From 7c6fc1800f537ed73e9abaeeaf0610edd4a49f4b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 21 Jun 2024 15:03:28 +0200
Subject: [PATCH 1/5] Replace busybox:ubuntu-14.04 image with
 busybox:1.36.1-glibc

---
 config/job_conf.yml.interactivetools                   |  4 ++--
 doc/source/admin/jobs.md                               |  2 +-
 doc/source/admin/special_topics/interactivetools.rst   |  4 ++--
 doc/source/admin/special_topics/mulled_containers.rst  |  2 +-
 lib/galaxy/config/sample/job_conf.sample.yml           |  8 ++++----
 lib/galaxy/config/sample/job_conf.xml.sample_advanced  | 10 +++++-----
 test/functional/tools/catDocker.xml                    |  2 +-
 test/functional/tools/job_environment_default.xml      |  2 +-
 .../tools/job_environment_default_legacy.xml           |  2 +-
 .../tools/job_environment_explicit_isolated_home.xml   |  2 +-
 .../tools/job_environment_explicit_shared_home.xml     |  2 +-
 test/functional/tools/tool_directory_docker.xml        |  2 +-
 test/integration/test_coexecution.py                   |  6 +++---
 test/integration/test_kubernetes_runner.py             |  6 +++---
 test/unit/app/jobs/test_job_configuration.py           |  2 +-
 15 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/config/job_conf.yml.interactivetools b/config/job_conf.yml.interactivetools
index dfc00fb46b46..5ac519ebd4f2 100644
--- a/config/job_conf.yml.interactivetools
+++ b/config/job_conf.yml.interactivetools
@@ -41,8 +41,8 @@ execution:
 
       #docker_cmd: /usr/local/custom_docker/docker
       #docker_host:
-      #docker_container_id_override: busybox:ubuntu-14.04
-      #docker_default_container_id: busybox:ubuntu-14.04
+      #docker_container_id_override: busybox:1.36.1-glibc
+      #docker_default_container_id: busybox:1.36.1-glibc
       #require_container: true
       #container_monitor: true
       #container_monitor_result: file
diff --git a/doc/source/admin/jobs.md b/doc/source/admin/jobs.md
index 5d87c9c429c9..dcb7f75a3f74 100644
--- a/doc/source/admin/jobs.md
+++ b/doc/source/admin/jobs.md
@@ -159,7 +159,7 @@ execution:
       k8s_namespace: default
       runner: pulsar_k8s
       docker_enabled: true
-      docker_default_container_id: busybox:ubuntu-14.04
+      docker_default_container_id: busybox:1.36.1-glibc
       pulsar_app_config:
         message_queue_url: 'amqp://guest:guest@host.docker.internal:5672//'
     local_environment:
diff --git a/doc/source/admin/special_topics/interactivetools.rst b/doc/source/admin/special_topics/interactivetools.rst
index 698c2d1d3d73..6d032c02d05c 100644
--- a/doc/source/admin/special_topics/interactivetools.rst
+++ b/doc/source/admin/special_topics/interactivetools.rst
@@ -172,8 +172,8 @@ An example ``job_conf.yml`` file as seen in ``config/job_conf.yml.interactivetoo
 
           #docker_cmd: /usr/local/custom_docker/docker
           #docker_host:
-          #docker_container_id_override: busybox:ubuntu-14.04
-          #docker_default_container_id: busybox:ubuntu-14.04
+          #docker_container_id_override: busybox:1.36.1-glibc
+          #docker_default_container_id: busybox:1.36.1-glibc
           #require_container: true
           #container_monitor: true
           #container_monitor_result: file
diff --git a/doc/source/admin/special_topics/mulled_containers.rst b/doc/source/admin/special_topics/mulled_containers.rst
index 38e883667c53..332a9806b73d 100644
--- a/doc/source/admin/special_topics/mulled_containers.rst
+++ b/doc/source/admin/special_topics/mulled_containers.rst
@@ -16,7 +16,7 @@ requirement field.
 
     <requirements>
         <!-- Container based dependency handling -->
-        <container type="docker">busybox:ubuntu-14.04</container>
+        <container type="docker">busybox:1.36.1-glibc</container>
         <!-- Conda based dependency handling -->
         <requirement type="package" version="8.22">gnu_coreutils</requirement>
     </requirements>
diff --git a/lib/galaxy/config/sample/job_conf.sample.yml b/lib/galaxy/config/sample/job_conf.sample.yml
index 27f8522ecfef..849aabba1eec 100644
--- a/lib/galaxy/config/sample/job_conf.sample.yml
+++ b/lib/galaxy/config/sample/job_conf.sample.yml
@@ -513,13 +513,13 @@ execution:
       # trust tool's specified container - a destination wide override
       # can be set. This will cause all jobs on this destination to use
       # that docker image.
-      #docker_container_id_override: busybox:ubuntu-14.04
+      #docker_container_id_override: busybox:1.36.1-glibc
 
       # Likewise, if deployer wants to use docker for isolation and
       # does trust tool's specified container - but also wants tool's not
       # configured to run in a container the following option can provide
       # a fallback. -->
-      #docker_default_container_id: busybox:ubuntu-14.04
+      #docker_default_container_id: busybox:1.36.1-glibc
 
       # If the destination should be secured to only allow containerized jobs
       # the following parameter may be set for the job destination. Some tools
@@ -633,7 +633,7 @@ execution:
         - type: docker
           shell: '/bin/sh'
           resolve_dependencies: false
-          identifier: 'busybox:ubuntu-14.04'
+          identifier: 'busybox:1.36.1-glibc'
         - type: singularity
           shell: '/bin/sh'
           resolve_dependencies: false
@@ -642,7 +642,7 @@ execution:
         - type: docker
           shell: '/bin/sh'
           resolve_dependencies: false
-          identifier: 'busybox:ubuntu-14.04'
+          identifier: 'busybox:1.36.1-glibc'
         - type: singularity
           shell: '/bin/sh'
           resolve_dependencies: false
diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index bf6b739175d5..3864072cc5d0 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -588,13 +588,13 @@
                trust tool's specified container - a destination wide override
                can be set. This will cause all jobs on this destination to use
                that docker image. -->
-          <!-- <param id="docker_container_id_override">busybox:ubuntu-14.04</param> -->
+          <!-- <param id="docker_container_id_override">busybox:1.36.1-glibc'</param> -->
 
           <!-- Likewise, if deployer wants to use docker for isolation and
                does trust tool's specified container - but also wants tool's not
                configured to run in a container the following option can provide
                a fallback. -->
-          <!-- <param id="docker_default_container_id">busybox:ubuntu-14.04</param> -->
+          <!-- <param id="docker_default_container_id">busybox:1.36.1-glibc'</param> -->
 
           <!-- If the destination should be secured to only allow containerized jobs
                the following parameter may be set for the job destination. Some tools do
@@ -674,11 +674,11 @@
                the enabled container types for this destination will be used.
           -->
           <param id="container_override">
-              <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:ubuntu-14.04</container>
+              <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:1.36.1-glibc'</container>
               <container type="singularity" shell="/bin/sh" resolve_dependencies="false">/path/to/default/container</container>
           </param>
           <param id="container">
-              <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:ubuntu-14.04</container>
+              <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:1.36.1-glibc'</container>
               <container type="singularity" shell="/bin/sh" resolve_dependencies="false">/path/to/default/container</container>
           </param>
         </destination>
@@ -966,7 +966,7 @@
             container ID will be passed along to condor as
             the docker_image submission parameter.
             -->
-            <!-- <param id="docker_default_container_id">busybox:ubuntu-14.04</param> -->
+            <!-- <param id="docker_default_container_id">busybox:1.36.1-glibc'</param> -->
         </destination>
 
         <!-- Jobs can be re-submitted for various reasons (to the same destination or others,
diff --git a/test/functional/tools/catDocker.xml b/test/functional/tools/catDocker.xml
index 5cef7257ca16..5abfe4fbfb29 100644
--- a/test/functional/tools/catDocker.xml
+++ b/test/functional/tools/catDocker.xml
@@ -1,7 +1,7 @@
 <tool id="catdc" name="Concatenate datasets (in docker)" version="1.0.0">
     <description>tail-to-head</description>
     <requirements>
-        <container type="docker">busybox:ubuntu-14.04</container>
+        <container type="docker">busybox:1.36.1-glibc</container>
     </requirements>
     <command><![CDATA[
 echo "Galaxy slots passed through contain as \$GALAXY_SLOTS" &&
diff --git a/test/functional/tools/job_environment_default.xml b/test/functional/tools/job_environment_default.xml
index c51108cb4f3a..f901e9c273ae 100644
--- a/test/functional/tools/job_environment_default.xml
+++ b/test/functional/tools/job_environment_default.xml
@@ -1,6 +1,6 @@
 <tool id="job_environment_default" name="job_environment_default" version="0.1.0" profile="18.01">
     <requirements>
-        <container type="docker">busybox:ubuntu-14.04</container>
+        <container type="docker">busybox:1.36.1-glibc</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 mktemp -d &&
diff --git a/test/functional/tools/job_environment_default_legacy.xml b/test/functional/tools/job_environment_default_legacy.xml
index 3d3e49de6e75..2e2782d52944 100644
--- a/test/functional/tools/job_environment_default_legacy.xml
+++ b/test/functional/tools/job_environment_default_legacy.xml
@@ -1,6 +1,6 @@
 <tool id="job_environment_default_legacy" name="job_environment_default_legacy" version="0.1.0">
     <requirements>
-        <container type="docker">busybox:ubuntu-14.04</container>
+        <container type="docker">busybox:1.36.1-glibc</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 mktemp -d &&
diff --git a/test/functional/tools/job_environment_explicit_isolated_home.xml b/test/functional/tools/job_environment_explicit_isolated_home.xml
index b665f87384d7..906a8cfdd62b 100644
--- a/test/functional/tools/job_environment_explicit_isolated_home.xml
+++ b/test/functional/tools/job_environment_explicit_isolated_home.xml
@@ -1,6 +1,6 @@
 <tool id="job_environment_explicit_isolated_home" name="job_environment_explicit_isolated_home" version="0.1.0">
     <requirements>
-        <container type="docker">busybox:ubuntu-14.04</container>
+        <container type="docker">busybox:1.36.1-glibc</container>
     </requirements>
     <command use_shared_home="false"><![CDATA[
 mktemp -d &&
diff --git a/test/functional/tools/job_environment_explicit_shared_home.xml b/test/functional/tools/job_environment_explicit_shared_home.xml
index 8e23c3924b41..9b24267df664 100644
--- a/test/functional/tools/job_environment_explicit_shared_home.xml
+++ b/test/functional/tools/job_environment_explicit_shared_home.xml
@@ -1,6 +1,6 @@
 <tool id="job_environment_explicit_shared_home" name="job_environment_explicit_shared_home" version="0.1.0" profile="18.01">
     <requirements>
-        <container type="docker">busybox:ubuntu-14.04</container>
+        <container type="docker">busybox:1.36.1-glibc</container>
     </requirements>
     <command use_shared_home="true"><![CDATA[
 mktemp -d &&
diff --git a/test/functional/tools/tool_directory_docker.xml b/test/functional/tools/tool_directory_docker.xml
index fa408789f340..dc24490279ce 100644
--- a/test/functional/tools/tool_directory_docker.xml
+++ b/test/functional/tools/tool_directory_docker.xml
@@ -1,6 +1,6 @@
 <tool id="tool_directory_docker" name="tool_directory_docker" version="1.0.0">
     <requirements>
-        <container type="docker">busybox:ubuntu-14.04</container>
+        <container type="docker">busybox:1.36.1-glibc</container>
     </requirements>
     <command><![CDATA[
 cp '$__tool_directory__/tool_directory.xml' output1
diff --git a/test/integration/test_coexecution.py b/test/integration/test_coexecution.py
index 3bfb97561d44..7e7543443dc7 100644
--- a/test/integration/test_coexecution.py
+++ b/test/integration/test_coexecution.py
@@ -66,7 +66,7 @@
       k8s_namespace: ${k8s_namespace}
       runner: pulsar_k8s
       docker_enabled: true
-      docker_default_container_id: busybox:ubuntu-14.04
+      docker_default_container_id: busybox:1.36.1-glibc
       pulsar_app_config:
         message_queue_url: '${container_amqp_url}'
       env:
@@ -145,7 +145,7 @@ def job_config(template_str: str, jobs_directory: str) -> str:
       runner: pulsar_tes
       tes_url: ${tes_url}
       docker_enabled: true
-      docker_default_container_id: busybox:ubuntu-14.04
+      docker_default_container_id: busybox:1.36.1-glibc
       pulsar_app_config:
         message_queue_url: '${container_amqp_url}'
       env:
@@ -204,7 +204,7 @@ def job_config(template_str: str, jobs_directory: str) -> str:
       runner: pulsar_tes
       tes_url: ${tes_url}
       docker_enabled: true
-      docker_default_container_id: busybox:ubuntu-14.04
+      docker_default_container_id: busybox:1.36.1-glibc
       pulsar_app_config:
         message_queue_url: '${container_amqp_url}'
       env:
diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py
index c751734353e2..9748d4b497b5 100644
--- a/test/integration/test_kubernetes_runner.py
+++ b/test/integration/test_kubernetes_runner.py
@@ -133,21 +133,21 @@ def job_config(jobs_directory: str) -> Config:
             <param id="limits_cpu">1.1</param>
             <param id="limits_memory">100M</param>
             <param id="docker_enabled">true</param>
-            <param id="docker_default_container_id">busybox:ubuntu-14.04</param>
+            <param id="docker_default_container_id">busybox:1.36.1-glibc</param>
             <env id="SOME_ENV_VAR">42</env>
         </destination>
         <destination id="k8s_destination_walltime_short" runner="k8s_walltime_short">
             <param id="limits_cpu">1.1</param>
             <param id="limits_memory">100M</param>
             <param id="docker_enabled">true</param>
-            <param id="docker_default_container_id">busybox:ubuntu-14.04</param>
+            <param id="docker_default_container_id">busybox:1.36.1-glibc</param>
             <env id="SOME_ENV_VAR">42</env>
         </destination>
         <destination id="k8s_destination_no_cleanup" runner="k8s_no_cleanup">
             <param id="limits_cpu">1.1</param>
             <param id="limits_memory">100M</param>
             <param id="docker_enabled">true</param>
-            <param id="docker_default_container_id">busybox:ubuntu-14.04</param>
+            <param id="docker_default_container_id">busybox:1.36.1-glibc</param>
             <env id="SOME_ENV_VAR">42</env>
         </destination>
         <destination id="local_dest" runner="local">
diff --git a/test/unit/app/jobs/test_job_configuration.py b/test/unit/app/jobs/test_job_configuration.py
index 56ba267fb11c..58f2ed5ff288 100644
--- a/test/unit/app/jobs/test_job_configuration.py
+++ b/test/unit/app/jobs/test_job_configuration.py
@@ -322,7 +322,7 @@ def test_container_tag_in_destination(self):
         assert len(container) == 2
         container0 = container[0]
         assert container0["type"] == "docker"
-        assert container0["identifier"] == "busybox:ubuntu-14.04"
+        assert container0["identifier"] == "busybox:1.36.1-glibc"
 
         container_override = container_dest.params["container_override"]
         assert len(container_override) == 2

From bcca24b47bb824317bed26d511663dd03521f7e7 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 19 Jun 2024 12:19:14 +0100
Subject: [PATCH 2/5] Prepare for NumPy 2.0

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

diff --git a/lib/galaxy/model/custom_types.py b/lib/galaxy/model/custom_types.py
index f36b4b9a6130..762c203eade4 100644
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -32,7 +32,7 @@ class SafeJsonEncoder(json.JSONEncoder):
     def default(self, obj):
         if isinstance(obj, numpy.int_):
             return int(obj)
-        elif isinstance(obj, numpy.float_):
+        elif isinstance(obj, numpy.float64):
             return float(obj)
         elif isinstance(obj, bytes):
             return unicodify(obj)

From 98690d960495555236f7f87ec149d1b432225778 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 21 Jun 2024 13:17:14 -0400
Subject: [PATCH 3/5] Pinia plugin fixes when using component mounting
 utilities.  This has changed multiple times in descendant branches so this is
 a flattened, cleaned up version for application against 24.0.

---
 client/src/utils/mountVueComponent.js | 28 ++++++++++++++++++++-------
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/client/src/utils/mountVueComponent.js b/client/src/utils/mountVueComponent.js
index 0e0ee949728d..2e47c3cabbee 100644
--- a/client/src/utils/mountVueComponent.js
+++ b/client/src/utils/mountVueComponent.js
@@ -4,8 +4,12 @@
 
 import BootstrapVue from "bootstrap-vue";
 import { iconPlugin, localizationPlugin, vueRxShortcutPlugin } from "components/plugins";
+import { createPinia, getActivePinia, PiniaVuePlugin } from "pinia";
 import Vue from "vue";
 
+// Load Pinia
+Vue.use(PiniaVuePlugin);
+
 // Bootstrap components
 Vue.use(BootstrapVue);
 
@@ -18,15 +22,25 @@ Vue.use(vueRxShortcutPlugin);
 // font-awesome svg icon registration/loading
 Vue.use(iconPlugin);
 
-export const mountVueComponent = (ComponentDefinition) => {
+function getOrCreatePinia() {
+    // We sometimes use this utility mounting function in a context where there
+    // is no existing vue application or pinia store (e.g. individual charts
+    // displayed in an iframe).
+    // To support both use cases, we will create a new pinia store and attach it
+    // to the vue application that is created for the component if missing.
+    return getActivePinia() || createPinia();
+}
+
+export function mountVueComponent(ComponentDefinition) {
     const component = Vue.extend(ComponentDefinition);
-    return (propsData, el) => new component({ propsData, el });
-};
+    return function (propsData, el) {
+        return new component({ propsData, el, pinia: getOrCreatePinia() });
+    };
+}
 
-export const replaceChildrenWithComponent = (el, ComponentDefinition, propsData = {}) => {
+export function replaceChildrenWithComponent(el, ComponentDefinition, propsData = {}) {
     const container = document.createElement("div");
     el.replaceChildren(container);
-    const component = Vue.extend(ComponentDefinition);
-    const mountFn = (propsData, el) => new component({ propsData, el });
+    const mountFn = mountVueComponent(ComponentDefinition);
     return mountFn(propsData, container);
-};
+}

From 2fd90d1d9c46a0afa4dcc70727d6ab6456b09179 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 24 Jun 2024 10:02:08 +0100
Subject: [PATCH 4/5] Install node from setup-node action

---
 .github/workflows/lint_openapi_schema.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/lint_openapi_schema.yml b/.github/workflows/lint_openapi_schema.yml
index 464d1cef825f..4269db840770 100644
--- a/.github/workflows/lint_openapi_schema.yml
+++ b/.github/workflows/lint_openapi_schema.yml
@@ -28,6 +28,11 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Get full Python version
         id: full-python-version
         shell: bash

From 7ceef4b279ecc4d96a7cae11349cd2638dccc2db Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Mon, 24 Jun 2024 14:02:02 +0200
Subject: [PATCH 5/5] Drop extra quote

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/config/sample/job_conf.xml.sample_advanced | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index 3864072cc5d0..dc67a4763d74 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -588,13 +588,13 @@
                trust tool's specified container - a destination wide override
                can be set. This will cause all jobs on this destination to use
                that docker image. -->
-          <!-- <param id="docker_container_id_override">busybox:1.36.1-glibc'</param> -->
+          <!-- <param id="docker_container_id_override">busybox:1.36.1-glibc</param> -->
 
           <!-- Likewise, if deployer wants to use docker for isolation and
                does trust tool's specified container - but also wants tool's not
                configured to run in a container the following option can provide
                a fallback. -->
-          <!-- <param id="docker_default_container_id">busybox:1.36.1-glibc'</param> -->
+          <!-- <param id="docker_default_container_id">busybox:1.36.1-glibc</param> -->
 
           <!-- If the destination should be secured to only allow containerized jobs
                the following parameter may be set for the job destination. Some tools do
@@ -674,11 +674,11 @@
                the enabled container types for this destination will be used.
           -->
           <param id="container_override">
-              <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:1.36.1-glibc'</container>
+              <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:1.36.1-glibc</container>
               <container type="singularity" shell="/bin/sh" resolve_dependencies="false">/path/to/default/container</container>
           </param>
           <param id="container">
-              <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:1.36.1-glibc'</container>
+              <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:1.36.1-glibc</container>
               <container type="singularity" shell="/bin/sh" resolve_dependencies="false">/path/to/default/container</container>
           </param>
         </destination>
@@ -966,7 +966,7 @@
             container ID will be passed along to condor as
             the docker_image submission parameter.
             -->
-            <!-- <param id="docker_default_container_id">busybox:1.36.1-glibc'</param> -->
+            <!-- <param id="docker_default_container_id">busybox:1.36.1-glibc</param> -->
         </destination>
 
         <!-- Jobs can be re-submitted for various reasons (to the same destination or others,