush=True):
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 698942a7d00..c364aa063a2 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -656,6 +656,18 @@ class GalaxyRBACAgent(RBACAgent):
         self.sa_session.flush()
         return assoc
 
+    def create_user_role(self, user, app):
+        # Create private user role if necessary
+        if self.app.security_agent.get_private_user_role(user):
+            self.app.security_agent.create_private_user_role(user)
+        # Create default user permissions if necessary
+        if not user.default_permissions:
+            if hasattr(self.app.config, "new_user_dataset_access_role_default_private"):
+                permissions = self.app.config.new_user_dataset_access_role_default_private
+                self.app.security_agent.user_set_default_permissions(user, default_access_private=permissions)
+            else:
+                self.app.security_agent.user_set_default_permissions(user, history=True, dataset=True)
+
     def create_private_user_role(self, user):
         # Create private role
         role = self.model.Role(name=user.email, description='Private Role for ' + user.email, type=self.model.Role.types.PRIVATE)
diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index e4f35a8cf41..34ed238999c 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -712,9 +712,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
            - add the disk usage of the current session to the user's total disk usage
         """
         self.user_checks(user)
-        # Make sure that user has a private role
-        if not self.app.security_agent.get_private_user_role(user):
-            self.app.security_agent.create_private_user_role(user)
+        self.app.security_agent.create_user_role(user, self.app)
         # Set the previous session
         prev_galaxy_session = self.galaxy_session
         prev_galaxy_session.is_valid = False

From fe81adf429a522b6583baa2457ba9946a48e0d75 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 27 Dec 2019 14:58:36 -0500
Subject: [PATCH 042/101] Use parsed local parameter in user role
 initialization helper

---
 lib/galaxy/model/security.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index c364aa063a2..1e28f29082e 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -658,15 +658,15 @@ class GalaxyRBACAgent(RBACAgent):
 
     def create_user_role(self, user, app):
         # Create private user role if necessary
-        if self.app.security_agent.get_private_user_role(user):
-            self.app.security_agent.create_private_user_role(user)
+        if app.security_agent.get_private_user_role(user):
+            app.security_agent.create_private_user_role(user)
         # Create default user permissions if necessary
         if not user.default_permissions:
-            if hasattr(self.app.config, "new_user_dataset_access_role_default_private"):
-                permissions = self.app.config.new_user_dataset_access_role_default_private
-                self.app.security_agent.user_set_default_permissions(user, default_access_private=permissions)
+            if hasattr(app.config, "new_user_dataset_access_role_default_private"):
+                permissions = app.config.new_user_dataset_access_role_default_private
+                app.security_agent.user_set_default_permissions(user, default_access_private=permissions)
             else:
-                self.app.security_agent.user_set_default_permissions(user, history=True, dataset=True)
+                app.security_agent.user_set_default_permissions(user, history=True, dataset=True)
 
     def create_private_user_role(self, user):
         # Create private role

From b318f6ad082bee4b1e67e5fd779ce37064f2ecc8 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 27 Dec 2019 15:01:50 -0500
Subject: [PATCH 043/101] Create private user role only if user role is not
 available

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

diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 1e28f29082e..206a2040c75 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -658,7 +658,7 @@ class GalaxyRBACAgent(RBACAgent):
 
     def create_user_role(self, user, app):
         # Create private user role if necessary
-        if app.security_agent.get_private_user_role(user):
+        if not app.security_agent.get_private_user_role(user):
             app.security_agent.create_private_user_role(user)
         # Create default user permissions if necessary
         if not user.default_permissions:

From 09a23326ef05a479c3bee854300e31dd71ece245 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 27 Dec 2019 15:07:16 -0500
Subject: [PATCH 044/101] Use local security agent instead of app in create
 user roles

---
 lib/galaxy/model/security.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 206a2040c75..6505d60f521 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -658,15 +658,15 @@ class GalaxyRBACAgent(RBACAgent):
 
     def create_user_role(self, user, app):
         # Create private user role if necessary
-        if not app.security_agent.get_private_user_role(user):
-            app.security_agent.create_private_user_role(user)
+        if not self.get_private_user_role(user):
+            self.create_private_user_role(user)
         # Create default user permissions if necessary
         if not user.default_permissions:
             if hasattr(app.config, "new_user_dataset_access_role_default_private"):
                 permissions = app.config.new_user_dataset_access_role_default_private
-                app.security_agent.user_set_default_permissions(user, default_access_private=permissions)
+                self.user_set_default_permissions(user, default_access_private=permissions)
             else:
-                app.security_agent.user_set_default_permissions(user, history=True, dataset=True)
+                self.user_set_default_permissions(user, history=True, dataset=True)
 
     def create_private_user_role(self, user):
         # Create private role

From d6703f54f6a236d4fae25adb2e4c7731d1262de4 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 28 Dec 2019 16:42:25 -0500
Subject: [PATCH 045/101] Version 19.9.1 of tool-util (tag
 galaxy-tool-util-19.9.1).

---
 packages/tool_util/HISTORY.rst                        | 2 +-
 packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
index 52c2df7066e..6612c61b83a 100644
--- a/packages/tool_util/HISTORY.rst
+++ b/packages/tool_util/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.9.1.dev0
+19.9.1 (2019-12-28)
 ---------------------
 
 
diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
index 0ee2dfac196..3a4ac74fc90 100644
--- a/packages/tool_util/galaxy/project_galaxy_tool_util.py
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.1.dev0'
+__version__ = '19.9.1'
 
 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 2e91dd121ffc71e8fe7de132f64f38a2c2c3700d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 28 Dec 2019 16:43:30 -0500
Subject: [PATCH 046/101] Starting work on tool-util 19.9.2

---
 packages/tool_util/HISTORY.rst                        | 6 ++++++
 packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
index 6612c61b83a..cec433c3e50 100644
--- a/packages/tool_util/HISTORY.rst
+++ b/packages/tool_util/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+19.9.2.dev0
+---------------------
+
+
+
 ---------------------
 19.9.1 (2019-12-28)
 ---------------------
diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
index 3a4ac74fc90..c9c01454c57 100644
--- a/packages/tool_util/galaxy/project_galaxy_tool_util.py
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.1'
+__version__ = '19.9.2.dev0'
 
 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 67b7148d09a090f0223f98e1a69693ddc9196353 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Dec 2019 19:15:20 +0100
Subject: [PATCH 047/101] Test return code

---
 lib/galaxy/jobs/runners/util/cli/shell/local.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/jobs/runners/util/cli/shell/local.py b/lib/galaxy/jobs/runners/util/cli/shell/local.py
index 6132655b5ff..2af0e2c509a 100644
--- a/lib/galaxy/jobs/runners/util/cli/shell/local.py
+++ b/lib/galaxy/jobs/runners/util/cli/shell/local.py
@@ -34,6 +34,8 @@ class LocalShell(BaseShellExec):
     True
     >>> exec_result.stdout.strip() == u'Hello World'
     True
+    >>> exec_result.returncode
+    0
     >>> exec_result = exec_python("import time; time.sleep(10)", timeout=1, timeout_check_interval=.1)
     >>> exec_result.stdout == u''
     True

From 3859735c27b894aaa30dec2f62206e7bee001596 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Dec 2019 19:13:17 +0100
Subject: [PATCH 048/101] Fix LocalShell returncode

It appears polling once after completionn is necessary to get the
correct returncode.
---
 lib/galaxy/jobs/runners/util/cli/shell/local.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/jobs/runners/util/cli/shell/local.py b/lib/galaxy/jobs/runners/util/cli/shell/local.py
index 2af0e2c509a..c4deeeb3624 100644
--- a/lib/galaxy/jobs/runners/util/cli/shell/local.py
+++ b/lib/galaxy/jobs/runners/util/cli/shell/local.py
@@ -65,6 +65,8 @@ class LocalShell(BaseShellExec):
             kill_pg(p.pid)
             return Bunch(stdout=u'', stderr=TIMEOUT_ERROR_MESSAGE, returncode=TIMEOUT_RETURN_CODE)
         outf.seek(0)
+        # Need to poll once to establish return code
+        p.poll()
         return Bunch(stdout=_read_str(outf), stderr=_read_str(p.stderr), returncode=p.returncode)
 
 

From 50ab5397b6dfa985b8d98ec772ede52e25cf1419 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 20 Nov 2019 20:57:16 +0100
Subject: [PATCH 049/101] Fix none type exception in provided metadata
 handling.

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

diff --git a/lib/galaxy/tool_util/provided_metadata.py b/lib/galaxy/tool_util/provided_metadata.py
index 6c68d4488b6..b8be575e4c4 100644
--- a/lib/galaxy/tool_util/provided_metadata.py
+++ b/lib/galaxy/tool_util/provided_metadata.py
@@ -110,7 +110,7 @@ class LegacyToolProvidedMetadata(BaseToolProvidedMetadata):
                     line = stringify_dictionary_keys(json.loads(line))
                     assert 'type' in line
                 except Exception:
-                    log.exception('(%s) Got JSON data from tool, but data is improperly formatted or no "type" key in data' % job_wrapper.job_id)
+                    log.exception('(%s) Got JSON data from tool, but data is improperly formatted or no "type" key in data' % getattr(job_wrapper, "job_id", None))
                     log.debug('Offending data was: %s' % line)
                     continue
                 # Set the dataset id if it's a dataset entry and isn't set.

From 3626950f6ed88c2c2e29d5f31c598aaf76e4c4b9 Mon Sep 17 00:00:00 2001
From: xgaia <xgaia@gmx.com>
Date: Mon, 6 Jan 2020 15:13:15 +0100
Subject: [PATCH 050/101] add missing env

---
 tools/interactive/interactivetool_askomics.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/interactive/interactivetool_askomics.xml b/tools/interactive/interactivetool_askomics.xml
index cc18516e770..94cf111a2f3 100644
--- a/tools/interactive/interactivetool_askomics.xml
+++ b/tools/interactive/interactivetool_askomics.xml
@@ -16,6 +16,7 @@
         <environment_variable name="USER_LAST_NAME">Galaxy</environment_variable>
         <environment_variable name="USER_USERNAME">${__user_name__}</environment_variable>
         <environment_variable name="USER_EMAIL">${__user_email__}</environment_variable>
+        <environment_variable name="USER_APIKEY">${__user_name__}</environment_variable>
         <!-- Galaxy info -->
         <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
         <environment_variable name="GALAXY_API_KEY" inject="api_key" />

From 5f15d5caa4402d0a5ac162f663e10c8530a7f564 Mon Sep 17 00:00:00 2001
From: xgaia <xgaia@gmx.com>
Date: Mon, 6 Jan 2020 15:17:06 +0100
Subject: [PATCH 051/101] upgrade tool to 3.2.1

---
 tools/interactive/interactivetool_askomics.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/interactive/interactivetool_askomics.xml b/tools/interactive/interactivetool_askomics.xml
index 94cf111a2f3..e2ec52f1144 100644
--- a/tools/interactive/interactivetool_askomics.xml
+++ b/tools/interactive/interactivetool_askomics.xml
@@ -1,7 +1,7 @@
 <tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="1.0">
     <description>a visual SPARQL query builder</description>
     <requirements>
-        <container type="docker">askomics/flaskomics-with-dependencies:3.2.0</container>
+        <container type="docker">askomics/flaskomics-with-dependencies:3.2.1</container>
     </requirements>
     <entry_points>
         <entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">

From 54e8dc64e3d3ddc2816432c4df9d02f09da9a180 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Jan 2020 12:32:51 -0500
Subject: [PATCH 052/101] Add static-safe mapping to config management; was
 previously only defined in uwsgi default args which not everything uses.

---
 lib/galaxy/config/config_manage.py            | 6 ++++++
 lib/galaxy/config/sample/galaxy.yml.sample    | 5 +++++
 lib/galaxy/config/sample/reports.yml.sample   | 5 +++++
 lib/galaxy/config/sample/tool_shed.yml.sample | 5 +++++
 lib/galaxy/config/script.py                   | 3 +++
 5 files changed, 24 insertions(+)

diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py
index aacfea0c046..f88eff40452 100644
--- a/lib/galaxy/config/config_manage.py
+++ b/lib/galaxy/config/config_manage.py
@@ -101,6 +101,12 @@ UWSGI_OPTIONS = OrderedDict([
         'default': '/favicon.ico=static/favicon.ico',
         'type': 'str',
     }),
+    ('static-safe', {
+        'key': 'static-safe',
+        'desc': """Allow serving images out of `client`.  Most modern Galaxy interfaces bundle all of this, but some older pages still serve these via symlink, requiring this rule.""",
+        'default': 'client/galaxy/images',
+        'type': 'str',
+    }),
     ('master', {
         'desc': """Enable the master process manager. Disabled by default for maximum compatibility with CTRL+C, but should be enabled for use with --daemon and/or production deployments.""",
         'default': False,
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index eccf4c67895..9fa6e76623f 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -50,6 +50,11 @@ uwsgi:
   # Mapping to serve the favicon.
   static-map: /favicon.ico=static/favicon.ico
 
+  # Allow serving images out of `client`.  Most modern Galaxy interfaces
+  # bundle all of this, but some older pages still serve these via
+  # symlink, requiring this rule.
+  static-safe: client/galaxy/images
+
   # Enable the master process manager. Disabled by default for maximum
   # compatibility with CTRL+C, but should be enabled for use with
   # --daemon and/or production deployments.
diff --git a/lib/galaxy/config/sample/reports.yml.sample b/lib/galaxy/config/sample/reports.yml.sample
index a0d21cbc3a0..b207fd53bd7 100644
--- a/lib/galaxy/config/sample/reports.yml.sample
+++ b/lib/galaxy/config/sample/reports.yml.sample
@@ -32,6 +32,11 @@ uwsgi:
   # Mapping to serve the favicon.
   static-map: /favicon.ico=static/favicon.ico
 
+  # Allow serving images out of `client`.  Most modern Galaxy interfaces
+  # bundle all of this, but some older pages still serve these via
+  # symlink, requiring this rule.
+  static-safe: client/galaxy/images
+
   # Enable the master process manager. Disabled by default for maximum
   # compatibility with CTRL+C, but should be enabled for use with
   # --daemon and/or production deployments.
diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample
index b8e5b169221..236e4b7430c 100644
--- a/lib/galaxy/config/sample/tool_shed.yml.sample
+++ b/lib/galaxy/config/sample/tool_shed.yml.sample
@@ -32,6 +32,11 @@ uwsgi:
   # Mapping to serve the favicon.
   static-map: /favicon.ico=static/favicon.ico
 
+  # Allow serving images out of `client`.  Most modern Galaxy interfaces
+  # bundle all of this, but some older pages still serve these via
+  # symlink, requiring this rule.
+  static-safe: client/galaxy/images
+
   # Enable the master process manager. Disabled by default for maximum
   # compatibility with CTRL+C, but should be enabled for use with
   # --daemon and/or production deployments.
diff --git a/lib/galaxy/config/script.py b/lib/galaxy/config/script.py
index f8bcb54cd66..03cfc0cd22f 100644
--- a/lib/galaxy/config/script.py
+++ b/lib/galaxy/config/script.py
@@ -37,6 +37,7 @@ DEFAULT_DB_CONN = 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIAT
 SAMPLES_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sample'))
 GALAXY_CONFIG_TEMPLATE_FILE = os.path.join(SAMPLES_PATH, 'galaxy.yml.sample')
 STATIC_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'web', 'framework', 'static'))
+CLIENT_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'client'))
 
 MSG_CONFIG_SUMMARY = """
 For help on configuring Galaxy, consult the documentation at: \n {}
@@ -55,6 +56,7 @@ GALAXY_CONFIG_SUBSTITUTIONS = {
     '  static-map: /static/style=static/style/blue': '  static-map: /static=${static_path}/style/blue',
     '  static-map: /static=static': '  static-map: /static=${static_path}',
     '  static-map: /favicon.ico=static/favicon.ico': '  static-map: /static=${static_path}/favicon.ico',
+    '  static-safe: client/galaxy/images': '  ${client_path}/galaxy/images',
     '  virtualenv: .venv': '  #venv: .venv   # not used when running installed',
     '  pythonpath: lib': '  #pythonpath: lib  # not used  when running installed',
     '  #config_dir: false': '  config_dir: ${config_dir}',
@@ -147,6 +149,7 @@ def _handle_galaxy_yml(args, config_dir, data_dir):
         uwsgi_transport=uwsgi_transport,
         config_dir=config_dir,
         data_dir=data_dir,
+        client_dir=CLIENT_PATH,
         static_path=STATIC_PATH,
         database_connection=args.db_conn,
     )

From f682307d19374cf6755c73ea9411703b7002fa7c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 7 Jan 2020 09:23:13 -0500
Subject: [PATCH 053/101] Fix tool shed tests for #9168.

---
 lib/galaxy/webapps/tool_shed/security/__init__.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/galaxy/webapps/tool_shed/security/__init__.py b/lib/galaxy/webapps/tool_shed/security/__init__.py
index 17fc5bd5afe..b212e674e6e 100644
--- a/lib/galaxy/webapps/tool_shed/security/__init__.py
+++ b/lib/galaxy/webapps/tool_shed/security/__init__.py
@@ -34,6 +34,9 @@ class RBACAgent(object):
         """
         return [x for x in [self.permitted_actions.get(action_string) for action_string in permitted_action_strings] if x is not None]
 
+    def create_user_role(self, user, app):
+        raise Exception("Unimplemented Method")
+
     def create_private_user_role(self, user):
         raise Exception("Unimplemented Method")
 
@@ -128,6 +131,9 @@ class CommunityRBACAgent(RBACAgent):
         self.associate_components(role=role, user=user)
         return role
 
+    def create_user_role(self, user, app):
+        self.get_private_user_role(user, auto_create=True)
+
     def get_item_actions(self, action, item):
         # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation
         return [permission for permission in item.actions if permission.action == action.action]

From e64bdd20e71cadbd7ff8bd8be09c819458d86497 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 12 Nov 2019 19:43:29 -0500
Subject: [PATCH 054/101] remove unused toolshed_updater mako function

---
 .../admin/tool_shed_repository/common.mako    | 20 -------------------
 .../admin/tool_shed_repository/common.mako    | 20 -------------------
 2 files changed, 40 deletions(-)

diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/common.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/common.mako
index 16f9d793f5b..d2783be488b 100644
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/common.mako
+++ b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/common.mako
@@ -376,26 +376,6 @@
     </script>
 </%def>
 
-<%def name="tool_dependency_installation_updater()">
-    <%
-        can_update = False
-        if query.count():
-            # Get the first tool dependency to get to the tool shed repository.
-            tool_dependency = query[0]
-            tool_shed_repository = tool_dependency.tool_shed_repository
-            can_update = tool_shed_repository.tool_dependencies_being_installed or tool_shed_repository.missing_tool_dependencies
-    %>
-    %if can_update:
-        <script type="text/javascript">
-            config.addInitialization(function() {
-                console.log("common.mako, tool_dependency_installation_updater");
-                // Tool dependency installation status updater
-                tool_dependency_status_updater( [${ ",".join( [ '{"id" : "%s", "status" : "%s"}' % ( trans.security.encode_id( td.id ), td.status ) for td in query ] ) } ] );
-            });
-        </script>
-    %endif
-</%def>
-
 <%def name="repository_installation_updater()">
     <%
         can_update = False
diff --git a/templates/admin/tool_shed_repository/common.mako b/templates/admin/tool_shed_repository/common.mako
index 16f9d793f5b..d2783be488b 100644
--- a/templates/admin/tool_shed_repository/common.mako
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -376,26 +376,6 @@
     </script>
 </%def>
 
-<%def name="tool_dependency_installation_updater()">
-    <%
-        can_update = False
-        if query.count():
-            # Get the first tool dependency to get to the tool shed repository.
-            tool_dependency = query[0]
-            tool_shed_repository = tool_dependency.tool_shed_repository
-            can_update = tool_shed_repository.tool_dependencies_being_installed or tool_shed_repository.missing_tool_dependencies
-    %>
-    %if can_update:
-        <script type="text/javascript">
-            config.addInitialization(function() {
-                console.log("common.mako, tool_dependency_installation_updater");
-                // Tool dependency installation status updater
-                tool_dependency_status_updater( [${ ",".join( [ '{"id" : "%s", "status" : "%s"}' % ( trans.security.encode_id( td.id ), td.status ) for td in query ] ) } ] );
-            });
-        </script>
-    %endif
-</%def>
-
 <%def name="repository_installation_updater()">
     <%
         can_update = False

From 2023eb8c85f23135229f2df166e7ade7d8155ec1 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 12 Nov 2019 19:51:58 -0500
Subject: [PATCH 055/101] Remove unused tool_dependency_status_updates

---
 .../admin/tool_shed_repository/common.mako    | 56 -------------------
 .../admin/tool_shed_repository/common.mako    | 56 -------------------
 2 files changed, 112 deletions(-)

diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/common.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/common.mako
index d2783be488b..fcd2ff6a9a8 100644
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/common.mako
+++ b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/common.mako
@@ -258,62 +258,6 @@
     %endif
 </%def>
 
-<%def name="dependency_status_updater()">
-    <script type="text/javascript">
-        config.addInitialization(function() {
-            console.log("common.mako, dependency_status_updater");
-
-            // Tool dependency status updater - used to update the installation status on the Tool Dependencies Grid.
-            // Looks for changes in tool dependency installation status using an async request. Keeps calling itself
-            // (via setTimeout) until dependency installation status is neither 'Installing' nor 'Building'.
-            window.tool_dependency_status_updater = function( dependency_status_list ) {
-                // See if there are any items left to track
-                var empty = true;
-                for ( var item in dependency_status_list ) {
-                    //alert( "item" + item.toSource() );
-                    //alert( "dependency_status_list[item] " + dependency_status_list[item].toSource() );
-                    //alert( "dependency_status_list[item]['status']" + dependency_status_list[item]['status'] );
-                    if ( dependency_status_list[item]['status'] != 'Installed' ) {
-                        empty = false;
-                        break;
-                    }
-                }
-                if ( ! empty ) {
-                    setTimeout( function() { 
-                        tool_dependency_status_updater_callback( dependency_status_list )
-                    }, 3000 );
-                }
-            };
-
-            var tool_dependency_status_updater_callback = function( dependency_status_list ) {
-                var ids = [];
-                var status_list = [];
-                $.each( dependency_status_list, function( index, dependency_status ) {
-                    ids.push( dependency_status[ 'id' ] );
-                    status_list.push( dependency_status[ 'status' ] );
-                });
-                // Make ajax call
-                $.ajax( {
-                    type: "POST",
-                    url: "${h.url_for( controller='admin_toolshed', action='tool_dependency_status_updates' )}",
-                    dataType: "json",
-                    data: { ids: ids.join( "," ), status_list: status_list.join( "," ) },
-                    success : function( data ) {
-                        $.each( data, function( index, val ) {
-                            // Replace HTML
-                            var cell1 = $( "#ToolDependencyStatus-" + val[ 'id' ] );
-                            cell1.html( val[ 'html_status' ] );
-                            dependency_status_list[ index ] = val;
-                        });
-                        tool_dependency_status_updater( dependency_status_list );
-                    },
-                });
-            };
-
-        });
-    </script>
-</%def>
-
 <%def name="repository_installation_status_updater()">
     <script type="text/javascript">
         config.addInitialization(function() {
diff --git a/templates/admin/tool_shed_repository/common.mako b/templates/admin/tool_shed_repository/common.mako
index d2783be488b..fcd2ff6a9a8 100644
--- a/templates/admin/tool_shed_repository/common.mako
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -258,62 +258,6 @@
     %endif
 </%def>
 
-<%def name="dependency_status_updater()">
-    <script type="text/javascript">
-        config.addInitialization(function() {
-            console.log("common.mako, dependency_status_updater");
-
-            // Tool dependency status updater - used to update the installation status on the Tool Dependencies Grid.
-            // Looks for changes in tool dependency installation status using an async request. Keeps calling itself
-            // (via setTimeout) until dependency installation status is neither 'Installing' nor 'Building'.
-            window.tool_dependency_status_updater = function( dependency_status_list ) {
-                // See if there are any items left to track
-                var empty = true;
-                for ( var item in dependency_status_list ) {
-                    //alert( "item" + item.toSource() );
-                    //alert( "dependency_status_list[item] " + dependency_status_list[item].toSource() );
-                    //alert( "dependency_status_list[item]['status']" + dependency_status_list[item]['status'] );
-                    if ( dependency_status_list[item]['status'] != 'Installed' ) {
-                        empty = false;
-                        break;
-                    }
-                }
-                if ( ! empty ) {
-                    setTimeout( function() { 
-                        tool_dependency_status_updater_callback( dependency_status_list )
-                    }, 3000 );
-                }
-            };
-
-            var tool_dependency_status_updater_callback = function( dependency_status_list ) {
-                var ids = [];
-                var status_list = [];
-                $.each( dependency_status_list, function( index, dependency_status ) {
-                    ids.push( dependency_status[ 'id' ] );
-                    status_list.push( dependency_status[ 'status' ] );
-                });
-                // Make ajax call
-                $.ajax( {
-                    type: "POST",
-                    url: "${h.url_for( controller='admin_toolshed', action='tool_dependency_status_updates' )}",
-                    dataType: "json",
-                    data: { ids: ids.join( "," ), status_list: status_list.join( "," ) },
-                    success : function( data ) {
-                        $.each( data, function( index, val ) {
-                            // Replace HTML
-                            var cell1 = $( "#ToolDependencyStatus-" + val[ 'id' ] );
-                            cell1.html( val[ 'html_status' ] );
-                            dependency_status_list[ index ] = val;
-                        });
-                        tool_dependency_status_updater( dependency_status_list );
-                    },
-                });
-            };
-
-        });
-    </script>
-</%def>
-
 <%def name="repository_installation_status_updater()">
     <script type="text/javascript">
         config.addInitialization(function() {

From 4383237cc580482249e674d7932350393f5794c3 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 12 Nov 2019 19:53:20 -0500
Subject: [PATCH 056/101] Remove tool_dependency_status_updates from
 admin_toolshed controller.

---
 .../galaxy/controllers/admin_toolshed.py      | 21 -------------------
 1 file changed, 21 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 8ceffa4a0f5..618d90fbd68 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1164,27 +1164,6 @@ class AdminToolshed(AdminGalaxy):
                                    message=message,
                                    status=status)
 
-    @web.json
-    def tool_dependency_status_updates(self, trans, ids=None, status_list=None):
-        # Avoid caching
-        trans.response.headers['Pragma'] = 'no-cache'
-        trans.response.headers['Expires'] = '0'
-        # Create new HTML for any ToolDependency records whose status that has changed.
-        rval = []
-        if ids is not None and status_list is not None:
-            ids = util.listify(ids)
-            status_list = util.listify(status_list)
-            for tup in zip(ids, status_list):
-                id, status = tup
-                tool_dependency = trans.install_model.context.query(trans.install_model.ToolDependency).get(trans.security.decode_id(id))
-                if tool_dependency.status != status:
-                    rval.append(dict(id=id,
-                                     status=tool_dependency.status,
-                                     html_status=unicodify(trans.fill_template("admin/tool_shed_repository/tool_dependency_installation_status.mako",
-                                                                               tool_dependency=tool_dependency),
-                                                           'utf-8')))
-        return rval
-
     @web.expose
     @web.require_admin
     def uninstall_tool_dependencies(self, trans, **kwd):

From 03de9f0c517aa1ca96ad5250fa40465b187212ab Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 12 Nov 2019 19:56:27 -0500
Subject: [PATCH 057/101] Remove tool dependency manage makos from tool shed.

---
 .../manage_repository_tool_dependencies.mako  | 107 ------------------
 .../uninstall_tool_dependencies.mako          |  63 -----------
 2 files changed, 170 deletions(-)
 delete mode 100644 lib/tool_shed/webapp/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
 delete mode 100644 lib/tool_shed/webapp/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako

diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
deleted file mode 100644
index a1a84517339..00000000000
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
+++ /dev/null
@@ -1,107 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
-<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "library" )}
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ${common_misc_javascripts()}
-</%def>
-
-${render_galaxy_repository_actions( repository )}
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="card">
-    <div class="card-header">Tool shed repository '${repository.name|h}' tool dependencies</div>
-        <%
-            can_install = False
-            can_uninstall = False
-        %>
-        <br/><br/>
-        <table class="grid">
-            <tr><th>Name</th><th>Version</th><th>Type</th><th>Status</th><th>Error</th></tr>
-            %for tool_dependency in repository.tool_dependencies:
-                <%
-                    if tool_dependency.error_message:
-                        from tool_shed.util.basic_util import to_html_string
-                        error_message = to_html_string( tool_dependency.error_message )
-                    else:
-                        error_message = ''
-                    if not can_install:
-                        if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                                       trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
-                            can_install = True
-                    if not can_uninstall:
-                        if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                                           trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
-                            can_uninstall = True
-                %>
-                <tr>
-                    <td>
-                        %if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
-                            <a target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='browse', tool_dependency_ids=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">
-                                ${tool_dependency.name|h}
-                            </a>
-                        %else:
-                            ${tool_dependency.name|h}
-                        %endif
-                    </td>
-                    <td>${tool_dependency.version|h}</td>
-                    <td>${tool_dependency.type|h}</td>
-                    <td>${tool_dependency.status|h}</td>
-                    <td>${error_message}</td>
-                </tr>
-            %endfor
-        </table>
-        %if can_install:
-            <br/>
-            <form name="install_tool_dependencies" id="install_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='install', repository_id=trans.security.encode_id( repository.id ) )}" method="post" >
-                <div class="form-row">
-                    Check each tool dependency that you want to install and click <b>Install</b>.
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <input type="checkbox" id="checkAllUninstalled" name="select_all_uninstalled_tool_dependencies_checkbox" value="true" onclick="checkAllUninstalledToolDependencyIdFields(1);"/><b>Select/unselect all tool dependencies</b>
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    ${render_select(uninstalled_tool_dependencies_select_field)}
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <input type="submit" name="install_button" value="Install"/></td>
-                </div>
-            </form>
-            <br/>
-        %endif
-        %if can_uninstall:
-            <br/>
-            <form name="uninstall_tool_dependencies" id="uninstall_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='uninstall', repository_id=trans.security.encode_id( repository.id ) )}" method="post" >
-                <div class="form-row">
-                    Check each tool dependency that you want to uninstall and click <b>Uninstall</b>.
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <input type="checkbox" id="checkAllInstalled" name="select_all_installed_tool_dependencies_checkbox" value="true" onclick="checkAllInstalledToolDependencyIdFields(1);"/><b>Select/unselect all tool dependencies</b>
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    ${render_select(installed_tool_dependencies_select_field)}
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <input type="submit" name="uninstall_button" value="Uninstall"/></td>
-                </div>
-            </form>
-            <br/>
-        %endif
-    </div>
-</div>
diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
deleted file mode 100644
index 321d5f708d2..00000000000
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
+++ /dev/null
@@ -1,63 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
-
-<% import os %>
-
-${render_galaxy_repository_actions( repository )}
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="card">
-    <div class="card-header">Uninstall tool dependencies</div>
-    <div class="card-body">
-        <form name="uninstall_tool_dependenceies" id="uninstall_tool_dependenceies" action="${h.url_for( controller='admin_toolshed', action='uninstall_tool_dependencies' )}" method="post" >       
-            <div class="form-row">
-                <table class="grid">
-                    <tr>
-                        <th>Name</th>
-                        <th>Version</th>
-                        <th>Type</th>
-                        <th>Install directory</th>
-                    </tr>
-                    %for tool_dependency in tool_dependencies:
-                        <input type="hidden" name="tool_dependency_ids" value="${trans.security.encode_id( tool_dependency.id )}"/>
-                        <%
-                            if tool_dependency.type == 'package':
-                                install_dir = os.path.join( trans.app.tool_dependency_dir,
-                                                            tool_dependency.name,
-                                                            tool_dependency.version,
-                                                            tool_dependency.tool_shed_repository.owner,
-                                                            tool_dependency.tool_shed_repository.name,
-                                                            tool_dependency.tool_shed_repository.installed_changeset_revision )
-                            elif tool_dependency.type == 'set_environment':
-                                install_dir = os.path.join( trans.app.tool_dependency_dir,
-                                                            'environment_settings',
-                                                            tool_dependency.name,
-                                                            tool_dependency.tool_shed_repository.owner,
-                                                            tool_dependency.tool_shed_repository.name,
-                                                            tool_dependency.tool_shed_repository.installed_changeset_revision )
-                            if not os.path.exists( install_dir ):
-                                install_dir = "This dependency's installation directory does not exist, click <b>Uninstall</b> to reset for installation."
-                        %>
-                        <tr>
-                            <td>${tool_dependency.name|h}</td>
-                            <td>${tool_dependency.version|h}</td>
-                            <td>${tool_dependency.type|h}</td>
-                            <td>${install_dir|h}</td>
-                        </tr>
-                    %endfor
-                </table>
-                <div style="clear: both"></div>
-            </div>
-            <div class="form-row">
-                <input type="submit" name="uninstall_tool_dependencies_button" value="Uninstall"/>
-                <div class="toolParamHelp" style="clear: both;">
-                    Click to uninstall the tool dependencies listed above.
-                </div>
-            </div>
-        </form>
-    </div>
-</div>

From 0a00428d8af1dbbd23940c4dd8fb3db0e2a1fa0d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 12 Nov 2019 20:10:04 -0500
Subject: [PATCH 058/101] Remove more unused makos from tool shed.

---
 ...install_tool_dependencies_with_update.mako |  94 ----------------
 .../monitor_repository_installation.mako      |  70 ------------
 .../purge_repository_confirmation.mako        |  74 -------------
 .../reselect_tool_panel_section.mako          | 101 ------------------
 4 files changed, 339 deletions(-)
 delete mode 100644 lib/tool_shed/webapp/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
 delete mode 100644 lib/tool_shed/webapp/templates/admin/tool_shed_repository/monitor_repository_installation.mako
 delete mode 100644 lib/tool_shed/webapp/templates/admin/tool_shed_repository/purge_repository_confirmation.mako
 delete mode 100644 lib/tool_shed/webapp/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako

diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
deleted file mode 100644
index 366eeb3bd3c..00000000000
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
+++ /dev/null
@@ -1,94 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
-
-<% import os %>
-
-${render_galaxy_repository_actions( repository )}
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="warningmessage">
-    <p>
-        The updates to the <b>${repository.name}</b> repository require the following packages.  Click the <b>Install</b> button to install them.
-        Installing some packages may take a while, but you can continue to use Galaxy during installation.
-    </p> 
-</div>
-  
-<div class="card">
-    <div class="card-body">
-        <form name="install_tool_dependencies_with_update" id="install_tool_dependencies_with_update" action="${h.url_for( controller='admin_toolshed', action='install_tool_dependencies_with_update' )}" method="post" >
-            <input type="hidden" name="updating_repository_id" value="${updating_repository_id|h}"/>
-            <input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev|h}"/>
-            <input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision|h}"/>
-            <input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata|h}"/>
-            <input type="hidden" name="encoded_relative_install_dir" value="${encoded_relative_install_dir|h}"/>
-            <input type="hidden" name="encoded_tool_dependencies_dict" value="${encoded_tool_dependencies_dict|h}"/>
-            %if tool_dependencies_dict:
-                %if install_tool_dependencies_check_box is not None:
-                    <div class="form-row">
-                        <label>Handle tool dependencies?</label>
-                        <% disabled = trans.app.tool_dependency_dir is None %>
-                        ${render_checkbox(install_tool_dependencies_check_box, disabled=disabled)}
-                        <div class="toolParamHelp" style="clear: both;">
-                            %if disabled:
-                                Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
-                            %else:
-                                Un-check to skip automatic handling of these tool dependencies.
-                            %endif
-                        </div>
-                    </div>
-                    <div style="clear: both"></div>
-                %endif
-                <div class="form-row">
-                    <table class="grid">
-                        <tr><td colspan="4" bgcolor="#D8D8D8"><b>New tool dependencies included in update</b></td></tr>
-                        <tr>
-                            <th>Name</th>
-                            <th>Version</th>
-                            <th>Install directory</th>
-                        </tr>
-                        %for key, requirements_dict in tool_dependencies_dict.items():
-                            <%
-                                readme_text = None
-                                if key == 'set_environment':
-                                    key_name = ', '.join( [ environment_variable[ 'name' ] for environment_variable in requirements_dict ] )
-                                    key_version = ''
-                                    install_dir = ''
-                                else:
-                                    key_items = key.split( '/' )
-                                    key_name = key_items[ 0 ]
-                                    key_version = key_items[ 1 ]
-                                    readme_text = requirements_dict.get( 'readme', None )
-                                    install_dir = os.path.join( trans.app.tool_dependency_dir,
-                                                                key_name,
-                                                                key_version,
-                                                                repository.owner,
-                                                                repository.name,
-                                                                repository.installed_changeset_revision )
-                            %>
-                            %if not os.path.exists( install_dir ):
-                                <tr>
-                                    <td>${key_name|h}</td>
-                                    <td>${key_version|h}</td>
-                                    <td>${install_dir|h}</td>
-                                </tr>
-                                %if readme_text:
-                                    <tr><td colspan="4" bgcolor="#FFFFCC">${key_name|h} ${key_version|h} requirements and installation information</td></tr>
-                                    <tr><td colspan="4"><pre>${readme_text}</pre></td></tr>
-                                %endif
-                            %endif
-                        %endfor
-                    </table>
-                    <div style="clear: both"></div>
-                </div>
-            %endif
-            <div class="form-row">
-                <input type="submit" name="install_tool_dependencies_with_update_button" value="Install"/>
-            </div>
-        </form>
-    </div>
-</div>
diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/monitor_repository_installation.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/monitor_repository_installation.mako
deleted file mode 100644
index e42c3f034c7..00000000000
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/monitor_repository_installation.mako
+++ /dev/null
@@ -1,70 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
-
-<%def name="javascripts()">
-   ${parent.javascripts()}
-   ${repository_installation_status_updater()}
-   ${repository_installation_updater()}
-   ${self.repository_installation_javascripts()}
-</%def>
-
-<%def name="repository_installation_javascripts()">
-    <script type="text/javascript">
-        %if context.get("initiate_repository_installation_ids"):
-            $(document).ready(function( ){
-                initiate_repository_installation( "${initiate_repository_installation_ids}", "${encoded_kwd}", "${reinstalling}" );
-            });
-        %endif
-        var initiate_repository_installation = function ( iri_ids, encoded_kwd, reinstalling ) {
-            // Make ajax call
-            $.ajax( {
-                type: "POST",
-                url: "${h.url_for( controller='admin_toolshed', action='install_repositories' )}",
-                dataType: "html",
-                data: { tool_shed_repository_ids: iri_ids, encoded_kwd: encoded_kwd, reinstalling: reinstalling },
-                success : function ( data ) {
-                    console.log( "Initializing repository installation succeeded" );
-                }
-            });
-        };
-    </script>
-</%def>
-
-%if context.get("message"):
-    ${render_msg( message, status )}
-%endif
-
-%if tool_shed_repositories:
-    <div class="card">
-        <div class="card-header">Monitor installing tool shed repositories</div>
-        <div class="card-body overflow-auto">
-            <table class="grid">
-                <tr>
-                    <td>Name</td>
-                    <td>Description</td>
-                    <td>Owner</td>
-                    <td>Revision</td>
-                    <td>Status</td>
-                </tr>
-                %for tool_shed_repository in tool_shed_repositories:
-                    <%
-                        encoded_repository_id = trans.security.encode_id( tool_shed_repository.id )
-                        ids_of_tool_dependencies_missing_or_being_installed = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies_missing_or_being_installed ]
-                        link_to_manage_tool_dependencies = tool_shed_repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ]
-                    %>
-                    <tr>
-                        <td>${tool_shed_repository.name|h}</td>
-                        <td>${tool_shed_repository.description}</td>
-                        <td>${tool_shed_repository.owner}</td>
-                        <td>${tool_shed_repository.changeset_revision}</td>
-                        <td><div id="RepositoryStatus-${encoded_repository_id}">${tool_shed_repository.status|h}</div></td>
-                    </tr>
-                %endfor
-            </table>
-            <br clear="left"/>
-        </div>
-    </div>
-%else:
-    ${render_msg("There is no repository being installed.", "info")}
-%endif
diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/purge_repository_confirmation.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/purge_repository_confirmation.mako
deleted file mode 100644
index 36a7f562b66..00000000000
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/purge_repository_confirmation.mako
+++ /dev/null
@@ -1,74 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "library" )}
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-</%def>
-
-${render_galaxy_repository_actions( repository )}
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="warningmessage">
-    <p>
-        Purging the repository named <b>${repository.name|h}</b> will result in deletion of all records for the
-        following associated items from the database.  Click the <b>Purge</b> button to purge this repository
-        and its associated items.
-    </p>
-</div>
-
-<div class="card">
-    <div class="card-header">Purge tool shed repository <b>${repository.name|h}</b></div>
-        <form name="purge_repository" id="purge_repository" action="${h.url_for( controller='admin_toolshed', action='purge_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
-            <%
-                tool_versions = 0
-                tool_dependencies = 0
-                required_repositories = 0
-                orphan_repository_repository_dependency_association_records = 0
-                orphan_repository_dependency_records = 0
-                # Count this repository's tool version lineage chain links that will be purged.
-                for tool_version in repository.tool_versions:
-                    for tool_version_association in tool_version.parent_tool_association:
-                        tool_versions += 1
-                    for tool_version_association in tool_version.child_tool_association:
-                        tool_versions += 1
-                    tool_versions += 1
-                # Count this repository's associated tool dependencies that will be purged.
-                for tool_dependency in repository.tool_dependencies:
-                    tool_dependencies += 1
-                # Count this repository's associated required repositories that will be purged.
-                for rrda in repository.required_repositories:
-                    required_repositories += 1
-                # Count any "orphan" repository_dependency records associated with the repository but not with any
-                # repository_repository_dependency_association records that will be purged.
-                for orphan_repository_dependency in \
-                    trans.sa_session.query( trans.app.install_model.RepositoryDependency ) \
-                                    .filter( trans.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id ):
-                    for orphan_rrda in \
-                        trans.sa_session.query( trans.app.install_model.RepositoryRepositoryDependencyAssociation ) \
-                                        .filter( trans.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == orphan_repository_dependency.id ):
-                        orphan_repository_repository_dependency_association_records += 1
-                    orphan_repository_dependency_records += 1
-            %>
-            <table class="grid">
-                <tr><td>Tool version records</td><td>${tool_versions|h}</td><tr>
-                <tr><td>Tool dependency records</td><td>${tool_dependencies|h}</td><tr>
-                <tr><td>Repository dependency records</td><td>${required_repositories|h}</td><tr>
-                <tr><td>Orphan repository_repository_dependency_association records</td><td>${orphan_repository_repository_dependency_association_records|h}</td><tr>
-                <tr><td>Orphan repository_dependency records</td><td>${orphan_repository_dependency_records|h}</td><tr>
-            </table>
-            <div style="clear: both"></div>
-            <div class="form-row">
-                <input type="submit" name="purge_repository_button" value="Purge"/>
-            </div>
-        </form>
-    </div>
-</div>
diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
deleted file mode 100644
index d901b6d08e8..00000000000
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
+++ /dev/null
@@ -1,101 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
-<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
-<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "library" )}
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ${container_javascripts()}
-</%def>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="card">
-    <div class="card-body">
-        <form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='reinstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
-            <div class="form-row">
-                <input type="hidden" name="repo_info_dict" value="${encoded_repo_info_dict}" />
-            </div>
-            <div style="clear: both"></div>
-            <% readme_files_dict = containers_dict.get( 'readme_files', None ) %>
-            %if readme_files_dict:
-                <div class="form-row">
-                    <table class="colored" width="100%">
-                        <th bgcolor="#EBD9B2">Repository README files - may contain important installation or license information</th>
-                    </table>
-                </div>
-                ${render_readme_section( containers_dict )}
-                <div style="clear: both"></div>
-            %endif
-            %if has_repository_dependencies or includes_tool_dependencies:
-                <div class="form-row">
-                    <table class="colored" width="100%">
-                        <th bgcolor="#EBD9B2">Confirm dependency installation</th>
-                    </table>
-                </div>
-                ${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
-            %endif
-            %if shed_tool_conf_select_field:
-                <div class="form-row">
-                    <table class="colored" width="100%">
-                        <th bgcolor="#EBD9B2">Choose the configuration file whose tool_path setting will be used for installing repositories</th>
-                    </table>
-                </div>
-                <%
-                    if len( shed_tool_conf_select_field.options ) == 1:
-                        select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be "
-                        select_help += "installed using its <b>tool_path</b> setting."
-                    else:
-                        select_help = "Your Galaxy instance is configured with %d shed-related tool configuration files, " % len( shed_tool_conf_select_field.options )
-                        select_help += "so select the file whose <b>tool_path</b> setting you want used for installing repositories."
-                %>
-                <div class="form-row">
-                    <label>Shed tool configuration file:</label>
-                    ${render_select(shed_tool_conf_select_field)}
-                    <div class="toolParamHelp" style="clear: both;">
-                        ${select_help|h}
-                    </div>
-                </div>
-                <div style="clear: both"></div>
-            %else:
-                <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf|h}"/>
-            %endif
-            %if includes_tools_for_display_in_tool_panel:
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    ${render_checkbox(no_changes_check_box)}
-                    <label style="display: inline;">No changes</label>
-                    <div class="toolParamHelp" style="clear: both;">
-                        Uncheck and select a different tool panel section to load the tools into a different section in the tool panel.
-                    </div>
-                </div>
-                <div class="form-row">
-                    <label>Add new tool panel section:</label>
-                    <input name="new_tool_panel_section_label" type="textfield" value="" size="40"/>
-                    <div class="toolParamHelp" style="clear: both;">
-                        Add a new tool panel section to contain the installed tools (optional).
-                    </div>
-                </div>
-                <div class="form-row">
-                    <label>Select existing tool panel section:</label>
-                    ${render_select(tool_panel_section_select_field)}
-                    <div class="toolParamHelp" style="clear: both;">
-                        Choose an existing section in your tool panel to contain the installed tools (optional).  
-                    </div>
-                </div>
-            %endif
-            <div class="form-row">
-                <input type="submit" name="select_tool_panel_section_button" value="Install"/>
-            </div>
-        </form>
-    </div>
-</div>

From 6b10f5c114e79e9e5a67cd8c1993bdedbe5fa209 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 12 Nov 2019 20:14:35 -0500
Subject: [PATCH 059/101] Remove unused tool shed mako.

---
 .../deactivate_or_uninstall_repository.mako   | 208 ------------------
 1 file changed, 208 deletions(-)
 delete mode 100644 lib/tool_shed/webapp/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako

diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
deleted file mode 100644
index 111832fea44..00000000000
--- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
+++ /dev/null
@@ -1,208 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
-<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
-<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
-
-<%
-repository = context.get( 'repository', None )
-if isinstance( repository, list ):
-    repositories = repository
-else:
-    repositories = [ repository ]
-%>
-
-%if len( repositories ) == 1:
-    ${render_galaxy_repository_actions( repositories[0] )}
-%endif
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="card">
-<form name="deactivate_or_uninstall_repository" id="deactivate_or_uninstall_repository" action="${ h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository' ) }" method="post" >
-%for repository in repositories:
-    <input type="hidden" name="id" value="${ trans.security.encode_id( repository.id ) | h }" />
-    <div class="card-header">${repository.name|h}</div>
-    <div class="card-body">
-            <div class="form-row">
-                <label>Description:</label>
-                ${repository.description|h}
-                <div style="clear: both"></div>
-            </div>
-            <div class="form-row">
-                <label>Revision:</label>
-                ${repository.changeset_revision|h}</a>
-            </div>
-            <div class="form-row">
-                <label>Tool shed:</label>
-                ${repository.tool_shed|h}
-                <div style="clear: both"></div>
-            </div>
-            <div class="form-row">
-                <label>Owner:</label>
-                ${repository.owner|h}
-            </div>
-            <div class="form-row">
-                <label>Deleted:</label>
-                ${repository.deleted|h}
-            </div>
-            <div class="form-row">
-                <%
-                    can_deactivate_repository = repository.can_deactivate
-                    can_uninstall_repository = repository.can_uninstall
-                %>
-                %if can_deactivate_repository:
-                    <table width="100%" border="0" cellpadding="0" cellspacing="0">
-                        <tr>
-                            <td bgcolor="#D8D8D8">
-                                <label>Deactivating this repository will result in the following:</label>
-                            </td>
-                        </tr>
-                    </table>
-                    <div class="toolParamHelp" style="clear: both;">
-                            * The repository and all of its contents will remain on disk and can still be used by dependent items.
-                    </div>
-                    %if repository.includes_tools_for_display_in_tool_panel:
-                        <div class="toolParamHelp" style="clear: both;">
-                            * The repository's tools will not be loaded into the tool panel.
-                        </div>
-                    %endif
-                    %if repository.includes_tool_dependencies:
-                        <div class="toolParamHelp" style="clear: both;">
-                            * The repository's installed tool dependencies will remain on disk.
-                        </div>
-                    %endif
-                    %if repository.includes_datatypes:
-                        <div class="toolParamHelp" style="clear: both;">
-                            * The repository's datatypes, datatype converters and display applications will be eliminated from the datatypes registry.
-                        </div>
-                    %endif
-                    <div class="toolParamHelp" style="clear: both;">
-                        * The repository record's deleted column in the tool_shed_repository database table will be set to True.
-                    </div>
-                    <br/>
-                %endif
-                %if can_uninstall_repository:
-                    <table width="100%" border="0" cellpadding="0" cellspacing="0">
-                        <tr>
-                            <td bgcolor="#D8D8D8">
-                                <label>Uninstalling this repository will result in the following:</label>
-                            </td>
-                        </tr>
-                    </table>
-                    <div class="toolParamHelp" style="clear: both;">
-                        * The repository and all of its contents will be removed from disk and can no longer be used by dependent items.
-                    </div>
-                    %if repository.includes_tools_for_display_in_tool_panel:
-                        <div class="toolParamHelp" style="clear: both;">
-                            * The repository's tool tag sets will be removed from the tool config file in which they are defined.
-                        </div>
-                    %endif
-                    %if repository.includes_tool_dependencies:
-                        <div class="toolParamHelp" style="clear: both;">
-                            * The repository's installed tool dependencies will be removed from disk and can no longer be used by dependent items.
-                        </div>
-                        <div class="toolParamHelp" style="clear: both;">
-                            * Each associated tool dependency record's status column in the tool_dependency database table will be set to 'Uninstalled'.
-                        </div>
-                    %endif
-                    %if repository.includes_datatypes:
-                        <div class="toolParamHelp" style="clear: both;">
-                            * The repository's datatypes, datatype converters and display applications will be eliminated from the datatypes registry.
-                        </div>
-                    %endif
-                    <div class="toolParamHelp" style="clear: both;">
-                        * The repository record's deleted column in the tool_shed_repository database table will be set to True.
-                    </div>
-                    <div class="toolParamHelp" style="clear: both;">
-                        * The repository record's uninstalled column in the tool_shed_repository database table will be set to True.
-                    </div>
-                    <div style="clear: both"></div>
-                    <br/>
-                    <%
-                        irm = trans.app.installed_repository_manager
-                        repository_tup = irm.get_repository_tuple_for_installed_repository_manager( repository )
-
-                        # Get installed repositories that this repository requires.
-                        installed_dependent_repositories = []
-                        installed_runtime_dependent_tool_dependencies = []
-                        installed_dependent_repositories = irm.installed_dependent_repositories_of_installed_repositories.get( repository_tup, [] )
-
-                        # Get this repository's installed tool dependencies.
-                        installed_tool_dependencies = irm.installed_tool_dependencies_of_installed_repositories.get( repository_tup, [] )
-
-                        # Get installed runtime dependent tool dependencies of this repository's installed tool dependencies.
-                        installed_runtime_dependent_tool_dependencies = []
-                        for itd_tup in installed_tool_dependencies:
-                            installed_dependent_td_tups = \
-                                irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.get( itd_tup, [] )
-                            if installed_dependent_td_tups:
-                                installed_runtime_dependent_tool_dependencies.extend( installed_dependent_td_tups )
-                    %>
-                    %if installed_dependent_repositories or installed_runtime_dependent_tool_dependencies:
-                        <table width="100%" border="0" cellpadding="0" cellspacing="0">
-                            <tr>
-                                <td bgcolor="#D8D8D8">
-                                    <label>Uninstalling this repository will affect the following dependent items:</label>
-                                </td>
-                            </tr>
-                        </table>
-                        %if installed_dependent_repositories:
-                            <label>Dependent repositories:</label>
-                            <ul>
-                            %for installed_dependent_repository_tup in installed_dependent_repositories:
-                                <%
-                                    tool_shed, name, owner, installed_changeset_revision = installed_dependent_repository_tup
-                                %>
-                                <li>Revision <b>${ installed_changeset_revision | h}</b> of repository <b>${name | h}</b> owned by <b>${owner | h}</b></li>
-                            %endfor
-                            </ul>
-                        %endif
-                        %if installed_runtime_dependent_tool_dependencies:
-                            <label>Runtime dependent tool dependencies of this repository's tool dependencies:</label>
-                            <ul>
-                                %for td_tup in installed_runtime_dependent_tool_dependencies:
-                                    <%
-                                        tool_shed_repository_id, name, version, type = td_tup
-                                        containing_repository = irm.get_containing_repository_for_tool_dependency( td_tup )
-                                        repository_name = containing_repository.name
-                                        changeset_revision = containing_repository.changeset_revision
-                                        owner = containing_repository.owner
-                                    %>
-                                    <li>
-                                        Version <b>${version | h}</b> of ${type | h} <b>${name | h}</b> contained in revision
-                                        <b>${changeset_revision | h}</b> of repository <b>${repository_name | h}</b> owned by <b>${owner | h}</b>
-                                    </li>
-                                %endfor
-                            </ul>
-                        %endif
-                        <br/>
-                    %endif
-                %endif
-            </div>
-        </div>
-%endfor
-            <div class="form-row">
-                <%
-                    can_deactivate_repository = True in map( lambda x: x.can_deactivate, repositories )
-                    can_uninstall_repository = True in map( lambda x: x.can_uninstall, repositories )
-                %>
-                %if can_deactivate_repository and can_uninstall_repository:
-                    <% deactivate_uninstall_button_text = "Deactivate or Uninstall" %>
-                    ${render_checkbox(remove_from_disk_check_box)}
-                    <label for="remove_from_disk" style="display: inline;font-weight:normal;">Check to uninstall or leave blank to deactivate</label>
-                    <br/><br/>
-                %elif can_deactivate_repository:
-                    <% deactivate_uninstall_button_text = "Deactivate" %>
-                %else:
-                    <% deactivate_uninstall_button_text = "Uninstall" %>
-                    ##hack to mimic check box
-                    <input type="hidden" name="remove_from_disk" value="true"/>
-                %endif
-                <input type="submit" name="deactivate_or_uninstall_repository_button" value="${deactivate_uninstall_button_text|h}"/>
-            </div>
-        </form>
-    </div>
-</div>

From e18df9616300aaaf731bba32a524d6056d379ac5 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 13 Nov 2019 08:44:54 -0500
Subject: [PATCH 060/101] Remove unused browse repository from admin toolshed.

---
 .../galaxy/controllers/admin_toolshed.py      | 11 ------
 .../browse_repository.mako                    | 36 -------------------
 2 files changed, 47 deletions(-)
 delete mode 100644 templates/admin/tool_shed_repository/browse_repository.mako

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 618d90fbd68..b0778d2243c 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -57,17 +57,6 @@ class AdminToolshed(AdminGalaxy):
                                                         message=message,
                                                         status=status))
 
-    @web.expose
-    @web.require_admin
-    def browse_repository(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository = repository_util.get_installed_tool_shed_repository(trans.app, kwd['id'])
-        return trans.fill_template('/admin/tool_shed_repository/browse_repository.mako',
-                                   repository=repository,
-                                   message=message,
-                                   status=status)
-
     @web.legacy_expose_api
     @web.require_admin
     def browse_repositories(self, trans, **kwd):
diff --git a/templates/admin/tool_shed_repository/browse_repository.mako b/templates/admin/tool_shed_repository/browse_repository.mako
deleted file mode 100644
index 0931cd34f54..00000000000
--- a/templates/admin/tool_shed_repository/browse_repository.mako
+++ /dev/null
@@ -1,36 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
-<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "dynatree_skin/ui.dynatree" )}
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ## ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.dynatree" )}
-    ${browse_files(repository.name, repository.repo_files_directory(trans.app))}
-</%def>
-
-${render_galaxy_repository_actions( repository )}
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="card">
-    <div class="card-header">Browse ${repository.name|h} revision ${repository.changeset_revision} files</div>
-    <div class="card-body">
-        <div class="form-row" >
-            <label>Contents:</label>
-            <div id="tree" >
-                Loading...
-            </div>
-        </div>
-        <div class="form-row">
-            <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div>
-        </div>
-    </div>
-</div>

From 88a6fdd656eb11b6abcd10247df2437baf7d9d11 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 13 Nov 2019 11:52:24 -0500
Subject: [PATCH 061/101] Change update_tool_shed_status in tool shed twill
 test to test API endpoint.

---
 lib/tool_shed/test/base/twilltestcase.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index d5f92adbe4b..8aa315cb93d 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -1580,10 +1580,9 @@ class ShedTwillTestCase(FunctionalTestCase):
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def update_tool_shed_status(self):
-        params = {
-            'all_installed_repositories': True
-        }
-        self.visit_galaxy_url('/admin_toolshed/update_tool_shed_status_for_installed_repository', params=params)
+        api_key = get_master_api_key()
+        response = requests.get(self.galaxy_url + "/api/tool_shed_repositories/check_for_updates?key=" + api_key)
+        assert response.status_code != 403, response.content
 
     def upload_file(self,
                     repository,

From 4731e742ef8ec44054aa7b91df2ff80a28053494 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 7 Jan 2020 13:50:01 -0500
Subject: [PATCH 062/101] Cleanup now unused update check code?

---
 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py  | 9 ---------
 .../galaxy_install/grids/admin_toolshed_grids.py         | 4 ----
 2 files changed, 13 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index b0778d2243c..3662647a770 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1266,12 +1266,3 @@ class AdminToolshed(AdminGalaxy):
                                                         id=trans.security.encode_id(repository.id),
                                                         message=message,
                                                         status=status))
-
-    @web.expose
-    @web.require_admin
-    def update_tool_shed_status_for_installed_repository(self, trans, **kwd):
-        message, status = repository_util.check_for_updates(trans.app, trans.install_model, kwd.get('id', None))
-        return trans.response.send_redirect(web.url_for(controller='admin',
-                                                        action='repositories',
-                                                        message=message,
-                                                        status=status))
diff --git a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
index 289cad2458d..b78e6d22ea2 100644
--- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
+++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
@@ -150,10 +150,6 @@ class InstalledRepositoryGrid(grids.Grid):
                                               visible=False,
                                               filterable="standard"))
     global_actions = [
-        grids.GridAction(label="Update tool shed status",
-                         url_args=dict(controller='admin_toolshed',
-                                       action='update_tool_shed_status_for_installed_repository',
-                                       all_installed_repositories=True))
     ]
     operations = [grids.GridOperation(label="Update tool shed status",
                                       condition=(lambda item: not item.deleted),

From 6ba2fafa5ea18a841789917a0c41727e6c987191 Mon Sep 17 00:00:00 2001
From: xgaia <xgaia@gmx.com>
Date: Mon, 6 Jan 2020 15:13:15 +0100
Subject: [PATCH 063/101] add missing env

---
 tools/interactive/interactivetool_askomics.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/interactive/interactivetool_askomics.xml b/tools/interactive/interactivetool_askomics.xml
index cc18516e770..94cf111a2f3 100644
--- a/tools/interactive/interactivetool_askomics.xml
+++ b/tools/interactive/interactivetool_askomics.xml
@@ -16,6 +16,7 @@
         <environment_variable name="USER_LAST_NAME">Galaxy</environment_variable>
         <environment_variable name="USER_USERNAME">${__user_name__}</environment_variable>
         <environment_variable name="USER_EMAIL">${__user_email__}</environment_variable>
+        <environment_variable name="USER_APIKEY">${__user_name__}</environment_variable>
         <!-- Galaxy info -->
         <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
         <environment_variable name="GALAXY_API_KEY" inject="api_key" />

From 099da43ce8c3d4197067f99335704b5318b3134a Mon Sep 17 00:00:00 2001
From: xgaia <xgaia@gmx.com>
Date: Mon, 6 Jan 2020 15:17:06 +0100
Subject: [PATCH 064/101] upgrade tool to 3.2.1

---
 tools/interactive/interactivetool_askomics.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/interactive/interactivetool_askomics.xml b/tools/interactive/interactivetool_askomics.xml
index 94cf111a2f3..e2ec52f1144 100644
--- a/tools/interactive/interactivetool_askomics.xml
+++ b/tools/interactive/interactivetool_askomics.xml
@@ -1,7 +1,7 @@
 <tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="1.0">
     <description>a visual SPARQL query builder</description>
     <requirements>
-        <container type="docker">askomics/flaskomics-with-dependencies:3.2.0</container>
+        <container type="docker">askomics/flaskomics-with-dependencies:3.2.1</container>
     </requirements>
     <entry_points>
         <entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">

From cd3936bfb0f2004f479274c7a6fa7e16b2c145a8 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Tue, 7 Jan 2020 12:17:02 -0500
Subject: [PATCH 065/101] Check return value of quick_load

---
 lib/galaxy/tools/toolbox/base.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index cc0396fffd1..2e41377c793 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -839,8 +839,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             if os.path.isdir(child_path) and recursive:
                 self.__watch_directory(child_path, elems, integrated_elems, load_panel_dict, recursive)
             elif self._looks_like_a_tool(child_path):
-                quick_load(child_path, async_load=False)
-                tool_loaded = True
+                tool_loaded = quick_load(child_path, async_load=False)
         if (tool_loaded or force_watch) and self._tool_watcher:
             self._tool_watcher.watch_directory(directory, quick_load)
 

From 1cafdf9397fee4f08e8cb8391baaadc8d7d2926b Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Tue, 7 Jan 2020 12:54:45 -0500
Subject: [PATCH 066/101] Make it explicit

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tools/toolbox/base.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 2e41377c793..3c25ca9e23a 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -839,7 +839,8 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             if os.path.isdir(child_path) and recursive:
                 self.__watch_directory(child_path, elems, integrated_elems, load_panel_dict, recursive)
             elif self._looks_like_a_tool(child_path):
-                tool_loaded = quick_load(child_path, async_load=False)
+                tool_id = quick_load(child_path, async_load=False)
+                tool_loaded = bool(tool_id)
         if (tool_loaded or force_watch) and self._tool_watcher:
             self._tool_watcher.watch_directory(directory, quick_load)
 

From ed4f538d2cb35c6ca83fcaa5d4a8adbdd32b590b Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 8 Jan 2020 12:11:49 +0000
Subject: [PATCH 067/101] Full Python dependencies update

using `make update-dependencies`.
---
 .../default/pinned-dev-requirements.txt       | 22 ++++----
 .../pipfiles/default/pinned-requirements.txt  | 53 +++++++++----------
 2 files changed, 37 insertions(+), 38 deletions(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index d5784c22828..34360b2b315 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -4,20 +4,20 @@ alabaster==0.7.12
 argh==0.26.2
 atomicwrites==1.3.0
 attrs==19.3.0
-babel==2.7.0
+babel==2.8.0
 certifi==2019.11.28
 chardet==3.0.4
 commonmark==0.9.1
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-coverage==4.5.4
+coverage==5.0.2
 docutils==0.15.2
 funcsigs==1.0.2 ; python_version < '3.3'
-future==0.18.2
+future==0.18.2 ; python_version < '3'
 gunicorn==19.10.0
 idna==2.8
-imagesize==1.1.0
-importlib-metadata==1.2.0 ; python_version < '3.8'
+imagesize==1.2.0
+importlib-metadata==1.3.0 ; python_version < '3.8'
 jinja2==2.10.3
 lxml==4.4.2
 markdown==3.1.1
@@ -27,24 +27,24 @@ mock==3.0.5
 more-itertools==5.0.0
 nose==1.3.7
 nosehtml==0.4.5
-packaging==19.2
+packaging==20.0
 pathlib2==2.3.2 ; python_version < '3.6'
 pathtools==0.1.2
 pluggy==0.13.1
 port-for==0.4
 psutil==5.6.7
-py==1.8.0
+py==1.8.1
 pygithub3==0.5.1 ; python_version < '3'
 pygments==2.5.2
-pyparsing==2.4.5
+pyparsing==2.4.6
 pytest-cov==2.8.1
 pytest-html==1.22.1
 pytest-metadata==1.8.0
 pytest-postgresql==1.4.1
 pytest-pythonpath==0.7.3
-pytest==4.6.6
+pytest==4.6.9
 pytz==2019.3
-pyyaml==5.2
+pyyaml==5.3
 recommonmark==0.6.0
 requests==2.22.0
 scandir==1.10.0 ; python_version < '3.5'
@@ -60,5 +60,5 @@ twill==0.9.1 ; python_version < '3'
 typing==3.7.4.1 ; python_version < '3.5'
 urllib3==1.25.7 ; python_version == '2.7'
 watchdog==0.9.0
-wcwidth==0.1.7 ; sys_platform != 'win32'
+wcwidth==0.1.8 ; sys_platform != 'win32'
 zipp==0.6.0
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index b7ff526367a..c0463e70b71 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -18,7 +18,7 @@ azure-nspkg==3.0.2
 azure-storage-blob==1.3.1
 azure-storage-common==1.4.2
 azure-storage-nspkg==3.1.0
-babel==2.7.0
+babel==2.8.0
 bagit==1.7.0
 bcrypt==3.1.7
 bdbag==1.5.6
@@ -37,7 +37,7 @@ certifi==2019.11.28
 cffi==1.13.2
 chardet==3.0.4
 cheetah3==3.2.4
-cliff==2.16.0
+cliff==2.17.0
 cloudauthz==0.6.0
 cloudbridge==2.0.0
 cmd2==0.8.9
@@ -53,22 +53,21 @@ dictobj==0.4
 docopt==0.6.2
 docutils==0.15.2
 dogpile.cache==0.9.0
-ecdsa==0.14.1
+ecdsa==0.15
 enum34==1.1.6 ; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2 ; python_version < '3.3'
 functools32==3.2.3.post2 ; python_version < '3.2'
-future==0.18.2
 futures==3.3.0 ; python_version == '2.6' or python_version == '2.7'
 galaxy-sequence-utils==1.1.3
 google-api-python-client==1.7.8
 google-auth-httplib2==0.0.3
-google-auth==1.7.1
+google-auth==1.10.0
 gxformat2==0.10.1
 h5py==2.10.0
-httplib2==0.14.0
+httplib2==0.15.0
 idna==2.8
-importlib-metadata==1.2.0 ; python_version < '3.8'
+importlib-metadata==1.3.0 ; python_version < '3.8'
 ipaddress==1.0.23 ; python_version < '3.3'
 isa-rwval==0.10.7
 iso8601==0.1.12
@@ -78,13 +77,13 @@ jsonpatch==1.24
 jsonpointer==2.0
 jsonschema==3.2.0
 keystoneauth1==3.18.0
-kombu==4.6.6
+kombu==4.6.7
 lockfile==0.12.2
 lxml==4.4.2
 mako==1.1.0
 markdown==3.1.1
 markupsafe==1.1.1
-mercurial==5.2
+mercurial==5.2.2
 mistune==0.8.4
 monotonic==1.5
 more-itertools==5.0.0
@@ -96,25 +95,25 @@ mypy-extensions==0.4.3
 netaddr==0.7.19
 netifaces==0.10.9
 networkx==1.11
-nodeenv==1.3.3
+nodeenv==1.3.4
 nose==1.3.7
-numpy==1.16.5
+numpy==1.16.6
 oauth2client==4.1.3
 oauthlib==3.1.0
 openstacksdk==0.17.0
 os-client-config==1.33.0
 os-service-types==1.7.0
-osc-lib==1.14.1
-oslo.config==6.12.0
+osc-lib==1.15.0
+oslo.config==7.0.0
 oslo.context==2.23.0
-oslo.i18n==3.25.0
-oslo.log==3.45.0
+oslo.i18n==3.25.1
+oslo.log==3.45.2
 oslo.serialization==2.29.2
-oslo.utils==3.42.0
-packaging==19.2
-paramiko==2.7.0
+oslo.utils==3.42.1
+packaging==20.0
+paramiko==2.7.1
 parsley==1.3
-paste==3.2.3
+paste==3.2.4
 pastedeploy==2.0.1
 pastescript==3.2.0
 pathlib2==2.3.2 ; python_version < '3.6'
@@ -133,16 +132,16 @@ pyjwt==1.7.1
 pykwalify==1.7.0
 pynacl==1.3.0
 pyopenssl==19.1.0
-pyparsing==2.4.5
+pyparsing==2.4.6
 pyperclip==1.7.0
-pyrsistent==0.15.6
+pyrsistent==0.15.7
 pysam==0.15.2
 pysftp==0.2.9
 python-cinderclient==4.0.0
 python-dateutil==2.8.1
 python-genomespaceclient==1.2.0
 python-glanceclient==2.12.0
-python-jose==3.0.1
+python-jose==3.1.0
 python-keystoneclient==3.17.0
 python-neutronclient==6.9.0
 python-novaclient==11.0.0
@@ -150,7 +149,7 @@ python-openid==2.2.5 ; python_version < '3.0'
 python-swiftclient==3.6.0
 pytz==2019.3
 pyuwsgi==2.0.18.post0
-pyyaml==5.2
+pyyaml==5.3
 rdflib-jsonld==0.4.0
 rdflib==4.2.2
 repoze.lru==0.7
@@ -172,8 +171,8 @@ simplejson==3.17.0
 six==1.11.0
 social-auth-core[openidconnect]==3.1.0+gx0
 sqlalchemy-migrate==0.13.0
-sqlalchemy-utils==0.35.0
-sqlalchemy==1.3.11
+sqlalchemy-utils==0.36.1
+sqlalchemy==1.3.12
 sqlparse==0.3.0
 stevedore==1.31.0
 subprocess32==3.5.4 ; python_version < '3.0'
@@ -184,11 +183,11 @@ typing-extensions==3.7.4.1
 typing==3.7.4.1 ; python_version < '3.5'
 tzlocal==2.0.0
 unicodecsv==0.14.1 ; python_version < '3.0'
-uritemplate==3.0.0
+uritemplate==3.0.1
 urllib3==1.25.7 ; python_version == '2.7'
 vine==1.3.0
 warlock==1.3.3
-wcwidth==0.1.7 ; sys_platform != 'win32'
+wcwidth==0.1.8 ; sys_platform != 'win32'
 webencodings==0.5.1
 webob==1.8.5
 whoosh==2.7.4

From b75f46a006df2a076ed9f46b588cc7417bc8797a Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Jan 2020 16:04:00 -0500
Subject: [PATCH 068/101] Add require_login bypass for entire authnz
 controller.

---
 lib/galaxy/web/framework/webapp.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index 31dd71bd584..273eb40cc69 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -563,6 +563,10 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
                         return
                 except IndexError:
                     pass
+            authnz_controller_base = url_for(controller='authnz', action='index')
+            if self.request.path.startswith(authnz_controller_base):
+                #  All authnz requests pass through
+                return
             # redirect to root if the path is not in the list above
             if self.request.path not in allowed_paths:
                 login_url = url_for(controller='root', action='login', redirect=self.request.path)

From 6326a1eb8bbb2851f51245d777867cc0049f6764 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 26 Dec 2019 16:00:55 -0500
Subject: [PATCH 069/101] Job Lock component.

---
 .../scripts/components/admin/JobLock.vue      | 45 +++++++++++++++++++
 .../galaxy/scripts/components/admin/Jobs.vue  | 45 ++++++-------------
 2 files changed, 59 insertions(+), 31 deletions(-)
 create mode 100644 client/galaxy/scripts/components/admin/JobLock.vue

diff --git a/client/galaxy/scripts/components/admin/JobLock.vue b/client/galaxy/scripts/components/admin/JobLock.vue
new file mode 100644
index 00000000000..d613b8236b6
--- /dev/null
+++ b/client/galaxy/scripts/components/admin/JobLock.vue
@@ -0,0 +1,45 @@
+<template>
+    <b-form-group label="Administrative Job Lock" label-for="prevent-job-dispatching">
+        <b-form-checkbox id="prevent-job-dispatching" v-model="jobLock" switch>
+            Job dispatching is currently
+            <strong>{{ jobLockDisplay ? "locked" : "unlocked" }}</strong>
+        </b-form-checkbox>
+    </b-form-group>
+</template>
+
+<script>
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+export default {
+    data() {
+        return {
+            jobLock: false,
+            jobLockDisplay: false
+        };
+    },
+    watch: {
+        jobLock(newVal) {
+            this.handleJobLock(axios.put(`${getAppRoot()}api/job_lock`, { active: this.jobLock }));
+        }
+    },
+    methods: {
+        initJobLock() {
+            this.handleJobLock(axios.get(`${getAppRoot()}api/job_lock`));
+        },
+        handleJobLock(axiosPromise) {
+            axiosPromise
+                .then(response => {
+                    this.jobLock = response.data.active;
+                    this.jobLockDisplay = response.data.active;
+                })
+                .catch(error => {
+                    console.error(error);
+                });
+        }
+    },
+    created() {
+        this.initJobLock();
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/admin/Jobs.vue b/client/galaxy/scripts/components/admin/Jobs.vue
index ce60f9909a7..5ed69a8bea2 100644
--- a/client/galaxy/scripts/components/admin/Jobs.vue
+++ b/client/galaxy/scripts/components/admin/Jobs.vue
@@ -1,8 +1,17 @@
 <template>
     <div>
-        <h2 class="mb-3">
-            <span id="jobs-title">Jobs</span>
-        </h2>
+        <b-container class="mb-3">
+            <b-row>
+                <b-col md="6">
+                    <h2>
+                        <span id="jobs-title">Jobs</span>
+                    </h2>
+                </b-col>
+                <b-col>
+                    <job-lock />
+                </b-col>
+            </b-row>
+        </b-container>
         <b-alert v-if="this.message !== ''" :variant="galaxyKwdToBootstrap(status)" show>
             {{ message }}
         </b-alert>
@@ -41,14 +50,6 @@
                             </b-form-group>
                         </b-form>
                     </b-col>
-                    <b-col>
-                        <b-form-group label="Administrative Job Lock" label-for="prevent-job-dispatching">
-                            <b-form-checkbox id="prevent-job-dispatching" v-model="jobLock" switch>
-                                Job dispatching is currently
-                                <strong>{{ jobLockDisplay ? "locked" : "unlocked" }}</strong>
-                            </b-form-checkbox>
-                        </b-form-group>
-                    </b-col>
                 </b-row>
                 <b-row>
                     <b-col md="6">
@@ -179,6 +180,7 @@ import { getAppRoot } from "onload/loadConfig";
 import UtcDate from "components/UtcDate";
 import axios from "axios";
 import JobDetails from "./JobDetails";
+import JobLock from "./JobLock";
 
 function cancelJob(jobId, message) {
     const url = `${getAppRoot()}api/jobs/${jobId}`;
@@ -186,7 +188,7 @@ function cancelJob(jobId, message) {
 }
 
 export default {
-    components: { UtcDate, JobDetails },
+    components: { UtcDate, JobDetails, JobLock },
     data() {
         return {
             jobsItems: [],
@@ -202,8 +204,6 @@ export default {
             ],
             cutoff: 180,
             cutoffDisplay: 180,
-            jobLock: false,
-            jobLockDisplay: false,
             selectedStopJobIds: [],
             selectedJobId: null,
             allSelected: false,
@@ -217,9 +217,6 @@ export default {
         };
     },
     watch: {
-        jobLock(newVal) {
-            this.handleJobLock(axios.put(`${getAppRoot()}api/job_lock`, { active: this.jobLock }));
-        },
         selectedStopJobIds(newVal) {
             if (newVal.length === 0) {
                 this.indeterminate = false;
@@ -234,19 +231,6 @@ export default {
         }
     },
     methods: {
-        initJobLock() {
-            this.handleJobLock(axios.get(`${getAppRoot()}api/job_lock`));
-        },
-        handleJobLock(axiosPromise) {
-            axiosPromise
-                .then(response => {
-                    this.jobLock = response.data.active;
-                    this.jobLockDisplay = response.data.active;
-                })
-                .catch(error => {
-                    console.error(error);
-                });
-        },
         update() {
             this.busy = true;
             let params = [];
@@ -359,7 +343,6 @@ export default {
         }
     },
     created() {
-        this.initJobLock();
         this.update();
     }
 };

From a4b7191bda998f1e19a4717f657eb6c14d2ad3c2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Dec 2019 11:59:12 +0100
Subject: [PATCH 070/101] Run jenkins tests on github-ci

This allows running integration tests that require docker or kubernetes.
I've also broken up the tests to reduce runtime.
---
 .github/workflows/integration.yaml | 48 ++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 .github/workflows/integration.yaml

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
new file mode 100644
index 00000000000..a09ce91f644
--- /dev/null
+++ b/.github/workflows/integration.yaml
@@ -0,0 +1,48 @@
+name: Integration
+on: [push, pull_request]
+env:
+  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+jobs:
+
+  test:
+    name: Test
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.7, 2.7]
+        subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    - name: Setup Minikube
+      if: matrix.subset == 'kubernetes'
+      id: minikube
+      uses: CodingNagger/minikube-setup-action@v1.0.2
+    - name: Launch Minikube
+      if: matrix.subset == 'kubernetes'
+      run: eval ${{ steps.minikube.outputs.launcher }}
+    - name: Check pods
+      if: matrix.subset == 'kubernetes'
+      run: |
+        kubectl get pods
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache venv dir
+      uses: actions/cache@v1
+      id: cache-venv-galaxy
+      with:
+        path: .venv
+        key: cache-venv-galaxy-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+    - name: Run tests
+      run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'

From ab47f4e68bc88b076cd1a507d4b930abc760a7f2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 9 Jan 2020 11:03:02 +0100
Subject: [PATCH 071/101] Check conditional dependencies, even if no config
 file was found

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

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 29691a9c4a6..6a08851fc79 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -194,7 +194,7 @@ class ConditionalDependencies(object):
 
 def optional(config_file=None):
     if not config_file:
-        config_file = find_config_file(['galaxy', 'universe_wsgi'])
+        config_file = find_config_file(['galaxy', 'universe_wsgi'], include_samples=True)
     if not config_file:
         print("galaxy.dependencies.optional: no config file found", file=sys.stderr)
         return []

From f1a88e44ce39bf8e2074d1ec45a24e6009932b1d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Dec 2019 16:58:35 +0100
Subject: [PATCH 072/101] Bump paramiko version

---
 .../dependencies/pipfiles/default/pinned-requirements.txt       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index b7ff526367a..fb538ee3ebb 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -112,7 +112,7 @@ oslo.log==3.45.0
 oslo.serialization==2.29.2
 oslo.utils==3.42.0
 packaging==19.2
-paramiko==2.7.0
+paramiko==2.7.1
 parsley==1.3
 paste==3.2.3
 pastedeploy==2.0.1

From 5b09f6d74c60d39392194a4dacf4c235fe23d8d4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 30 Dec 2019 15:06:12 +0100
Subject: [PATCH 073/101] Disable strict host key checking during tests

And fix parsing of shell_strict_host_key_check
---
 lib/galaxy/jobs/runners/util/cli/shell/rsh.py | 5 +++--
 test/integration/test_cli_runners.py          | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/jobs/runners/util/cli/shell/rsh.py b/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
index 2352208229a..afdfd28ed1f 100644
--- a/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
+++ b/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
@@ -6,7 +6,8 @@ from pulsar.managers.util.retry import RetryActionExecutor
 
 from galaxy.util import (
     smart_str,
-    unicodify
+    string_as_bool,
+    unicodify,
 )
 from galaxy.util.bunch import Bunch
 from .local import LocalShell
@@ -43,7 +44,7 @@ class SecureShell(RemoteShell):
     SSH_NEW_KEY_STRING = 'Are you sure you want to continue connecting'
 
     def __init__(self, rsh='ssh', rcp='scp', private_key=None, port=None, strict_host_key_checking=True, **kwargs):
-        strict_host_key_checking = "yes" if strict_host_key_checking else "no"
+        strict_host_key_checking = "yes" if string_as_bool(strict_host_key_checking) else "no"
         options = ["-o", "StrictHostKeyChecking=%s" % strict_host_key_checking]
         options.extend(["-o", "ConnectTimeout=60"])
         if private_key:
diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index d09e6c07fd3..a116765a748 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -58,6 +58,7 @@ def cli_job_config(remote_connection, shell_plugin='ParamikoShell', job_plugin='
             <param id="shell_private_key">$private_key</param>
             <param id="shell_hostname">$hostname</param>
             <param id="shell_port">$port</param>
+            <param id="shell_strict_host_key_checking">False</param>
             <param id="embed_metadata_in_job">False</param>
             <env id="SOME_ENV_VAR">42</env>
         </destination>

From d33813c28d29f2839db344832eb9fe929eafa34d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 30 Dec 2019 15:35:40 +0100
Subject: [PATCH 074/101] Tweak paramiko missing hostkey policies

---
 lib/galaxy/jobs/runners/util/cli/shell/rsh.py | 11 ++++++-----
 test/unit/test_remote_shell.py                |  1 +
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/jobs/runners/util/cli/shell/rsh.py b/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
index afdfd28ed1f..c6c7e1fbd1a 100644
--- a/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
+++ b/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
@@ -41,11 +41,11 @@ class RemoteShell(LocalShell):
 
 
 class SecureShell(RemoteShell):
-    SSH_NEW_KEY_STRING = 'Are you sure you want to continue connecting'
 
     def __init__(self, rsh='ssh', rcp='scp', private_key=None, port=None, strict_host_key_checking=True, **kwargs):
-        strict_host_key_checking = "yes" if string_as_bool(strict_host_key_checking) else "no"
-        options = ["-o", "StrictHostKeyChecking=%s" % strict_host_key_checking]
+        options = []
+        if not string_as_bool(strict_host_key_checking):
+            options.extend(["-o", "StrictHostKeyChecking=no", "-o", "UserKnownHostsFile=/dev/null"])
         options.extend(["-o", "ConnectTimeout=60"])
         if private_key:
             options.extend(['-i', private_key])
@@ -56,13 +56,14 @@ class SecureShell(RemoteShell):
 
 class ParamikoShell(object):
 
-    def __init__(self, username, hostname, password=None, private_key=None, port=22, timeout=60, **kwargs):
+    def __init__(self, username, hostname, password=None, private_key=None, port=22, timeout=60, strict_host_key_checking=True, **kwargs):
         self.username = username
         self.hostname = hostname
         self.password = password
         self.private_key = private_key
         self.port = int(port) if port else port
         self.timeout = int(timeout) if timeout else timeout
+        self.strict_host_key_checking = string_as_bool(strict_host_key_checking)
         self.ssh = None
         self.retry_action_executor = RetryActionExecutor(max_retries=100, interval_max=300)
         self.connect()
@@ -70,7 +71,7 @@ class ParamikoShell(object):
     def connect(self):
         log.info("Attempting establishment of new paramiko SSH channel")
         self.ssh = paramiko.SSHClient()
-        self.ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
+        self.ssh.set_missing_host_key_policy(paramiko.RejectPolicy() if self.strict_host_key_checking else paramiko.WarningPolicy())
         self.ssh.connect(hostname=self.hostname,
                          port=self.port,
                          username=self.username,
diff --git a/test/unit/test_remote_shell.py b/test/unit/test_remote_shell.py
index d460509c3fd..f13305ba2be 100644
--- a/test/unit/test_remote_shell.py
+++ b/test/unit/test_remote_shell.py
@@ -23,6 +23,7 @@ class TestCliInterface(unittest.TestCase):
         cls.username = 'testuser'
         cls.shell_params = {'username': cls.username,
                             'private_key': cls.ssh_keys.private_key_file,
+                            'strict_host_key_checking': False,
                             'hostname': 'localhost'}
         cls.cli_interface = CliInterface()
 

From 9be9a5b5d22e20c799c932cb87112f1719fba1d4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 30 Dec 2019 20:35:45 +0100
Subject: [PATCH 075/101] Adjust uid of testuser inside slurm/pbs container

---
 test/integration/test_cli_runners.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index a116765a748..48cd4b3cf8f 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -12,7 +12,7 @@ from galaxy_test.driver import integration_util
 from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
 
 
-RemoteConnection = collections.namedtuple('remote_connection', ['hostname', 'username', 'password', 'port', 'private_key', 'public_key'])
+RemoteConnection = collections.namedtuple('remote_connection', ['hostname', 'username', 'port', 'private_key', 'public_key'])
 
 
 @integration_util.skip_unless_docker()
@@ -36,7 +36,8 @@ def start_ssh_docker(container_name, jobs_directory, port=10022, image='agaveapi
                           'nofile=2048:2048',
                           image]
     subprocess.check_call(START_SLURM_DOCKER)
-    return RemoteConnection('localhost', 'testuser', 'testuser', port, ssh_keys.private_key_file, ssh_keys.public_key_file)
+    subprocess.check_call(['docker', 'exec', container_name, 'usermod', '-u', str(os.getuid()), 'testuser'])
+    return RemoteConnection('localhost', 'testuser', port, ssh_keys.private_key_file, ssh_keys.public_key_file)
 
 
 def stop_ssh_docker(container_name, remote_connection):

From 1f9dc90f25ac4cc1460ebffc7080ea317a6ba5ff Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Jan 2020 19:05:26 +0100
Subject: [PATCH 076/101] Run ssh/cluster containers in privileged mode

---
 test/integration/test_cli_runners.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index 48cd4b3cf8f..bc3683fd68a 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -28,6 +28,7 @@ def start_ssh_docker(container_name, jobs_directory, port=10022, image='agaveapi
                           '--name',
                           container_name,
                           '--rm',
+                          '--privileged',  # for torque
                           '-v',
                           "{jobs_directory}:{jobs_directory}".format(jobs_directory=jobs_directory),
                           "-v",

From a7d4d6907477d736259bcaead4368efacd9cbbc6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 3 Jan 2020 13:10:34 +0100
Subject: [PATCH 077/101] Run fallback external_metadata when finishing job

That only affects the ShellJobRunner
---
 lib/galaxy/jobs/runners/cli.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/jobs/runners/cli.py b/lib/galaxy/jobs/runners/cli.py
index 2da5643a6ce..6508142674b 100644
--- a/lib/galaxy/jobs/runners/cli.py
+++ b/lib/galaxy/jobs/runners/cli.py
@@ -161,10 +161,6 @@ class ShellJobRunner(AsynchronousJobRunner):
                 if ajs.job_wrapper.get_state() == model.Job.states.DELETED:
                     continue
 
-                external_metadata = not asbool(ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB))
-                if external_metadata:
-                    self._handle_metadata_externally(ajs.job_wrapper, resolve_requirements=True)
-
                 log.debug("(%s/%s) job not found in batch state check" % (id_tag, external_job_id))
                 shell_params, job_params = self.parse_destination_params(ajs.job_destination.params)
                 shell, job_interface = self.get_cli_plugins(shell_params, job_params)
@@ -187,6 +183,9 @@ class ShellJobRunner(AsynchronousJobRunner):
                 ajs.running = True
             ajs.old_state = state
             if state == model.Job.states.OK:
+                external_metadata = not asbool(ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB))
+                if external_metadata:
+                    self.work_queue.put((self.handle_metadata_externally, ajs))
                 log.debug('(%s/%s) job execution finished, running job wrapper finish method' % (id_tag, external_job_id))
                 self.work_queue.put((self.finish_job, ajs))
             else:
@@ -194,6 +193,9 @@ class ShellJobRunner(AsynchronousJobRunner):
         # Replace the watch list with the updated version
         self.watched = new_watched
 
+    def handle_metadata_externally(self, ajs):
+        self._handle_metadata_externally(ajs.job_wrapper, resolve_requirements=True)
+
     def __handle_out_of_memory(self, ajs, external_job_id):
         shell_params, job_params = self.parse_destination_params(ajs.job_destination.params)
         shell, job_interface = self.get_cli_plugins(shell_params, job_params)

From cfe1ad7f859305e392b0fd4ed8a5a4225033a227 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 3 Jan 2020 13:11:55 +0100
Subject: [PATCH 078/101] Skip usermod on osx, isn't necessary with docker for
 mac

---
 test/integration/test_cli_runners.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index bc3683fd68a..c2277d85f9c 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -3,6 +3,7 @@ import collections
 import os
 import string
 import subprocess
+import sys
 import tempfile
 import unittest
 
@@ -37,7 +38,8 @@ def start_ssh_docker(container_name, jobs_directory, port=10022, image='agaveapi
                           'nofile=2048:2048',
                           image]
     subprocess.check_call(START_SLURM_DOCKER)
-    subprocess.check_call(['docker', 'exec', container_name, 'usermod', '-u', str(os.getuid()), 'testuser'])
+    if sys.platform != 'darwin':
+        subprocess.check_call(['docker', 'exec', container_name, 'usermod', '-u', str(os.getuid()), 'testuser'])
     return RemoteConnection('localhost', 'testuser', port, ssh_keys.private_key_file, ssh_keys.public_key_file)
 
 

From 55cf4451d044ebc7123069fbd12ce95fdf8f769e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 5 Jan 2020 12:53:33 +0100
Subject: [PATCH 079/101] CliRunner lint fix

---
 test/integration/test_cli_runners.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index c2277d85f9c..fb464bfa584 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -96,7 +96,7 @@ class BaseCliIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
         super(BaseCliIntegrationTestCase, cls).tearDownClass()
 
     @classmethod
-    def handle_galaxy_config_kwds(cls, config, ):
+    def handle_galaxy_config_kwds(cls, config):
         config["jobs_directory"] = cls.jobs_directory
         config["file_path"] = cls.jobs_directory
         config["job_config_file"] = cli_job_config(remote_connection=cls.remote_connection,

From d5fc7d426e2d1bc519a35288735dd47cb332273d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 3 Jan 2020 17:49:18 +0100
Subject: [PATCH 080/101] Fix interactivetool python 3 support and tests

- enables docker destination for interactivetool tests
- fixes a wrong argument in entrypoint management
- fixes the test setup that targeted a previous iteration (which was
  still called realtimetools)
- prevents deleting the working directory before python has a chance to
  start the container monitor (that's the sleep command)
- fixes some odd interactive tool test assertions
- uses unicode arguments in key_type_token_mapping.py.
  uwsgi arguments are always passed as bytestrings.
---
 lib/galaxy/jobs/__init__.py                   |  2 +-
 lib/galaxy/managers/interactivetool.py        |  2 +-
 lib/galaxy_ext/container_monitor/monitor.py   |  2 +-
 lib/galaxy_test/driver/driver_util.py         | 20 +++++++++++--------
 .../key_type_token_mapping.py                 | 13 ++++++++++--
 test/integration/test_containerized_jobs.py   |  5 +++++
 test/integration/test_interactivetools_api.py | 12 +++++------
 7 files changed, 36 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 9bb04908efd..8b9d67523ca 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -2111,7 +2111,7 @@ class JobWrapper(HasResourceParameters):
                 "connection_configuration": container.connection_configuration,
             }, f)
 
-        return "(python '%s'/lib/galaxy_ext/container_monitor/monitor.py &) " % exec_dir
+        return "(python '%s'/lib/galaxy_ext/container_monitor/monitor.py &); sleep 1 " % exec_dir
 
     @property
     def user(self):
diff --git a/lib/galaxy/managers/interactivetool.py b/lib/galaxy/managers/interactivetool.py
index dd740f96eb1..a6504c5c587 100644
--- a/lib/galaxy/managers/interactivetool.py
+++ b/lib/galaxy/managers/interactivetool.py
@@ -270,7 +270,7 @@ class InteractiveToolManager(object):
         entry_point = trans.sa_session.query(model.InteractiveToolEntryPoint).get(entry_point_id)
         if self.app.interactivetool_manager.can_access_entry_point(trans, entry_point):
             if entry_point.active:
-                return self.target_if_active(entry_point)
+                return self.target_if_active(trans, entry_point)
             elif entry_point.deleted:
                 raise exceptions.MessageException('InteractiveTool has ended. You will have to start a new one.')
             else:
diff --git a/lib/galaxy_ext/container_monitor/monitor.py b/lib/galaxy_ext/container_monitor/monitor.py
index b1e1447f1e0..86987b81e2d 100644
--- a/lib/galaxy_ext/container_monitor/monitor.py
+++ b/lib/galaxy_ext/container_monitor/monitor.py
@@ -22,7 +22,7 @@ def parse_ports(container_name, connection_configuration):
                                         preexec_fn=os.setpgrp)
             if exit_code == 0:
                 stdout_file.seek(0)
-                ports_raw = stdout_file.read()
+                ports_raw = stdout_file.read().decode('utf-8')
                 return ports_raw
 
 
diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py
index f6334b762ee..1475c8669e1 100644
--- a/lib/galaxy_test/driver/driver_util.py
+++ b/lib/galaxy_test/driver/driver_util.py
@@ -4,6 +4,7 @@ import fcntl
 import logging
 import os
 import random
+import re
 import shutil
 import signal
 import socket
@@ -62,13 +63,15 @@ INSTALLED_TOOL_PANEL_CONFIGS = [
 ]
 REALTIME_PROXY_TEMPLATE = string.Template(r"""
 uwsgi:
-  realtime_map: $tempdir/realtime_map.sqlite
-  python-raw: scripts/realtime/key_type_token_mapping.py
-  route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(realtime\.$test_host:$test_port)$ goto:realtime
+  http-raw-body: true
+  interactivetools_map: $tempdir/interactivetools_map.sqlite
+  python-raw: scripts/interactivetools/key_type_token_mapping.py
+  route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.$test_host:$test_port)$ goto:interactivetool
   route-run: goto:endendend
-  route-label: realtime
-  route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(realtime\.$test_host:$test_port)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $2 $1 $3 $4 $0 5
+  route-label: interactivetool
+  route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.$test_host:$test_port)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $1 $3 $2 $4 $0 5
   route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
+  route: .* break:404 Not Found
   route-label: endendend
 """)
 
@@ -729,8 +732,9 @@ def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=No
 
     enable_realtime_mapping = getattr(config_object, "enable_realtime_mapping", False)
     if enable_realtime_mapping:
-        config["galaxy"]["realtime_prefix"] = "realtime"
-        config["galaxy"]["realtime_map"] = os.path.join(tempdir, "realtime_map.sqlite")
+        config["galaxy"]["interactivetools_prefix"] = "interactivetool"
+        config["galaxy"]["interactivetools_map"] = os.path.join(tempdir, "interactivetools_map.sqlite")
+        config['galaxy']['interactivetools_enable'] = True
 
     yaml_config_path = os.path.join(tempdir, "galaxy.yml")
     with open(yaml_config_path, "w") as f:
@@ -743,7 +747,7 @@ def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=No
             old_contents = f.read()
         with open(yaml_config_path, "w") as f:
             test_port = str(port) if port else r"[0-9]+"
-            test_host = host or "localhost"
+            test_host = re.escape(host) if host else "localhost"
             uwsgi_section = REALTIME_PROXY_TEMPLATE.safe_substitute(test_host=test_host, test_port=test_port, tempdir=tempdir)
             f.write(uwsgi_section)
             f.write(old_contents)
diff --git a/scripts/interactivetools/key_type_token_mapping.py b/scripts/interactivetools/key_type_token_mapping.py
index fa096dfbd60..df6dff6506a 100644
--- a/scripts/interactivetools/key_type_token_mapping.py
+++ b/scripts/interactivetools/key_type_token_mapping.py
@@ -6,7 +6,7 @@ from time import time
 import uwsgi
 
 
-realtime_db_file = uwsgi.opt["interactivetools_map"]
+realtime_db_file = uwsgi.opt["interactivetools_map"].decode('utf-8')
 db_conn = sqlite3.connect(realtime_db_file)
 
 DATABASE_TABLE_NAME = 'gxitproxy'
@@ -51,6 +51,14 @@ class CacheList():
 key_type_token_mapped_cache = CacheList()
 
 
+def args_as_unicode(func):
+    def wrap_args(*args):
+        args = (arg.decode('utf-8') if isinstance(arg, bytes) else arg for arg in args)
+        return func(*args)
+    return wrap_args
+
+
+@args_as_unicode
 def key_type_token_mapper_cached(key, key_type, token, route_extra, url, ttl):
     global key_type_token_mapped_cache
     cache_key = (key, key_type, token)
@@ -58,11 +66,12 @@ def key_type_token_mapper_cached(key, key_type, token, route_extra, url, ttl):
     if entry is None:
         entry = key_type_token_mapper(key, key_type, token, route_extra, url)
         if entry is not None:
-            # Should we cache empt/not authorized entries, perhaps for shorter time?
+            # Should we cache empty/not authorized entries, perhaps for shorter time?
             key_type_token_mapped_cache.add_entry(cache_key, entry, ttl=float(ttl))
     return entry
 
 
+@args_as_unicode
 def key_type_token_mapper(key, key_type, token, route_extra, url):
     global db_conn
     # print 'key %s key_type %s token %s route_extra %s url %s\n' % (key, key_type, token, route_extra, url)
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index 626d63c5e63..d84f3060b8d 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -37,6 +37,11 @@ class ContainerizedIntegrationTestCase(integration_util.IntegrationTestCase):
         skip_if_container_type_unavailable(cls)
         super(ContainerizedIntegrationTestCase, cls).setUpClass()
 
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["job_config_file"] = DOCKERIZED_JOB_CONFIG_FILE
+        disable_dependency_resolution(config)
+
 
 def disable_dependency_resolution(config):
     # Disable tool dependency resolution.
diff --git a/test/integration/test_interactivetools_api.py b/test/integration/test_interactivetools_api.py
index e214e3eee80..f3ae60d4879 100644
--- a/test/integration/test_interactivetools_api.py
+++ b/test/integration/test_interactivetools_api.py
@@ -47,8 +47,7 @@ class InteractiveToolsIntegrationTestCase(ContainerizedIntegrationTestCase):
         assert isinstance(jobs, list)
         assert len(jobs) == 1
         job0 = jobs[0]
-        entry_points = self.wait_on_entry_points_active(job0["id"])
-        assert len(entry_points) == 2
+        entry_points = self.wait_on_entry_points_active(job0["id"], expected_num=2)
         entry_point0 = entry_points[0]
         entry_point1 = entry_points[1]
         target0 = self.entry_point_target(entry_point0["id"])
@@ -59,19 +58,18 @@ class InteractiveToolsIntegrationTestCase(ContainerizedIntegrationTestCase):
 
         content1 = self.wait_on_proxied_content(target1)
         assert content1 == "moo cow\n", content1
-        assert False
 
     def wait_on_proxied_content(self, target):
         def get_hosted_content():
             try:
                 scheme, rest = target.split("://", 1)
-                prefix, host_and_port = rest.split(".realtime.")
-                print(rest)
+                prefix, host_and_port = rest.split(".interactivetool.")
                 faked_host = rest
                 if "/" in rest:
                     faked_host = rest.split("/", 1)[0]
-                response = requests.get("%s://%s" % (scheme, host_and_port), timeout=1, headers={"Host": faked_host})
-                return response.content
+                url = "%s://%s" % (scheme, host_and_port)
+                response = requests.get(url, timeout=1, headers={"Host": faked_host})
+                return response.text
             except Exception as e:
                 print(e)
                 return None

From ef3215d8c463ed26531b72c378fe3f2cee65a3a4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 5 Jan 2020 14:36:56 +0100
Subject: [PATCH 081/101] Update build_mulled integration test for new API

The previous API doesn't allow container installation after 2445425bf96a4f834cae961d18860f9a18a60c60
---
 test/integration/test_containerized_jobs.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index d84f3060b8d..9702f7b2622 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -1,5 +1,6 @@
 """Integration tests for running tools in Docker containers."""
 
+import json
 import os
 import unittest
 
@@ -111,13 +112,18 @@ class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, Ru
         if not which('docker'):
             raise unittest.SkipTest("Docker not found on PATH, required for building images via involucro")
         resolver_type = self.build_mulled_resolver
-        tool_id = 'mulled_example_multi_1'
-        endpoint = "tools/%s/dependencies" % tool_id
-        data = {'id': tool_id, 'resolver_type': resolver_type}
+        tool_ids = ['mulled_example_multi_1']
+        endpoint = "dependency_resolvers/toolbox/install"
+        data = {'tool_ids': json.dumps(tool_ids), 'resolver_type': resolver_type, 'container_type': self.container_type, 'include_containers': True}
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
+        create_response = self._get("dependency_resolvers/toolbox", data={'tool_ids': tool_ids, 'container_type': self.container_type, 'include_containers': True, 'index_by': 'tools'}, admin=True)
         response = create_response.json()
-        assert any([True for d in response if d['dependency_type'] == self.container_type])
+        assert len(response) == 1
+        status = response[0]['status']
+        assert status[0]['model_class'] == 'ContainerDependency'
+        assert status[0]['dependency_type'] == self.container_type
+        assert status[0]['container_description']['identifier'].startswith('quay.io/local/mulled-v2-')
 
 
 class MappingContainerResolverTestCase(integration_util.IntegrationTestCase):

From be6ffc03bf970292cbe676bc3b31ada1b6cb3a61 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 5 Jan 2020 14:39:00 +0100
Subject: [PATCH 082/101] Fix mulled_build logic

---
 lib/galaxy/tool_util/deps/mulled/mulled_build.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
index 412994c3152..6150f312d3e 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -180,7 +180,7 @@ def mull_targets(
     if DEST_BASE_IMAGE:
         dest_base_image = DEST_BASE_IMAGE
     else:
-        dest_base_image = DEFAULT_EXTENDED_BASE_IMAGE if not any_target_requires_extended_base(targets) else DEST_BASE_IMAGE
+        dest_base_image = DEFAULT_EXTENDED_BASE_IMAGE if any_target_requires_extended_base(targets) else DEST_BASE_IMAGE
 
     targets = list(targets)
     if involucro_context is None:

From 9705d036631f7586eb2a133bf2593bda0e806385 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 5 Jan 2020 17:27:56 +0100
Subject: [PATCH 083/101] Install pykube if kubectl on path

May perhaps want to limit this to when we know we run integration tests,
but I don't think this harms anything for now.
---
 lib/galaxy/dependencies/__init__.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 6a08851fc79..4d398f0f230 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -11,7 +11,10 @@ import pkg_resources
 import yaml
 
 from galaxy.containers import parse_containers_config
-from galaxy.util import asbool
+from galaxy.util import (
+    asbool,
+    which,
+)
 from galaxy.util.properties import (
     find_config_file,
     load_app_properties
@@ -145,7 +148,7 @@ class ConditionalDependencies(object):
         return "galaxy.jobs.runners.pbs:PBSJobRunner" in self.job_runners
 
     def check_pykube(self):
-        return "galaxy.jobs.runners.kubernetes:KubernetesJobRunner" in self.job_runners
+        return "galaxy.jobs.runners.kubernetes:KubernetesJobRunner" in self.job_runners or which('kubectl')
 
     def check_chronos_python(self):
         return "galaxy.jobs.runners.chronos:ChronosJobRunner" in self.job_runners

From d0693ccbea88df07f3f0e69fc6295f26109bd7f2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 5 Jan 2020 17:41:18 +0100
Subject: [PATCH 084/101] Run and fix grt/export.py test

It used to take 35 minutes on jenkins, but it doesn't anymore, as we're
using a clean database for each test class.
---
 test/integration/test_scripts.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/integration/test_scripts.py b/test/integration/test_scripts.py
index cbedbd75f0e..bf73fb83cb2 100644
--- a/test/integration/test_scripts.py
+++ b/test/integration/test_scripts.py
@@ -116,7 +116,6 @@ class ScriptsIntegrationTestCase(integration_util.IntegrationTestCase):
         output = self._scripts_check_output(script, ["-c", config_file])
         assert "Complete" in output
 
-    @integration_util.skip_if_jenkins
     def test_grt_export(self):
         script = "grt/export.py"
         self._scripts_check_argparse_help(script)
@@ -134,7 +133,7 @@ class ScriptsIntegrationTestCase(integration_util.IntegrationTestCase):
         json_file = os.path.join(self.config_dir, json_files[0])
         with open(json_file, "r") as f:
             export = json.load(f)
-        assert export["version"] == 2
+        assert export["version"] == 3
 
     def test_admin_cleanup_datasets(self):
         self._scripts_check_argparse_help("cleanup_datasets/admin_cleanup_datasets.py")

From 44eac318b03764d06f58f49f4581855958c050e9 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 5 Jan 2020 19:04:45 +0100
Subject: [PATCH 085/101] Fix kubernetes tests on minikube

---
 test/integration/test_kubernetes_runner.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py
index 69966b6870c..62fe4640a82 100644
--- a/test/integration/test_kubernetes_runner.py
+++ b/test/integration/test_kubernetes_runner.py
@@ -1,5 +1,6 @@
 """Integration tests for the Kubernetes runner."""
-# Tested on docker for mac 18.06.1-ce-mac73 using the default kubernetes setup
+# Tested on docker for mac 18.06.1-ce-mac73 using the default kubernetes setup,
+# also works on minikube
 import collections
 import json
 import os
@@ -91,37 +92,40 @@ def job_config(jobs_directory):
             <param id="k8s_persistent_volume_claims">jobs-directory-claim:$jobs_directory,tool-directory-claim:$tool_directory</param>
             <param id="k8s_config_path">$k8s_config_path</param>
             <param id="k8s_galaxy_instance_id">gx-short-id</param>
+            <param id="k8s_run_as_user_id">$$uid</param>
         </plugin>
         <plugin id="k8s_walltime_short" type="runner" load="galaxy.jobs.runners.kubernetes:KubernetesJobRunner">
             <param id="k8s_persistent_volume_claims">jobs-directory-claim:$jobs_directory,tool-directory-claim:$tool_directory</param>
             <param id="k8s_config_path">$k8s_config_path</param>
             <param id="k8s_galaxy_instance_id">gx-short-id</param>
             <param id="k8s_walltime_limit">10</param>
+            <param id="k8s_run_as_user_id">$$uid</param>
         </plugin>
         <plugin id="k8s_no_cleanup" type="runner" load="galaxy.jobs.runners.kubernetes:KubernetesJobRunner">
             <param id="k8s_persistent_volume_claims">jobs-directory-claim:$jobs_directory,tool-directory-claim:$tool_directory</param>
             <param id="k8s_config_path">$k8s_config_path</param>
             <param id="k8s_galaxy_instance_id">gx-short-id</param>
             <param id="k8s_cleanup_job">never</param>
+            <param id="k8s_run_as_user_id">$$uid</param>
         </plugin>
     </plugins>
     <destinations default="k8s_destination">
         <destination id="k8s_destination" runner="k8s">
-            <param id="limits_cpu">1.9</param>
+            <param id="limits_cpu">1.1</param>
             <param id="limits_memory">10M</param>
             <param id="docker_enabled">true</param>
             <param id="docker_default_container_id">busybox:ubuntu-14.04</param>
             <env id="SOME_ENV_VAR">42</env>
         </destination>
         <destination id="k8s_destination_walltime_short" runner="k8s_walltime_short">
-            <param id="limits_cpu">1.9</param>
+            <param id="limits_cpu">1.1</param>
             <param id="limits_memory">10M</param>
             <param id="docker_enabled">true</param>
             <param id="docker_default_container_id">busybox:ubuntu-14.04</param>
             <env id="SOME_ENV_VAR">42</env>
         </destination>
         <destination id="k8s_destination_no_cleanup" runner="k8s_no_cleanup">
-            <param id="limits_cpu">1.9</param>
+            <param id="limits_cpu">1.1</param>
             <param id="limits_memory">10M</param>
             <param id="docker_enabled">true</param>
             <param id="docker_default_container_id">busybox:ubuntu-14.04</param>
@@ -182,7 +186,9 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
         super(BaseKubernetesIntegrationTestCase, cls).tearDownClass()
 
     @classmethod
-    def handle_galaxy_config_kwds(cls, config, ):
+    def handle_galaxy_config_kwds(cls, config):
+        # TODO: implement metadata setting as separate job, as service or side-car
+        config['retry_metadata_internally'] = True
         config["jobs_directory"] = cls.jobs_directory
         config["file_path"] = cls.jobs_directory
         config["job_config_file"] = cls.job_config.path

From 8b3ca7b5b8551471726880095a92da93a7456c90 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Jan 2020 13:11:09 +0100
Subject: [PATCH 086/101] Fix skip_unless_fixed_port

GALAXY_TEST_PORT is always set, GALAXY_TEST_PORT_RANDOM is set to 1
if GALAXY_TEST_PORT wasn't set externally.
---
 lib/galaxy_test/driver/integration_util.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy_test/driver/integration_util.py b/lib/galaxy_test/driver/integration_util.py
index 37a16a33383..6dbfe169654 100644
--- a/lib/galaxy_test/driver/integration_util.py
+++ b/lib/galaxy_test/driver/integration_util.py
@@ -47,7 +47,7 @@ def k8s_config_path():
 
 
 def skip_unless_fixed_port():
-    if os.environ.get("GALAXY_TEST_PORT"):
+    if os.environ.get("GALAXY_TEST_PORT_RANDOM") != "1":
         return _identity
 
     return skip("GALAXY_TEST_PORT must be set for this test.")

From 03e7ea25fbfdfdf9c159f120327d85f196f9e932 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 5 Jan 2020 19:50:32 +0100
Subject: [PATCH 087/101] Fix tool watcher unit tests; sleep needs to happen
 after watching the file

---
 test/unit/tools/test_watcher.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/test/unit/tools/test_watcher.py b/test/unit/tools/test_watcher.py
index 352a4a8a32c..e6eb7389ab1 100644
--- a/test/unit/tools/test_watcher.py
+++ b/test/unit/tools/test_watcher.py
@@ -16,15 +16,17 @@ def test_watcher():
     with __test_directory() as t:
         tool_path = path.join(t, "test.xml")
         toolbox = Toolbox()
-        open(tool_path, "w").write("a")
+        with open(tool_path, "w") as f:
+            f.write("a")
         tool_watcher = watcher.get_tool_watcher(toolbox, bunch.Bunch(
             watch_tools=True
         ))
         tool_watcher.start()
-        time.sleep(1)
         tool_watcher.watch_file(tool_path, "cool_tool")
+        time.sleep(2)
         assert not toolbox.was_reloaded("cool_tool")
-        open(tool_path, "w").write("b")
+        with open(tool_path, "w") as f:
+            f.write("b")
         wait_for_reload(lambda: toolbox.was_reloaded("cool_tool"))
         tool_watcher.shutdown()
         assert tool_watcher.observer is None
@@ -41,10 +43,12 @@ def test_tool_conf_watcher():
 
     with __test_directory() as t:
         tool_conf_path = path.join(t, "test_conf.xml")
-        open(tool_conf_path, "w").write("a")
+        with open(tool_conf_path, "w", 1) as t:
+            t.write("a")
         conf_watcher.watch_file(tool_conf_path)
-        time.sleep(1)
-        open(tool_conf_path, "w").write("b")
+        time.sleep(2)
+        with open(tool_conf_path, 'wb', 0) as t:
+            t.write(b"b")
         wait_for_reload(lambda: callback.called)
         conf_watcher.shutdown()
         assert conf_watcher.thread is None

From 33638c67963791d36e8c296a27e667ce0aed349d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 7 Jan 2020 16:44:23 +0100
Subject: [PATCH 088/101] Don't set GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
 if GALAXY_TEST_DB_URI is set

The actual database to target is generated dynamically, but since
GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION takes precedence the
wrong database is used.
---
 run_tests.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/run_tests.sh b/run_tests.sh
index 78ca1b2e911..77c7871043c 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -602,6 +602,7 @@ if [ -z "$skip_common_startup" ]; then
             export GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
     fi
     ./scripts/common_startup.sh $skip_venv $no_create_venv $no_replace_pip $replace_pip $skip_client_build --dev-wheels || exit 1
+    unset GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
 fi
 
 . ./scripts/common_startup_functions.sh

From 1e4ec5c843e28def7a672c246524cf972663eba8 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@gmail.com>
Date: Mon, 6 Jan 2020 10:56:38 +0000
Subject: [PATCH 089/101] Use `@pytest.mark.skipif` decorator

---
 test/unit/tools/test_watcher.py | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/test/unit/tools/test_watcher.py b/test/unit/tools/test_watcher.py
index e6eb7389ab1..f1e0c12a21b 100644
--- a/test/unit/tools/test_watcher.py
+++ b/test/unit/tools/test_watcher.py
@@ -4,15 +4,14 @@ from contextlib import contextmanager
 from os import path
 from shutil import rmtree
 
+import pytest
+
 from galaxy.tools.toolbox import watcher
 from galaxy.util import bunch
 
 
+@pytest.mark.skipif(not watcher.can_watch, reason="watchdog not available")
 def test_watcher():
-    if not watcher.can_watch:
-        from nose.plugins.skip import SkipTest
-        raise SkipTest()
-
     with __test_directory() as t:
         tool_path = path.join(t, "test.xml")
         toolbox = Toolbox()
@@ -32,23 +31,20 @@ def test_watcher():
         assert tool_watcher.observer is None
 
 
+@pytest.mark.skipif(not watcher.can_watch, reason="watchdog not available")
 def test_tool_conf_watcher():
-    if not watcher.can_watch:
-        from nose.plugins.skip import SkipTest
-        raise SkipTest()
-
     callback = CallbackRecorder()
     conf_watcher = watcher.get_tool_conf_watcher(callback.call)
     conf_watcher.start()
 
     with __test_directory() as t:
         tool_conf_path = path.join(t, "test_conf.xml")
-        with open(tool_conf_path, "w", 1) as t:
-            t.write("a")
+        with open(tool_conf_path, "w") as f:
+            f.write("a")
         conf_watcher.watch_file(tool_conf_path)
         time.sleep(2)
-        with open(tool_conf_path, 'wb', 0) as t:
-            t.write(b"b")
+        with open(tool_conf_path, "w") as f:
+            f.write("b")
         wait_for_reload(lambda: callback.called)
         conf_watcher.shutdown()
         assert conf_watcher.thread is None

From e7abcb030b4b92576fe91caa841c9200d1b7b344 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 6 Jan 2020 19:08:02 +0100
Subject: [PATCH 090/101] Fix integration test case for database set through
 env var

---
 test/integration/test_scripts.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/integration/test_scripts.py b/test/integration/test_scripts.py
index bf73fb83cb2..bd115a6c03b 100644
--- a/test/integration/test_scripts.py
+++ b/test/integration/test_scripts.py
@@ -184,7 +184,10 @@ class ScriptsIntegrationTestCase(integration_util.IntegrationTestCase):
         config_dir = self.config_dir
         path = os.path.join(config_dir, "galaxy.yml")
         self._test_driver.temp_directories.extend([config_dir])
+        config = self._raw_config
+        # Update config dict with database_connection, which might be set through env variables
+        config['database_connection'] = self._app.config.database_connection
         with open(path, "w") as f:
-            yaml.dump({"galaxy": self._raw_config}, f)
+            yaml.dump({"galaxy": config}, f)
 
         return path

From 5824a734edc3130fca087b45d9132f9ec82f757d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Jan 2020 11:23:36 +0100
Subject: [PATCH 091/101] Use pytest.mark.skip, shows failure reason with -rxXs

---
 lib/galaxy_test/driver/integration_util.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy_test/driver/integration_util.py b/lib/galaxy_test/driver/integration_util.py
index 6dbfe169654..59e3ef17b86 100644
--- a/lib/galaxy_test/driver/integration_util.py
+++ b/lib/galaxy_test/driver/integration_util.py
@@ -31,7 +31,7 @@ def skip_if_jenkins(cls):
 def skip_unless_executable(executable):
     if which(executable):
         return _identity
-    return skip("PATH doesn't contain executable %s" % executable)
+    return pytest.mark.skip("PATH doesn't contain executable %s" % executable)
 
 
 def skip_unless_docker():
@@ -50,7 +50,7 @@ def skip_unless_fixed_port():
     if os.environ.get("GALAXY_TEST_PORT_RANDOM") != "1":
         return _identity
 
-    return skip("GALAXY_TEST_PORT must be set for this test.")
+    return pytest.mark.skip("GALAXY_TEST_PORT must be set for this test.")
 
 
 class IntegrationInstance(UsesApiTestCaseMixin):

From 797fc57b0ab60737570a8c9bd1985b9162d8b13a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 9 Jan 2020 11:10:02 +0100
Subject: [PATCH 092/101] Decorate class to skip, not class setup method

---
 test/integration/test_cli_runners.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index fb464bfa584..7ac42b5f333 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -12,11 +12,9 @@ from galaxy_test.base.ssh_util import generate_ssh_keys
 from galaxy_test.driver import integration_util
 from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
 
-
 RemoteConnection = collections.namedtuple('remote_connection', ['hostname', 'username', 'port', 'private_key', 'public_key'])
 
 
-@integration_util.skip_unless_docker()
 def start_ssh_docker(container_name, jobs_directory, port=10022, image='agaveapi/slurm'):
     ssh_keys = generate_ssh_keys()
     START_SLURM_DOCKER = ['docker',
@@ -77,6 +75,7 @@ def cli_job_config(remote_connection, shell_plugin='ParamikoShell', job_plugin='
     return job_conf.name
 
 
+@integration_util.skip_unless_docker()
 class BaseCliIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
 
     @classmethod

From b58bf622523d2ed017f700095783b78d6d5c5332 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 9 Jan 2020 14:07:29 +0100
Subject: [PATCH 093/101] Print output when exception occurs

---
 test/integration/test_scripts.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/test/integration/test_scripts.py b/test/integration/test_scripts.py
index bd115a6c03b..b718f1ec6ca 100644
--- a/test/integration/test_scripts.py
+++ b/test/integration/test_scripts.py
@@ -178,7 +178,12 @@ class ScriptsIntegrationTestCase(integration_util.IntegrationTestCase):
         clean_env = {
             "PATH": os.environ.get("PATH", None),
         }  # Don't let testing environment variables interfere with config.
-        return unicodify(subprocess.check_output(cmd, cwd=cwd, env=clean_env))
+        try:
+            return unicodify(subprocess.check_output(cmd, cwd=cwd, env=clean_env))
+        except Exception as e:
+            if isinstance(e, subprocess.CalledProcessError):
+                raise Exception("%s\nOutput was:\n%s" % (unicodify(e), e.output))
+            raise
 
     def write_config_file(self):
         config_dir = self.config_dir

From 1c27a3021e129bbd37b6423c51836ec1e32c16ba Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Thu, 9 Jan 2020 17:20:54 +0100
Subject: [PATCH 094/101] Rename @erasche to @hexylena and correct
 inconsistencies

---
 CONTRIBUTORS.md                               |  2 +-
 .../interactive_environments.svg              |  2 +-
 doc/source/dev/interactive_environments.rst   |  2 +-
 doc/source/releases/15.05.rst                 | 20 ++++++------
 doc/source/releases/15.07.rst                 | 24 +++++++-------
 doc/source/releases/15.07_announce.rst        | 16 +++++-----
 doc/source/releases/15.10.rst                 | 24 +++++++-------
 doc/source/releases/16.01.rst                 | 24 +++++++-------
 doc/source/releases/16.04.rst                 | 14 ++++----
 doc/source/releases/16.07.rst                 | 18 +++++------
 doc/source/releases/16.10.rst                 |  6 ++--
 doc/source/releases/17.01.rst                 | 14 ++++----
 doc/source/releases/17.05.rst                 | 18 +++++------
 doc/source/releases/17.09.rst                 | 32 +++++++++----------
 doc/source/releases/17.09_announce.rst        |  2 +-
 doc/source/releases/18.01.rst                 | 18 +++++------
 doc/source/releases/18.05.rst                 | 12 +++----
 doc/source/releases/18.05_announce.rst        |  2 +-
 doc/source/releases/18.09.rst                 | 14 ++++----
 doc/source/releases/19.01.rst                 |  4 +--
 doc/source/releases/19.01_announce.rst        |  2 +-
 doc/source/releases/19.05.rst                 | 12 +++----
 doc/source/releases/19.05_announce.rst        |  2 +-
 23 files changed, 142 insertions(+), 142 deletions(-)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index 830f2384304..800d4762594 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -124,7 +124,7 @@ The following individuals have contributed code to Galaxy:
 * Chinmay Rao <chinmay@bx.psu.edu>
 * Matt Ralston <mrals89@gmail.com>
 * ramezrawas <ramezrawas@gmail.com>
-* Eric Rasche <esr@tamu.edu> <rasche.eric@gmail.com> <rasche.eric@yandex.ru>
+* Helena Rasche <helena.rasche@gmail.com>
 * Athos Ribeiro <athoscr@fedoraproject.org>
 * Andrew Robinson <Andrew.Robinson@latrobe.edu.au>
 * Devon Ryan <dpryan79@gmail.com>
diff --git a/doc/source/admin/special_topics/interactive_environments.svg b/doc/source/admin/special_topics/interactive_environments.svg
index 88f5de92c8d..55c81e4c55f 100644
--- a/doc/source/admin/special_topics/interactive_environments.svg
+++ b/doc/source/admin/special_topics/interactive_environments.svg
@@ -484,7 +484,7 @@
         <dc:title>Galaxy Jupyter Graphic</dc:title>
         <dc:creator>
           <cc:Agent>
-            <dc:title>Björn Grüning, Torsten Houwaart, Eric Rasche</dc:title>
+            <dc:title>Björn Grüning, Torsten Houwaart, Helena Rasche</dc:title>
           </cc:Agent>
         </dc:creator>
         <dc:language>en_US</dc:language>
diff --git a/doc/source/dev/interactive_environments.rst b/doc/source/dev/interactive_environments.rst
index 0f173bec0cd..0686a18c21d 100644
--- a/doc/source/dev/interactive_environments.rst
+++ b/doc/source/dev/interactive_environments.rst
@@ -553,4 +553,4 @@ If everything went well, at this point you should see a directory listing show u
 .. image:: interactive_environments_success.png
 
 If you find yourself encountering difficulties, the "Hello, World" IE is
-available in a `GitHub repo <https://github.com/erasche/hello-world-interactive-environment/releases/tag/v15.10>`__, and there are people on the IRC channel who can help debug.
+available in a `GitHub repo <https://github.com/hexylena/hello-world-interactive-environment/releases/tag/v15.10>`__, and there are people on the IRC channel who can help debug.
diff --git a/doc/source/releases/15.05.rst b/doc/source/releases/15.05.rst
index 5de92f86cfc..7877b56a6c6 100644
--- a/doc/source/releases/15.05.rst
+++ b/doc/source/releases/15.05.rst
@@ -55,10 +55,10 @@ Enhancements
   `Pull Request 143`_
 * Add NCBI SRA datatype - thanks to Matt Shirley. `Pull Request 87`_
 * Stronger toolbox filtering. `Pull Request 119`_
-* Allow updating Tool Shed repositories via the API - thanks to Eric Rasche.
+* Allow updating Tool Shed repositories via the API - thanks to Helena Rasche.
   `Pull Request 30`_
 * Expose category list in show call for Tool Shed repositories - thanks to
-  Eric Rasche. `Pull Request 29`_
+  Helena Rasche. `Pull Request 29`_
 * Add API endpoint to create Tool Shed repositories. `Pull Request 2`_
 * Do not configure Galaxy to use the test Tool Shed by default.
   `Pull Request 38`_
@@ -67,7 +67,7 @@ Enhancements
 * Enhance multi-selection widgets to allow key combinations ``Ctrl-A``
   and ``Ctrl-X``. e8564d7_, `Trello <https://trello.com/c/3QhD5l5h>`__
 * New, consistent button for displaying citation BibTeX. `Pull Request 19`_
-* Improved ``README`` reflecting move to Github - thanks in part to Eric
+* Improved ``README`` reflecting move to Github - thanks in part to Helena
   Rasche. `PR #2 (old repo)
   <https://github.com/galaxyproject/galaxy-beta1/pull/2>`__,
   226e826_, 2650d09_, 7d5dde8_
@@ -87,14 +87,14 @@ Enhancements
 * Preserve spaces in ``Count1`` tool (``tools/filters/uniq.xml``) - thanks to
   Peter Cock. `Pull Request 13`_
 * `Interactive Environments`_ improvements and fixes from multiple
-  developers including Eric Rasche and  Björn Grüning. `Pull Request 69`_,
+  developers including Helena Rasche and  Björn Grüning. `Pull Request 69`_,
   `Pull Request 73`_, `Pull Request 131`_, `Pull Request 135`_,
   `Pull Request 152`_, `Pull Request 197`_
-* Enable multi-part upload for exporting files with the GenomeSpace export 
+* Enable multi-part upload for exporting files with the GenomeSpace export
   tool. `Pull Request 74`_, `Trello <https://trello.com/c/28O46iln>`__
 * Large refactoring, expansion, and increase in test coverage for "managers".
   `Pull Request 76`_
-* Improved display of headers in tool help. 157eba6_, 
+* Improved display of headers in tool help. 157eba6_,
   `Biostar <https://biostar.usegalaxy.org/p/11211/>`__
 * Uniform configuration of "From" field for sent emails - thanks to Nicola
   Soranzo. `Pull Request 23`_
@@ -112,8 +112,8 @@ Enhancements
 * Add test tool demonstrating citing a Github repository. 65def71_
 * Add option to track all automated changes to the integrated tool panel.
   10bb492_
-* Make tool version explicit in all distribution tool - thanks to Peter Cock. 
-  `Pull Request 14`_. 
+* Make tool version explicit in all distribution tool - thanks to Peter Cock.
+  `Pull Request 14`_.
 * Relocate the external metadata setting script. `Pull Request 7`_
 * Parameterize script used to pull new builds from the UCSC Browser.
   e4e5df0_
@@ -141,7 +141,7 @@ Fixes
   properly. `Pull Request 198`_, `Trello <https://trello.com/c/WVlaLsOh>`__
 * Fix scatter plot API communications for certain proxied Galaxy instances -
   thanks to @yhoogstrate. `Pull Request 89`_
-* Fix bug in collectl_ job metrics plugin - thanks to Carrie Ganote. 
+* Fix bug in collectl_ job metrics plugin - thanks to Carrie Ganote.
   `Pull Request 231`_
 * Fix late validation of tool parameters. `Pull Request 115`_
 * Fix ``fasta_to_tabular_converter.py`` (for implicit conversion) - thanks to
@@ -161,7 +161,7 @@ Fixes
 * Fix to remove redundant version ids in tool version selector.
   `Pull Request 244`_
 * Fix for downloading metadata files. `Pull Request 234`_
-* Fix for history failing to render if it contains more exotic dataset 
+* Fix for history failing to render if it contains more exotic dataset
   collection types. `Pull Request 196`_
 * Fixes for BaseURLToolParameter. `Pull Request 247`_
 * Fix to suppress pysam binary incompatibility warning when using datatypes
diff --git a/doc/source/releases/15.07.rst b/doc/source/releases/15.07.rst
index b27322668f0..2c6d7676a61 100644
--- a/doc/source/releases/15.07.rst
+++ b/doc/source/releases/15.07.rst
@@ -12,7 +12,7 @@ Enhancements
 .. enhancements
 
 * Interactive environment (IE) framework updates including a new IE for RStudio.
-  (Thanks to a team effort spearheaded by `@erasche <https://github.com/erasche>`__.)
+  (Thanks to a team effort spearheaded by `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 229`_, `Pull Request 230`_
 * Rework workflow editor to use newer tool form components and allow construction
   of workflows with tools explicitly producing output collections.
@@ -27,8 +27,8 @@ Enhancements
   focus on the API documentation. (Thanks to `@nsoranzo
   <https://github.com/nsoranzo>`__.)
   `Pull Request 399`_, `Pull Request 405`_
-* Add EDAM IDs to Galaxy datatypes. (Thanks to a team effort initiated by `@erasche
-  <https://github.com/erasche>`__.)
+* Add EDAM IDs to Galaxy datatypes. (Thanks to a team effort initiated by `@hexylena
+  <https://github.com/hexylena>`__.)
   `Pull Request 80`_, `Pull Request 342`_
 * Improved reports app sorting and bug fixes thanks to
   Daniel Bouchard (`@Airistotal <https://github.com/Airistotal>`__). Even more
@@ -66,11 +66,11 @@ Enhancements
   <https://github.com/Christian-B>`__.) `Pull Request 441`_
 * Add emboss datatypes (previously migrated to Tool Shed). (Thanks to `@bgruening
   <https://github.com/bgruening>`__.) `Pull Request 148`_
-* Add new Hmmer & Stockholm datatypes. (Thanks to `@erasche
-  <https://github.com/erasche>`__.) `Pull Request 218`_
-* Add an RData datatype. (Thanks to `@erasche
-  <https://github.com/erasche>`__.) `Pull Request 239`_
-* Add mauve XMFA datatype (Thanks to `@erasche <https://github.com/erasche>`__.)
+* Add new Hmmer & Stockholm datatypes. (Thanks to `@hexylena
+  <https://github.com/hexylena>`__.) `Pull Request 218`_
+* Add an RData datatype. (Thanks to `@hexylena
+  <https://github.com/hexylena>`__.) `Pull Request 239`_
+* Add mauve XMFA datatype (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 270`_
 * Add ConnectivityTable (\*.ct) (RNA 2D structure format) datatype.
   (Thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
@@ -114,10 +114,10 @@ Enhancements
   `Pull Request 186`_
 * Switch visualizations registry to entry_point config definition for 
   built-in visualizations. `Pull Request 243`_
-* Set default value for IE sig proxy (Thanks to `@erasche
-  <https://github.com/erasche>`__.) `Pull Request 197`_
+* Set default value for IE sig proxy (Thanks to `@hexylena
+  <https://github.com/hexylena>`__.) `Pull Request 197`_
 * Other smaller interactive environment updates. (Thanks to
-  `@erasche <https://github.com/erasche>`__.)
+  `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 412`_
 * Refuse to load interactive debugging middleware under uwsgi.
   `Pull Request 200`_
@@ -179,7 +179,7 @@ Enhancements
 * Add configurable Docker hostname (Thanks to `@bgruening
   <https://github.com/bgruening>`__.) `Pull Request 356`_
 * Improve XML styling of display applications. 
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 364`_
 * README improvements including - adding shields for Biostar, IRC, and Travis.
   `Pull Request 368`_, `Pull Request 369`_
diff --git a/doc/source/releases/15.07_announce.rst b/doc/source/releases/15.07_announce.rst
index ca02d6dc81e..ef7e21708ad 100644
--- a/doc/source/releases/15.07_announce.rst
+++ b/doc/source/releases/15.07_announce.rst
@@ -10,7 +10,7 @@ Highlights
 
 **Interactive Environments**
   The interactive environments (IE) framework features several updates this release
-  and Galaxy is now distributed with a new IE for RStudio implemented by Eric Rasche.
+  and Galaxy is now distributed with a new IE for RStudio implemented by Helena Rasche.
 
 **Workflow Editor Enhancements**
   The workflow editor has been significantly revamped - it now uses newer tool form
@@ -18,9 +18,9 @@ Highlights
   output collections.
 
 **Policies for Committers and Pull Requests**
-  The process for adding committers to the project and fielding pull requests has 
+  The process for adding committers to the project and fielding pull requests has
   been formalized and documented in the source code. Three new committers have been
-  added to the project - Björn Grüning, Nicola Soranzo, and Eric Rasche.
+  added to the project - Björn Grüning, Nicola Soranzo, and Helena Rasche.
 
 
 `Github <https://github.com/galaxyproject/galaxy>`__
@@ -28,17 +28,17 @@ Highlights
 
 New
   .. code-block:: shell
-  
+
       % git clone -b master https://github.com/galaxyproject/galaxy.git
 
 Update to latest stable release
   .. code-block:: shell
-  
+
       % git checkout master && pull --ff-only origin master
 
 Update to exact version
   .. code-block:: shell
-  
+
       % git checkout v15.07
 
 
@@ -47,8 +47,8 @@ Update to exact version
 
 Upgrade
   .. code-block:: shell
-  
-      % hg pull 
+
+      % hg pull
       % hg update latest_15.07
 
 
diff --git a/doc/source/releases/15.10.rst b/doc/source/releases/15.10.rst
index 3ff09495280..5e517291f41 100644
--- a/doc/source/releases/15.10.rst
+++ b/doc/source/releases/15.10.rst
@@ -32,10 +32,10 @@ Enhancements
 * Add ``regex_replace`` tool dependency install action.
   `Pull Request 457`_
 * Document Galaxy interactive environments (GIEs).
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 803`_
-* Explicit project procedure language on reversions and WIP. (Thanks to `@erasche
-  <https://github.com/erasche>`__.)
+* Explicit project procedure language on reversions and WIP. (Thanks to `@hexylena
+  <https://github.com/hexylena>`__.)
   `Pull Request 556`_
 * Readme improvemenets - GitHub issues, security email contact and CI testing
   (Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
@@ -97,7 +97,7 @@ Enhancements
 * Expose tool config file path to admins via the API.
   `Pull Request 652`_
 * Add Galaxy developer documentation section to docs.
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 654`_
 * Password reset improvements.
   `Pull Request 655`_
@@ -115,7 +115,7 @@ Enhancements
 * Set a default value for copy history dialog radio input (to copy *all*).
   `Pull Request 693`_
 * Remove various code duplication.
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 694`_
 * Use ``setup.py`` for Python all installations during dependency installation.
   (Thanks to `@bgruening <https://github.com/bgruening>`__.)
@@ -163,13 +163,13 @@ Enhancements
   <https://github.com/scholtalbers>`__.)
   `Pull Request 777`_
 * Unify the docker command, command_inject, and command_wrapper (Thanks to
-  `@erasche <https://github.com/erasche>`__.)
+  `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 782`_
 * Test case to prevent regression of `#753
   <https://github.com/galaxyproject/galaxy/issues/753>`__.
   `Pull Request 784`_
 * Refactor interactive environment launching to use Docker's ``-P`` option.
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 790`_
 * Print ``has_metrics`` class name instead of object memory address. (Thanks to
   `@nsoranzo <https://github.com/nsoranzo>`__.)
@@ -205,7 +205,7 @@ Enhancements
   `Pull Request 847`_
 * Remove unused ``echo`` tool
   `Pull Request 848`_
-* Update interactive environments for this release. (Thanks to `@erasche <https://github.com/erasche>`__.)
+* Update interactive environments for this release. (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 849`_
 * Enhancements for IPython interactive environment allowing it run in certain
   deployments.
@@ -296,10 +296,10 @@ Fixes
   (Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
   `Pull Request 596`_
 * Fix bug in reload API where id wasn't recognised.
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 619`_
 * Correct typo in tool shed action handler code.
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 561`_
 * Small fixes for UI functional tests.
   `Pull Request 485`_, `Pull Request 487`_
@@ -404,7 +404,7 @@ Fixes
 * Tool form error messages and rerun fixes.
   `Pull Request 766`_
 * Quote value to fix configparser error in interactive environments.
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 775`_
 * Fix upload event binding.
   `Pull Request 778`_
@@ -425,7 +425,7 @@ Fixes
   (Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
   `Pull Request 838`_
 * Expose all API keys to admins under ``REMOTE_USER``.
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 873`_
 * Various fixes for data libraries.
   `Pull Request 878`_
diff --git a/doc/source/releases/16.01.rst b/doc/source/releases/16.01.rst
index 1fd79ee567e..2534f6eb049 100644
--- a/doc/source/releases/16.01.rst
+++ b/doc/source/releases/16.01.rst
@@ -58,7 +58,7 @@ Enhancements
   `Pull Request 1405`_
 * Add search on username/any for API calls to user and use Select2 for sharing
   workflows/pages/histories
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1111`_
 * Improve masthead and scratchbook UI and architecture.
   `Pull Request 1407`_, `Pull Request 1424`_
@@ -113,7 +113,7 @@ Enhancements
   environment variables.
   `Pull Request 564`_, `Pull Request 889`_
 * Reorganize history menu
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 985`_
 * Look up installed tools from different toolshed(s)
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
@@ -141,7 +141,7 @@ Enhancements
   (thanks to `@scholtalbers <https://github.com/scholtalbers>`__.)
   `Pull Request 912`_
 * Add an API script to upload directory as a data library
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 918`_
 * Enable dockerized toolshed tests.
   `Pull Request 942`_
@@ -197,7 +197,7 @@ Enhancements
 * Use common exceptions in tools.
   `Pull Request 874`_
 * Refactor the remote user middleware for complexity
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 875`_
 * Allowed for capitalized package names such as R in unlinked tool shed
   dependency resolver
@@ -221,7 +221,7 @@ Enhancements
 * Add Workflow editor UI for step labels.
   `Pull Request 1251`_
 * Ease the grunt uglify process
-  (Thanks to `@erasche <https://github.com/erasche>`__.)
+  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1238`_
 * Add beta run workflow form based on the newer tool form code.
   `Pull Request 1249`_
@@ -260,7 +260,7 @@ Enhancements
 * Unify and abstract code for checking if file looks like a tool definition.
   `Pull Request 1368`_
 * Added hashes to pip requirements file
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1393`_
 * Interactive environment updates
   (thanks to `@bgruening <https://github.com/bgruening>`__.)
@@ -376,10 +376,10 @@ Fixes
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
   `Pull Request 863`_
 * Bump version of sqlite3 in nodejs proxy
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 866`_
 * Expose API keys to admins under ``REMOTE_USER``
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 872`_
 * Bug fix for tool shed repository API
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
@@ -394,7 +394,7 @@ Fixes
   error.
   `Pull Request 908`_
 * Bug fix for condor runner changes made this release cycle
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 909`_
 * Change user preference datatype to text.
   `Pull Request 916`_
@@ -404,14 +404,14 @@ Fixes
 * Revise tool URL building.
   `Pull Request 947`_
 * Fix for code checking if a file seems to a tool definition file
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 949`_
 * Fix base panels to include scripts as the last element of the body.
   `Pull Request 969`_
 * Grid batch operation fixes.
   `Pull Request 971`_
 * Fix extra files path URL problem.
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 991`_
 * Fixes broken env-var declarations for tools with weird chars in their names
   (thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
@@ -485,7 +485,7 @@ Fixes
 * Fix for creating workflow outputs on initial workflow upload.
   `Pull Request 1330`_
 * Don't query on unencoded IDs for error form
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1340`_
 * If ``GALAXY_SLOTS`` is defined in the environment, use it for the local runner.
   `Pull Request 1346`_
diff --git a/doc/source/releases/16.04.rst b/doc/source/releases/16.04.rst
index c3bc54c31fc..41b68a87d10 100644
--- a/doc/source/releases/16.04.rst
+++ b/doc/source/releases/16.04.rst
@@ -38,7 +38,7 @@ Enhancements
 * disable 'hg push' to TS repositories
   `Pull Request 2033`_
 * Generic GIE Launcher, GIE Image Chooser, multiple datasets
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1403`_
 * The entire Python source code is now continuously checked with flake8 for
   PEP-8 style consistency and common errors. The last 3500 errors were fixed in
@@ -49,7 +49,7 @@ Enhancements
 .. enhancement
 
 * Implement new GIE proxy
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1807`_
 * Workflow editor overview click navigation
   `Pull Request 1843`_
@@ -58,7 +58,7 @@ Enhancements
 * datalibs: introduce folder management; fix various glitches; refactor
   `Pull Request 1562`_
 * Add makefile target for release process
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1433`_
 * libraries: provide select all/none options when importing
   `Pull Request 1970`_
@@ -152,7 +152,7 @@ Enhancements
 * Implement dataset empty input validator.
   `Pull Request 1808`_
 * Makefile help target + formatting
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1824`_
 * Add license and repository information to package.json.
   `Pull Request 1829`_
@@ -228,7 +228,7 @@ Enhancements
 * make new beta TS tools installation via API configurable
   `Pull Request 2088`_
 * Patch in visual separation of section parameters
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2091`_
 * Add sample supervisor config
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
@@ -447,7 +447,7 @@ Fixes
 * Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako .
   `Pull Request 1972`_
 * Remove duplicate help target
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 1980`_
 * Fix booleans in workflow editor
   `Pull Request 1990`_
@@ -477,7 +477,7 @@ Fixes
 * Show sections in workflow run
   `Pull Request 2087`_
 * Workflow section fix backport
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2092`_
 * Run external local set_metadata jobs in the job's working directory
   `Pull Request 2094`_
diff --git a/doc/source/releases/16.07.rst b/doc/source/releases/16.07.rst
index 911f6d0b029..af7dee0c852 100644
--- a/doc/source/releases/16.07.rst
+++ b/doc/source/releases/16.07.rst
@@ -35,7 +35,7 @@ Highlighted Enhancements
   (thanks to `@BalthazarPavot <https://github.com/BalthazarPavot>`__.)
   `Pull Request 2664`_
 * Nicer bug report emails
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2143`_
 * Tools with auto_format='true' now connectable in workflow editor
   (thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
@@ -160,7 +160,7 @@ Enhancements
 * Remove backported importlib and ordereddict.
   `Pull Request 2380`_
 * Note on updating tool testing
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2381`_
 * Docker swarm support for Galaxy Interactive Environments (GIEs)
   `Pull Request 2386`_, `Pull Request 2392`_
@@ -238,7 +238,7 @@ Enhancements
 * Allow users to purge datasets by default.
   `Pull Request 2553`_
 * Add Jupyter IE to the allowed visualizations for BAM datasets
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2572`_
 * Python3: port 215 files
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__, `@tshtatland <https://github.com/tshtatland>`__, `@xiaoqian1984 <https://github.com/xiaoqian1984>`__, `@alanryanwang <https://github.com/alanryanwang>`__ and `@ericenns <https://github.com/ericenns>`__.)
@@ -392,14 +392,14 @@ Fixes
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
   `Pull Request 2223`_
 * Sanitize poorly escaped input value in run workflow form
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2231`_
 * Multi-data collection reductions in repeat blocks are broken.
   `Pull Request 2233`_
 * Encode collection reduce in serializable fashion
   `Pull Request 2241`_
 * Cast everything to a string
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2252`_
 * Use standard model.orm.now for toolshed's password reset token datetime math
   `Pull Request 2261`_
@@ -426,7 +426,7 @@ Fixes
 * Build: remove redundant webpack step in makefile
   `Pull Request 2327`_
 * Unicodify has different semantics to str, causing bug reporter bug
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2336`_
 * Wrap statsd timing middleware more closely around the core application
   `Pull Request 2342`_
@@ -441,7 +441,7 @@ Fixes
   (thanks to `@bgruening <https://github.com/bgruening>`__.)
   `Pull Request 2394`_
 * Check variable's presence before calling str methods
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2408`_
 * UI, history: correctly handle index API defaults
   `Pull Request 2413`_
@@ -482,10 +482,10 @@ Fixes
 * Initialize objectstore for fix_set_dataset_sizes script
   `Pull Request 2544`_
 * Fix old bug in non-allowed_images.yml GIEs
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2548`_
 * More defensive GIE Proxying
-  (thanks to `@erasche <https://github.com/erasche>`__.)
+  (thanks to `@hexylena <https://github.com/hexylena>`__.)
   `Pull Request 2552`_
 * Fixes for showing min/max labels in Trackster.
   `Pull Request 2555`_
diff --git a/doc/source/releases/16.10.rst b/doc/source/releases/16.10.rst
index 7ffb4f35fc1..0d582855502 100644
--- a/doc/source/releases/16.10.rst
+++ b/doc/source/releases/16.10.rst
@@ -221,7 +221,7 @@ Enhancements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 3033`_
 * Remove outdated warning on ID_SECRET
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3046`_
 * Add Galaxy architecture slides documentation to project.
   `Pull Request 3060`_, `Pull Request 3091`_
@@ -330,10 +330,10 @@ Fixes
   (thanks to `@sszakony <https://github.com/sszakony>`__).
   `Pull Request 2808`_
 * Allow NodeJS proxy to do reverse proxying
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 2817`_
 * Fixes for the RStudio interactive environment
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 2818`_
 * Acquire lock before attempting to install conda
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
diff --git a/doc/source/releases/17.01.rst b/doc/source/releases/17.01.rst
index 9b8fbfc723f..d5fb6489487 100644
--- a/doc/source/releases/17.01.rst
+++ b/doc/source/releases/17.01.rst
@@ -50,20 +50,20 @@ Enhancements
   `Pull Request 3217`_
 * Many improvements to the job information page - including
   exposing certain job metrics to non-admin users
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3344`_, `Pull Request 3256`_,
   `Pull Request 3340`_
 * Formalize decision to increase time between releases to four months. The next release
   will be 17.05.
   `Pull Request 3271`_
 * Add API endpoint to determine who the current user is
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3423`_
 * Extend API version information for Docker-based Galaxy instances
   (thanks to `@manabuishii <https://github.com/manabuishii>`__).
   `Pull Request 3411`_
 * Implement a more complete Genbank datatype with sniffer
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3339`_
 * Add additional image datatypes
   (thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__).
@@ -114,7 +114,7 @@ Enhancements
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 3328`_
 * Allow admins to see API keys under when using remote user authentication from proxies.
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3338`_
 * Limit adjusting Galaxy's Python environment to legacy tools
   (discussed in Deprecation Notices section of release notes).
@@ -149,7 +149,7 @@ Fixes
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 3215`_
 * Fix user table header in admin view
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3200`_
 * Fix to adjust masthead and tool search.
   `Pull Request 3055`_
@@ -193,10 +193,10 @@ Fixes
   (thanks to `@manabuishii <https://github.com/manabuishii>`__).
   `Pull Request 3409`_
 * Fix login functionality for RStudio IEs
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3414`_
 * Fix accidental email exposure during history sharing
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3417`_
 * Fix UX problem when sharing objects with users.
   `Pull Request 3373`_
diff --git a/doc/source/releases/17.05.rst b/doc/source/releases/17.05.rst
index 803af07b415..f4aaf560071 100644
--- a/doc/source/releases/17.05.rst
+++ b/doc/source/releases/17.05.rst
@@ -38,7 +38,7 @@ Enhancements
   (thanks to `@anuprulez <https://github.com/anuprulez>`__ and `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 3601`_
 * Add script to encode or decode the IDs that Galaxy exposes to users and admins
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3622`_
 * Support Docker Engine swarm mode for Interactive Environments.
   `Pull Request 3666`_
@@ -50,7 +50,7 @@ Enhancements
 * Container interface abstraction.
   `Pull Request 3863`_
 * Graphite support
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3964`_
 * Normalize the handling of steps and missing tools for the workflow editor.
   `Pull Request 3181`_
@@ -187,7 +187,7 @@ Enhancements
 * i18n improvements and French localization.
   `Pull Request 3762`_
 * Should exit immediately to avoid index error
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3770`_
 * Made collection operations help sections slightly more readable.
   `Pull Request 3784`_
@@ -258,7 +258,7 @@ Enhancements
 * Change 'User' menu to 'Login or Register' for anonymous users.
   `Pull Request 3955`_
 * Stats docs
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3968`_
 * Enhance filenames with collection context when downloading datasets from
   GUI.
@@ -270,7 +270,7 @@ Enhancements
 * Update Jupyter image to 17.05 .
   `Pull Request 4007`_
 * Inline CSS in error report email
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3445`_
 * Improve routing for user preference views.
   `Pull Request 3446`_
@@ -340,7 +340,7 @@ Fixes
 * Fix margin style values for color picker element.
   `Pull Request 3965`_
 * 17.05 rstudio fixes / one small GIE fix
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3975`_
 * Fix transiently failing Selenium upload test.
   `Pull Request 3587`_
@@ -480,7 +480,7 @@ Fixes
 * Fix multiple collection reductions on multiple data parameters.
   `Pull Request 3875`_
 * Fix inability for viz to raise loading with non-ascii messages
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 3881`_
 * Fix new history endpoint providing custom builds metadata.
   `Pull Request 3887`_
@@ -525,7 +525,7 @@ Fixes
 * Use the configured tool_path when loading data managers.
   `Pull Request 3989`_
 * Typo in remote user / user preferences exception
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4015`_
 * Fix setting up explicit container resolution from a container resolution
   config file.
@@ -546,7 +546,7 @@ Fixes
 * Fix for S3ObjectStore _clean_cache method.
   `Pull Request 4055`_
 * Correct webhooks to use Galaxy.root and be compatible with proxy_prefix
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4065`_
 * Fix global grid action event handler.
   `Pull Request 4068`_
diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst
index da30a7417c6..d76a3e701d1 100644
--- a/doc/source/releases/17.09.rst
+++ b/doc/source/releases/17.09.rst
@@ -80,7 +80,7 @@ Enhancements
   `Pull Request 4466`_
 * Refactor tool error reporting into plugins and implement a new
   plugin for `influxdb <https://www.influxdata.com/>`__
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4305`_, `Pull Request 4533`_
 * Implement second toolshed installation UX targetting the API.
   `Pull Request 3626`_
@@ -120,10 +120,10 @@ Enhancements
   (thanks to `@arbernard <https://github.com/arbernard>`__).
   `Pull Request 4489`_
 * Nicer tool click targets for toolbox
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4470`_
 * Implement a "plain" bootstrap theme for the UX
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4470`_
 * Add Selenium tests for the "saved histories", "published histories", and
   "custom builds"
@@ -136,7 +136,7 @@ Enhancements
   `Pull Request 4576`_, `Pull Request 4561`_, `Pull Request 4531`_, `Pull Request 4564`_,
   `Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_, `Pull Request 4042`_
 * Prevent graphite from dying loudly
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4036`_
 * Updated parameters check for OpenID
   (thanks to `@VJalili <https://github.com/VJalili>`__).
@@ -164,12 +164,12 @@ Enhancements
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 4096`_
 * Security policy
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4113`_
 * Improved styling of workflow list.
   `Pull Request 4138`_
 * Swap over all URLs to new wiki location
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4141`_
 * Documentation fixes and improvements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -238,10 +238,10 @@ Enhancements
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 4271`_
 * More uniform backend code for generating page titles
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4272`_, `Pull Request 4578`_
 * Fix blockquote>p sizing
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4273`_
 * Expose more user properties to admins via the API.
   `Pull Request 4274`_
@@ -256,7 +256,7 @@ Enhancements
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 4284`_
 * Improve security via local network access restrictions
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4289`_
 * Enhancement for Phyloviz viz plugin
   (thanks to `@bgruening <https://github.com/bgruening>`__).
@@ -288,7 +288,7 @@ Enhancements
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 4368`_, `Pull Request 4380`_
 * Galactic Radio Telescope Update
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4376`_
 * Show minimum required galaxy version in tool shed and galaxy installation
   process
@@ -308,7 +308,7 @@ Enhancements
 * Generalize allow_library_path_paste to allow_path_paste.
   `Pull Request 4404`_
 * Small GRT bugfixes
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4408`_
 * Update conda channel order to sync with Bioconda
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -335,7 +335,7 @@ Enhancements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 4456`_
 * Improvements to `Sentry <https://sentry.io/welcome/>`__ integration
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4457`_, `Pull Request 4471`_
 * Fix for GIEs to not automatically uppercase environment variables
   (thanks to `@xgaia <https://github.com/xgaia>`__).
@@ -359,7 +359,7 @@ Enhancements
 * Minor copy datasets dialog improvement.
   `Pull Request 4486`_
 * 41% reduction in freiburg galaxy startup time
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4495`_
 * Allow paramiko cli to recover from ssh timeout
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -473,7 +473,7 @@ Enhancements
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 4598`_
 * Remove various unreachable statements
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4603`_
 * Refactored a dataset variable to HDA
   (thanks to `@VJalili <https://github.com/VJalili>`__).
@@ -583,7 +583,7 @@ Fixes
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 4420`_
 * Some unicoding for local runner
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4426`_
 * Break connection in workflow editor if necessary
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -603,7 +603,7 @@ Fixes
 * Fix drag and drop from history for Firefox
   `Pull Request 4496`_
 * 2017-08 Security Patch
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4501`_
 * Fix history import if using symlink in database directory
   (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst
index cb9e14e9b29..708858fa4c8 100644
--- a/doc/source/releases/17.09_announce.rst
+++ b/doc/source/releases/17.09_announce.rst
@@ -141,7 +141,7 @@ Cross site scripting and session fixation
 
 Disclosed on the `mailing list <https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-August/025938.html>`__ in August 2017.
 
-Vulnerabilities were found by Eric Rasche and Manabu Ishii respectively. Detailed descriptions of these categories of vulnerabilities can be found at:
+Vulnerabilities were found by Helena Rasche and Manabu Ishii respectively. Detailed descriptions of these categories of vulnerabilities can be found at:
 
 - `<https://www.owasp.org/index.php/Cross-site_Scripting_(XSS)>`__
 - https://www.owasp.org/index.php/Session_fixation
diff --git a/doc/source/releases/18.01.rst b/doc/source/releases/18.01.rst
index f9bd8a0145e..549774b4547 100644
--- a/doc/source/releases/18.01.rst
+++ b/doc/source/releases/18.01.rst
@@ -45,7 +45,7 @@ Enhancements
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 4737`_
 * Implement a Github error report backend for
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4765`_
 * Add maintenance script to simplify setting up a cleanup cron job
   (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
@@ -136,7 +136,7 @@ Enhancements
 * Allow multiple simultaneous uploads via single POST.
   `Pull Request 4563`_
 * Various bits of proactive security-related hardening
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4604`_
 * Move test helper ``wait_for_dataset_collection`` for reuse
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -157,14 +157,14 @@ Enhancements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 4688`_
 * Nicer logging message for sentry
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4693`_
 * Use enumeration to provide history input index names.
   `Pull Request 4700`_
 * Cleanup delayed action in ``history-view.js``.
   `Pull Request 4704`_
 * Add logging during for script integrity exceptions
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4720`_
 * Fix to respect ``galaxy.json`` supplied metadata for empty outputs.
   `Pull Request 4722`_
@@ -187,7 +187,7 @@ Enhancements
   (thanks to `@pcm32 <https://github.com/pcm32>`__ and the `@phnmnl <https://github.com/phnmnl>`__ project).
   `Pull Request 4751`_
 * Send all influxdb stats to a single bucket
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 4758`_
 * PEP-8 fixes in random doctests.
   `Pull Request 4764`_
@@ -274,7 +274,7 @@ Enhancements
 * Document fastest way to iterate on client & client tests together.
   `Pull Request 5051`_
 * Support separate DSN for job sentry error reports
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5056`_
 * Build endpoint separation
   `Pull Request 5058`_
@@ -531,7 +531,7 @@ Fixes
   `Pull Request 5045`_
 * Safely handle possible ``None`` value encountered in processing and execution of
   post-job action arguments
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5050`_
 * Restore admin form routes.
   `Pull Request 5065`_
@@ -563,7 +563,7 @@ Fixes
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 5121`_
 * Fix attribute error that was missed during refactor of sentry
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5122`_
 * Fix connecting non-input modules to subworkflow inputs.
   `Pull Request 5140`_
@@ -664,7 +664,7 @@ Fixes
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 5357`_
 * Handle ``None`` in job owner in API
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5358`_
 * Fix form logic in deactivate or uninstall.
   `Pull Request 5363`_
diff --git a/doc/source/releases/18.05.rst b/doc/source/releases/18.05.rst
index 581b2a8cfe5..eab60edeb07 100644
--- a/doc/source/releases/18.05.rst
+++ b/doc/source/releases/18.05.rst
@@ -50,7 +50,7 @@ Enhancements
   `Pull Request 5479`_
 * Allow formatting `StatsD <https://github.com/etsy/statsd>`__ data for
   `InfluxDB <https://github.com/influxdata/influxdb>`__
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5742`_
 * Tool versions should follow `PEP 440 <https://www.python.org/dev/peps/pep-0440/>`__
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -145,10 +145,10 @@ Enhancements
 * Various improvements for API tests.
   `Pull Request 5697`_, `Pull Request 5699`_
 * Small log level improvement
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5715`_
 * Swap password checking for the constant time comparison algorithm
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5719`_
 * Upgrade clone failure logging to error
   (thanks to `@pvanheus <https://github.com/pvanheus>`__).
@@ -201,7 +201,7 @@ Enhancements
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 5924`_
 * Document Github bug reporter
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5928`_
 * Rewrite history structure display in `VueJS <https://vuejs.org/>`__
   (thanks to `@anuprulez <https://github.com/anuprulez>`__).
@@ -295,7 +295,7 @@ Fixes
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 5718`_
 * `Sentry <https://sentry.io/>`__ bug reports working for anonymous users
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5721`_
 * Add Galaxy `lib` directory to Python path for 2 scripts
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -366,7 +366,7 @@ Fixes
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 5917`_
 * Correct signal number in admin documentation
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5921`_
 * Fix error with data managers when trying to move_merge nonexistent
   extra_files dir
diff --git a/doc/source/releases/18.05_announce.rst b/doc/source/releases/18.05_announce.rst
index 551738931a5..571b6192d35 100644
--- a/doc/source/releases/18.05_announce.rst
+++ b/doc/source/releases/18.05_announce.rst
@@ -45,7 +45,7 @@ Highlights
 **GDPR Beta Mode**
   We introduce beta GDPR privacy mode. Admins can enable it to help them comply with the European Union law
   known as `General Data Protection Regulation <http://eur-lex.europa.eu/legal-content/en/TXT/?uri=CELEX:32016R0679>`__,
-  which goes into effect on May 25, 2018. Thanks to `@erasche <https://github.com/erasche>`__.
+  which goes into effect on May 25, 2018. Thanks to `@hexylena <https://github.com/hexylena>`__.
 
   `Pull Request 6069`_
 
diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index f133cae3d1a..d39ac530a90 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -54,7 +54,7 @@ Enhancements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6013`_
 * Add hostname metric
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 6021`_
 * Pause jobs with invalid inputs
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -88,7 +88,7 @@ Enhancements
 * Common dataset selector
   `Pull Request 6195`_
 * Permit numeric values of GRT instance ID in config
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 6200`_
 * Add the newick extension for the Newick datatype,
   (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
@@ -100,7 +100,7 @@ Enhancements
 * Charts filename download fix
   `Pull Request 6216`_
 * Wrap inputs in labels
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 6221`_
 * Workflow submit text links
   `Pull Request 6240`_
@@ -209,14 +209,14 @@ Enhancements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6469`_
 * Fix bug noticed in sentry
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 6474`_
 * Rulebuilder: Special case auto URL schema detection for SRA inputs.
   `Pull Request 6476`_
 * GRT: fix the upload logging init
   `Pull Request 6478`_
 * Add more information to the dataset template
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 6480`_
 * Use bootstrap vue classes for workflow import form
   `Pull Request 6489`_
@@ -344,7 +344,7 @@ Enhancements
 .. small_enhancement
 
 * Remove duplicate metric sending
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 6011`_
 * This strips the graphite-specific middleware
   `Pull Request 6018`_
@@ -670,7 +670,7 @@ Fixes
 * Redirect unidentified routes in admin panel
   `Pull Request 6551`_
 * Remove the sharing of toolbox in GRT
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 6553`_
 * Restore ``log_destination = stdout`` configuration option.
   `Pull Request 6555`_
diff --git a/doc/source/releases/19.01.rst b/doc/source/releases/19.01.rst
index e824f35d890..952205f9e8d 100644
--- a/doc/source/releases/19.01.rst
+++ b/doc/source/releases/19.01.rst
@@ -310,7 +310,7 @@ Fixes
 .. bug
 
 * Fixes to allow config schema to validate
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 5919`_
 * Patch `update.sh` to address dependency update issues on a macOS.
   `Pull Request 6694`_
@@ -414,7 +414,7 @@ Fixes
 * Fix resubmission on tool error detection.
   `Pull Request 7040`_
 * GRT: Rip out all parameters, round file sizes
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 7041`_
 * Pass through ``--daemon`` option to gunicorn
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
diff --git a/doc/source/releases/19.01_announce.rst b/doc/source/releases/19.01_announce.rst
index d8df49a5cf0..92bc2391b5c 100644
--- a/doc/source/releases/19.01_announce.rst
+++ b/doc/source/releases/19.01_announce.rst
@@ -21,7 +21,7 @@ Highlights
 **More Colorful Tags**
   Use consistently hashed randomized colors for history dataset name tags to increase visual
   distinction between tags, making it easier to track data flow in complex histories.
-  Thanks to `@erasche <https://github.com/erasche>`__.
+  Thanks to `@hexylena <https://github.com/hexylena>`__.
   `Pull Request 7072`_, `Pull Request 7081`_
 
 **Extensive Workflow Enhancements (continued)**
diff --git a/doc/source/releases/19.05.rst b/doc/source/releases/19.05.rst
index 160ab07a718..97592570e4a 100644
--- a/doc/source/releases/19.05.rst
+++ b/doc/source/releases/19.05.rst
@@ -46,7 +46,7 @@ Enhancements
   `Pull Request 7193`_, `Pull Request 7192`_, `Pull Request 7537`_,
   `Pull Request 7540`_, `Pull Request 7684`_, `Pull Request 7704`_
 * User facing release notes
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 7527`_
 * Implement dataset source and hash tracking.
   `Pull Request 7487`_, `Pull Request 4659`_, `Pull Request 7549`_
@@ -223,10 +223,10 @@ Enhancements
 * Automatically set ``cookie_path`` using ``url_for()``.
   `Pull Request 7404`_
 * Allow configuration location of user preferences extra configuration
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 7428`_
 * Add hover styling to target tool in tool panel
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 7437`_
 * Update Docker testing image
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -260,7 +260,7 @@ Enhancements
 * Refactor XSD output elements to share common output attributes.
   `Pull Request 7555`_
 * Improve linking between job conf handler assignment and documentation
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 7558`_
 * Refactor ``galaxy.web.security`` into ``galaxy.security.idencoding``.
   `Pull Request 7560`_
@@ -537,7 +537,7 @@ Fixes
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 7547`_
 * Correct db-self handler assignment method
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 7561`_
 * Fix database config doctests when env vars are in use for dburi
   `Pull Request 7562`_
@@ -549,7 +549,7 @@ Fixes
 * Update cloud imports to adhere with cloudbridge interface changes.
   `Pull Request 7586`_
 * Fix RStudio GIE
-  (thanks to `@erasche <https://github.com/erasche>`__).
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 7590`_, `Pull Request 7925`_
 * Fix styleguide.
   `Pull Request 7602`_
diff --git a/doc/source/releases/19.05_announce.rst b/doc/source/releases/19.05_announce.rst
index 557133feea8..7716266dfc8 100644
--- a/doc/source/releases/19.05_announce.rst
+++ b/doc/source/releases/19.05_announce.rst
@@ -14,7 +14,7 @@ Highlights
   oriented but will likely be even more so now. Features such as favoriting tools,
   improved workflow editor feedback, and an exciting new cellxgene GIE may have
   been featured in these release notes in the past but are now featured in the
-  user release notes instead. A huge thanks to `@erasche <https://github.com/erasche>`__
+  user release notes instead. A huge thanks to `@hexylena <https://github.com/hexylena>`__
   for getting the ball rolling on this initiative.
 
   Check out the `19.05 user release notes <https://docs.galaxyproject.org/en/release_19.05/releases/19.05_announce_user.html>`__.

From 9e9d08e98ee370a953b4b2d3ce45359df1f8d68b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 9 Jan 2020 18:17:10 +0100
Subject: [PATCH 095/101] Just make sure we're not using galaxy's isolated home
 dir

---
 test/integration/test_containerized_jobs.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index 9702f7b2622..6d6791e8ce8 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -62,7 +62,6 @@ class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, Ru
     job_config_file = DOCKERIZED_JOB_CONFIG_FILE
     build_mulled_resolver = 'build_mulled'
     container_type = 'docker'
-    default_container_home_dir = '/'
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -106,7 +105,7 @@ class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, Ru
         assert job_env.pwd.endswith("/working")
         # Should we change env_pass_through to just always include TMP and HOME for docker?
         # I'm not sure, if yes this would change.
-        assert job_env.home == self.default_container_home_dir, job_env.home
+        assert not job_env.home.endswith('/home')
 
     def test_build_mulled(self):
         if not which('docker'):
@@ -175,5 +174,3 @@ class SingularityJobsIntegrationTestCase(DockerizedJobsIntegrationTestCase):
     job_config_file = SINGULARITY_JOB_CONFIG_FILE
     build_mulled_resolver = 'build_mulled_singularity'
     container_type = 'singularity'
-    # singularity passes $HOME by default
-    default_container_home_dir = os.environ.get('HOME', '/')

From b09b7d53ce524eebde93db8c65d0a126d7f3ae75 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 9 Jan 2020 17:48:43 +0000
Subject: [PATCH 096/101] Write unicode strings to files opened with
 `io.open(path, w, encoding=utf-8)`

Otherwise under Python2 the following exception is raised:
```
$ python2
Python 2.7.17 (default, Nov  7 2019, 10:07:09)
[GCC 7.4.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import io
>>> with io.open('foo.txt', 'w', encoding='utf-8') as fh:
...     fh.write('foo')
...
Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
TypeError: write() argument 1 must be unicode, not str
```
---
 lib/galaxy/util/__init__.py |   2 +-
 scripts/grt/export.py       | 234 ++++++++++++++++++------------------
 2 files changed, 116 insertions(+), 120 deletions(-)

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 1e488ef1c4c..1dcb20b2303 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -271,7 +271,7 @@ def xml_to_string(elem, pretty=False):
     except TypeError as e:
         # we assume this is a comment
         if hasattr(elem, 'text'):
-            return "<!-- %s -->\n" % elem.text
+            return u"<!-- %s -->\n" % elem.text
         else:
             raise e
     if xml_str and pretty:
diff --git a/scripts/grt/export.py b/scripts/grt/export.py
index 32dc4641ddb..a782e4c8e34 100644
--- a/scripts/grt/export.py
+++ b/scripts/grt/export.py
@@ -146,150 +146,146 @@ def main(argv):
     blacklisted_tools = config['sanitization']['tools']
 
     annotate('export_jobs_start', 'Exporting Jobs')
-    handle_job = io.open(REPORT_BASE + '.jobs.tsv', 'w', encoding='utf-8')
-    handle_job.write('\t'.join(('id', 'tool_id', 'tool_version', 'state', 'create_time')) + '\n')
-    for offset_start in range(last_job_sent, end_job_id, args.batch_size):
-        logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
-        for job in sa_session.query(model.Job.id, model.Job.user_id, model.Job.tool_id, model.Job.tool_version, model.Job.state, model.Job.create_time) \
-                .filter(model.Job.id > offset_start) \
-                .filter(model.Job.id <= min(end_job_id, offset_start + args.batch_size)) \
-                .all():
-            # If the tool is blacklisted, exclude everywhere
-            if job[2] in blacklisted_tools:
-                continue
+    with io.open(REPORT_BASE + '.jobs.tsv', 'w', encoding='utf-8') as handle_job:
+        handle_job.write(u'\t'.join(('id', 'tool_id', 'tool_version', 'state', 'create_time')) + '\n')
+        for offset_start in range(last_job_sent, end_job_id, args.batch_size):
+            logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
+            for job in sa_session.query(model.Job.id, model.Job.user_id, model.Job.tool_id, model.Job.tool_version, model.Job.state, model.Job.create_time) \
+                    .filter(model.Job.id > offset_start) \
+                    .filter(model.Job.id <= min(end_job_id, offset_start + args.batch_size)) \
+                    .all():
+                # If the tool is blacklisted, exclude everywhere
+                if job[2] in blacklisted_tools:
+                    continue
 
-            try:
-                line = [
-                    str(job[0]),  # id
-                    job[2],  # tool_id
-                    job[3],  # tool_version
-                    job[4],  # state
-                    str(job[5])  # create_time
-                ]
-                cline = unicodify('\t'.join(line) + '\n')
-                handle_job.write(cline)
-            except Exception:
-                logging.warning("Unable to write out a 'handle_job' row. Ignoring the row.", exc_info=True)
-                continue
-            # meta counts
-            job_state_data[job[4]] += 1
-            active_users[job[1]] += 1
-            job_tool_map[job[0]] = job[2]
-
-    handle_job.close()
+                try:
+                    line = [
+                        str(job[0]),  # id
+                        job[2],  # tool_id
+                        job[3],  # tool_version
+                        job[4],  # state
+                        str(job[5])  # create_time
+                    ]
+                    cline = unicodify('\t'.join(line) + '\n')
+                    handle_job.write(cline)
+                except Exception:
+                    logging.warning("Unable to write out a 'handle_job' row. Ignoring the row.", exc_info=True)
+                    continue
+                # meta counts
+                job_state_data[job[4]] += 1
+                active_users[job[1]] += 1
+                job_tool_map[job[0]] = job[2]
     annotate('export_jobs_end')
 
     annotate('export_datasets_start', 'Exporting Datasets')
-    handle_datasets = io.open(REPORT_BASE + '.datasets.tsv', 'w', encoding='utf-8')
-    handle_datasets.write('\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name', 'type')) + '\n')
-    for offset_start in range(last_job_sent, end_job_id, args.batch_size):
-        logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
+    with io.open(REPORT_BASE + '.datasets.tsv', 'w', encoding='utf-8') as handle_datasets:
+        handle_datasets.write(u'\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name', 'type')) + '\n')
+        for offset_start in range(last_job_sent, end_job_id, args.batch_size):
+            logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
 
-        # four queries: JobToInputDatasetAssociation, JobToOutputDatasetAssociation, HistoryDatasetAssociation, Dataset
+            # four queries: JobToInputDatasetAssociation, JobToOutputDatasetAssociation, HistoryDatasetAssociation, Dataset
 
-        job_to_input_hda_ids = sa_session.query(model.JobToInputDatasetAssociation.job_id, model.JobToInputDatasetAssociation.dataset_id,
-            model.JobToInputDatasetAssociation.name) \
-            .filter(model.JobToInputDatasetAssociation.job_id > offset_start) \
-            .filter(model.JobToInputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
-            .all()
+            job_to_input_hda_ids = sa_session.query(model.JobToInputDatasetAssociation.job_id, model.JobToInputDatasetAssociation.dataset_id,
+                model.JobToInputDatasetAssociation.name) \
+                .filter(model.JobToInputDatasetAssociation.job_id > offset_start) \
+                .filter(model.JobToInputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
+                .all()
 
-        job_to_output_hda_ids = sa_session.query(model.JobToOutputDatasetAssociation.job_id, model.JobToOutputDatasetAssociation.dataset_id,
-            model.JobToOutputDatasetAssociation.name) \
-            .filter(model.JobToOutputDatasetAssociation.job_id > offset_start) \
-            .filter(model.JobToOutputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
-            .all()
+            job_to_output_hda_ids = sa_session.query(model.JobToOutputDatasetAssociation.job_id, model.JobToOutputDatasetAssociation.dataset_id,
+                model.JobToOutputDatasetAssociation.name) \
+                .filter(model.JobToOutputDatasetAssociation.job_id > offset_start) \
+                .filter(model.JobToOutputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
+                .all()
 
-        # add type and concat
-        job_to_hda_ids = [[list(i), "input"] for i in job_to_input_hda_ids] + [[list(i), "output"] for i in job_to_output_hda_ids]
+            # add type and concat
+            job_to_hda_ids = [[list(i), "input"] for i in job_to_input_hda_ids] + [[list(i), "output"] for i in job_to_output_hda_ids]
 
-        # put all of the hda_ids into a list
-        hda_ids = [i[0][1] for i in job_to_hda_ids]
+            # put all of the hda_ids into a list
+            hda_ids = [i[0][1] for i in job_to_hda_ids]
 
-        hdas = sa_session.query(model.HistoryDatasetAssociation.id, model.HistoryDatasetAssociation.dataset_id,
-            model.HistoryDatasetAssociation.extension) \
-            .filter(model.HistoryDatasetAssociation.id.in_(hda_ids)) \
-            .all()
+            hdas = sa_session.query(model.HistoryDatasetAssociation.id, model.HistoryDatasetAssociation.dataset_id,
+                model.HistoryDatasetAssociation.extension) \
+                .filter(model.HistoryDatasetAssociation.id.in_(hda_ids)) \
+                .all()
 
-        # put all the dataset ids into a list
-        dataset_ids = [i[1] for i in hdas]
+            # put all the dataset ids into a list
+            dataset_ids = [i[1] for i in hdas]
 
-        # get the sizes of the datasets
-        datasets = sa_session.query(model.Dataset.id, model.Dataset.total_size) \
-            .filter(model.Dataset.id.in_(dataset_ids)) \
-            .all()
+            # get the sizes of the datasets
+            datasets = sa_session.query(model.Dataset.id, model.Dataset.total_size) \
+                .filter(model.Dataset.id.in_(dataset_ids)) \
+                .all()
 
-        # datasets to dictionay for easy search
-        hdas = {i[0]: i[1:] for i in hdas}
-        datasets = {i[0]: i[1:] for i in datasets}
+            # datasets to dictionay for easy search
+            hdas = {i[0]: i[1:] for i in hdas}
+            datasets = {i[0]: i[1:] for i in datasets}
 
-        for job_to_hda in job_to_hda_ids:
+            for job_to_hda in job_to_hda_ids:
 
-            job = job_to_hda[0]  # job_id, hda_id, name
-            filetype = job_to_hda[1]  # input|output
+                job = job_to_hda[0]  # job_id, hda_id, name
+                filetype = job_to_hda[1]  # input|output
 
-            # No associated job
-            if job[0] not in job_tool_map:
-                continue
+                # No associated job
+                if job[0] not in job_tool_map:
+                    continue
 
-            # If the tool is blacklisted, exclude everywhere
-            if job_tool_map[job[0]] in blacklisted_tools:
-                continue
+                # If the tool is blacklisted, exclude everywhere
+                if job_tool_map[job[0]] in blacklisted_tools:
+                    continue
 
-            hda_id = job[1]
-            if hda_id is None:
-                continue
+                hda_id = job[1]
+                if hda_id is None:
+                    continue
 
-            dataset_id = hdas[hda_id][0]
-            if dataset_id is None:
-                continue
+                dataset_id = hdas[hda_id][0]
+                if dataset_id is None:
+                    continue
 
-            try:
-                line = [
-                    str(job[0]),  # Job ID
-                    str(hda_id),  # HDA ID
-                    str(hdas[hda_id][1]),  # Extension
-                    round_to_2sd(datasets[dataset_id][0]),  # File size
-                    job[2],  # Parameter name
-                    str(filetype)  # input/output
-                ]
-                cline = unicodify('\t'.join(line) + '\n')
-                handle_datasets.write(cline)
-            except Exception:
-                logging.warning("Unable to write out a 'handle_datasets' row. Ignoring the row.", exc_info=True)
-                continue
-    handle_datasets.close()
+                try:
+                    line = [
+                        str(job[0]),  # Job ID
+                        str(hda_id),  # HDA ID
+                        str(hdas[hda_id][1]),  # Extension
+                        round_to_2sd(datasets[dataset_id][0]),  # File size
+                        job[2],  # Parameter name
+                        str(filetype)  # input/output
+                    ]
+                    cline = unicodify('\t'.join(line) + '\n')
+                    handle_datasets.write(cline)
+                except Exception:
+                    logging.warning("Unable to write out a 'handle_datasets' row. Ignoring the row.", exc_info=True)
+                    continue
     annotate('export_datasets_end')
 
     annotate('export_metric_num_start', 'Exporting Metrics (Numeric)')
-    handle_metric_num = io.open(REPORT_BASE + '.metric_num.tsv', 'w', encoding='utf-8')
-    handle_metric_num.write('\t'.join(('job_id', 'plugin', 'name', 'value')) + '\n')
-    for offset_start in range(last_job_sent, end_job_id, args.batch_size):
-        logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
-        for metric in sa_session.query(model.JobMetricNumeric.job_id, model.JobMetricNumeric.plugin, model.JobMetricNumeric.metric_name, model.JobMetricNumeric.metric_value) \
-                .filter(model.JobMetricNumeric.job_id > offset_start) \
-                .filter(model.JobMetricNumeric.job_id <= min(end_job_id, offset_start + args.batch_size)) \
-                .all():
-            # No associated job
-            if metric[0] not in job_tool_map:
-                continue
-            # If the tool is blacklisted, exclude everywhere
-            if job_tool_map[metric[0]] in blacklisted_tools:
-                continue
+    with io.open(REPORT_BASE + '.metric_num.tsv', 'w', encoding='utf-8') as handle_metric_num:
+        handle_metric_num.write(u'\t'.join(('job_id', 'plugin', 'name', 'value')) + '\n')
+        for offset_start in range(last_job_sent, end_job_id, args.batch_size):
+            logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
+            for metric in sa_session.query(model.JobMetricNumeric.job_id, model.JobMetricNumeric.plugin, model.JobMetricNumeric.metric_name, model.JobMetricNumeric.metric_value) \
+                    .filter(model.JobMetricNumeric.job_id > offset_start) \
+                    .filter(model.JobMetricNumeric.job_id <= min(end_job_id, offset_start + args.batch_size)) \
+                    .all():
+                # No associated job
+                if metric[0] not in job_tool_map:
+                    continue
+                # If the tool is blacklisted, exclude everywhere
+                if job_tool_map[metric[0]] in blacklisted_tools:
+                    continue
 
-            try:
-                line = [
-                    str(metric[0]),  # job id
-                    metric[1],  # plugin
-                    metric[2],  # name
-                    str(metric[3])  # value
-                ]
+                try:
+                    line = [
+                        str(metric[0]),  # job id
+                        metric[1],  # plugin
+                        metric[2],  # name
+                        str(metric[3])  # value
+                    ]
 
-                cline = unicodify('\t'.join(line) + '\n')
-                handle_metric_num.write(cline)
-            except Exception:
-                logging.warning("Unable to write out a 'handle_metric_num' row. Ignoring the row.", exc_info=True)
-                continue
-    handle_metric_num.close()
+                    cline = unicodify('\t'.join(line) + '\n')
+                    handle_metric_num.write(cline)
+                except Exception:
+                    logging.warning("Unable to write out a 'handle_metric_num' row. Ignoring the row.", exc_info=True)
+                    continue
     annotate('export_metric_num_end')
 
     # Now on to outputs.

From 1b301049c08297303270bdbecc7a847aff2c9571 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Thu, 9 Jan 2020 19:12:12 +0100
Subject: [PATCH 097/101] Drop 2.7 from integration tests

---
 .github/workflows/integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index a09ce91f644..3a3e5437c63 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        python-version: [3.7, 2.7]
+        python-version: [3.7]
         subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']
     services:
       postgres:

From fdd65bbb81aed96a157104971e1f8259a5799bc4 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 9 Jan 2020 15:11:02 -0500
Subject: [PATCH 098/101] Log exceptions encountered while caching dynamic job
 rules and raise JobMappingException instead.

---
 lib/galaxy/jobs/mapper.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py
index 8d50ad0a9b8..fd5022f56e6 100644
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -15,6 +15,7 @@ DYNAMIC_DESTINATION_ID = "dynamic_legacy_from_url"
 
 ERROR_MESSAGE_NO_RULE_FUNCTION = "Galaxy misconfigured - cannot find dynamic rule function name for destination %s."
 ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND = "Galaxy misconfigured - no rule function named %s found in dynamic rule modules."
+ERROR_MESSAGE_RULE_EXCEPTION = "Galaxy misconfigured - encountered an unhandled exception while caching dynamic rule."
 
 
 class JobMappingException(Exception):
@@ -225,8 +226,11 @@ class JobRunnerMapper(object):
         return job_destination
 
     def __cache_job_destination(self, params, raw_job_destination=None):
-        self.cached_job_destination = self.__determine_job_destination(
-            params, raw_job_destination=raw_job_destination)
+        try:
+            self.cached_job_destination = self.__determine_job_destination(params, raw_job_destination=raw_job_destination)
+        except Exception:
+            log.exception("Caught unhandled exception while attempting to cache job destination:")
+            raise JobMappingException(ERROR_MESSAGE_RULE_EXCEPTION)
         return self.cached_job_destination
 
     def get_job_destination(self, params):

From 5bd9468281b9bd51679f5ae02487ae85c529d336 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 9 Jan 2020 15:36:14 -0500
Subject: [PATCH 099/101] Don't catch the custom dynamic rule exceptions, just
 raise them as-is.

---
 lib/galaxy/jobs/mapper.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py
index fd5022f56e6..d0b06cf6034 100644
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -228,6 +228,8 @@ class JobRunnerMapper(object):
     def __cache_job_destination(self, params, raw_job_destination=None):
         try:
             self.cached_job_destination = self.__determine_job_destination(params, raw_job_destination=raw_job_destination)
+        except (JobMappingException, JobNotReadyException):
+            raise
         except Exception:
             log.exception("Caught unhandled exception while attempting to cache job destination:")
             raise JobMappingException(ERROR_MESSAGE_RULE_EXCEPTION)

From b3910c1b5e0de8645b580168b5fc006e8cdf98fa Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 9 Jan 2020 16:45:21 -0500
Subject: [PATCH 100/101] Make a new exception class for problems with the
 dynamic mapper configuration itself.

---
 lib/galaxy/jobs/mapper.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py
index d0b06cf6034..25025e3803b 100644
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -15,7 +15,11 @@ DYNAMIC_DESTINATION_ID = "dynamic_legacy_from_url"
 
 ERROR_MESSAGE_NO_RULE_FUNCTION = "Galaxy misconfigured - cannot find dynamic rule function name for destination %s."
 ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND = "Galaxy misconfigured - no rule function named %s found in dynamic rule modules."
-ERROR_MESSAGE_RULE_EXCEPTION = "Galaxy misconfigured - encountered an unhandled exception while caching dynamic rule."
+ERROR_MESSAGE_RULE_EXCEPTION = "Encountered an unhandled exception while caching job destination dynamic rule."
+
+
+class JobMappingConfigurationException(Exception):
+    pass
 
 
 class JobMappingException(Exception):
@@ -158,12 +162,12 @@ class JobRunnerMapper(object):
                 rule_modules, expand_function_name)
             if not expand_function:
                 message = ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND % expand_function_name
-                raise Exception(message)
+                raise JobMappingConfigurationException(message)
         else:
             expand_function = self.__find_function_by_tool_id(rule_modules)
             if not expand_function:
                 message = ERROR_MESSAGE_NO_RULE_FUNCTION % destination
-                raise Exception(message)
+                raise JobMappingConfigurationException(message)
         return expand_function
 
     def __get_rule_modules_or_defaults(self, rules_module_name):
@@ -193,7 +197,7 @@ class JobRunnerMapper(object):
         elif expand_type in STOCK_RULES:
             expand_function = STOCK_RULES[expand_type]
         else:
-            raise Exception("Unhandled dynamic job runner type specified - %s" % expand_type)
+            raise JobMappingConfigurationException("Unhandled dynamic job runner type specified - %s" % expand_type)
 
         return self.__handle_rule(expand_function, destination)
 
@@ -228,7 +232,7 @@ class JobRunnerMapper(object):
     def __cache_job_destination(self, params, raw_job_destination=None):
         try:
             self.cached_job_destination = self.__determine_job_destination(params, raw_job_destination=raw_job_destination)
-        except (JobMappingException, JobNotReadyException):
+        except (JobMappingConfigurationException, JobMappingException, JobNotReadyException):
             raise
         except Exception:
             log.exception("Caught unhandled exception while attempting to cache job destination:")

From 104db46047197be5065e7329c88b1b0f689c02f8 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 10 Jan 2020 10:44:55 -0500
Subject: [PATCH 101/101] Add a comment explaining why the job mapper turns
 general exceptions into JobMappingExceptions.

---
 lib/galaxy/jobs/mapper.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py
index 25025e3803b..bf07063b1e5 100644
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -235,6 +235,8 @@ class JobRunnerMapper(object):
         except (JobMappingConfigurationException, JobMappingException, JobNotReadyException):
             raise
         except Exception:
+            # Other exceptions should not bubble up to the job wrapper since they can occur during the fail() method,
+            # causing jobs to become permanently stuck in a non-terminal state.
             log.exception("Caught unhandled exception while attempting to cache job destination:")
             raise JobMappingException(ERROR_MESSAGE_RULE_EXCEPTION)
         return self.cached_job_destination