Merge pull request galaxyproject#16675 from jmchilton/report_urls

Implement instance URLs in Galaxy markdown.

client/src/components/Markdown/Elements/InstanceUrl.vue

@@ -0,0 +1,31 @@
+<script setup lang="ts">
+import { computed } from "vue";
+
+import ExternalLink from "@/components/ExternalLink.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+interface InstanceUrlProps {
+    href?: string;
+    title?: string;
+    loading: boolean;
+}
+
+const props = withDefaults(defineProps<InstanceUrlProps>(), {
+    href: null,
+    title: null,
+});
+
+const effectiveTitle = computed(() => {
+    return props.title ? props.title : props.href;
+});
+</script>
+
+<template>
+    <p>
+        <LoadingSpan v-if="props.loading" message="Loading instance configuration"> </LoadingSpan>
+        <ExternalLink v-else-if="props.href" :href="props.href">
+            {{ effectiveTitle }}
+        </ExternalLink>
+        <i v-else> Configuration value unset, please contact Galaxy admin. </i>
+    </p>
+</template>

client/src/components/Markdown/MarkdownContainer.test.js

@@ -11,6 +11,13 @@ import MountTarget from "./MarkdownContainer.vue";
 jest.mock("utils/redirect");
 withPrefix.mockImplementation((url) => url);
 
+jest.mock("@/composables/config", () => ({
+    useConfig: jest.fn(() => ({
+        config: {},
+        isConfigLoaded: true,
+    })),
+}));
+
 const localVue = getLocalVue();
 const axiosMock = new MockAdapter(axios);
 

client/src/components/Markdown/MarkdownContainer.vue

@@ -1,13 +1,16 @@
 <script setup>
 import { computed, ref } from "vue";
 
+import { useConfig } from "@/composables/config";
+
 import HistoryDatasetAsImage from "./Elements/HistoryDatasetAsImage.vue";
 import HistoryDatasetCollectionDisplay from "./Elements/HistoryDatasetCollection/CollectionDisplay.vue";
 import HistoryDatasetDetails from "./Elements/HistoryDatasetDetails.vue";
 import HistoryDatasetDisplay from "./Elements/HistoryDatasetDisplay.vue";
 import HistoryDatasetIndex from "./Elements/HistoryDatasetIndex.vue";
 import HistoryDatasetLink from "./Elements/HistoryDatasetLink.vue";
 import HistoryLink from "./Elements/HistoryLink.vue";
+import InstanceUrl from "./Elements/InstanceUrl.vue";
 import InvocationTime from "./Elements/InvocationTime.vue";
 import JobMetrics from "./Elements/JobMetrics.vue";
 import JobParameters from "./Elements/JobParameters.vue";
@@ -17,6 +20,8 @@ import WorkflowDisplay from "./Elements/Workflow/WorkflowDisplay.vue";
 import WorkflowImage from "./Elements/Workflow/WorkflowImage.vue";
 import WorkflowLicense from "./Elements/Workflow/WorkflowLicense.vue";
 
+const { config, isConfigLoaded } = useConfig();
+
 const toggle = ref(false);
 const props = defineProps({
     name: {
@@ -83,6 +88,39 @@ const isVisible = computed(() => !isCollapsible.value || toggle.value);
             <div v-else-if="name == 'workflow_license'" class="workflow-license">
                 <WorkflowLicense :license-id="workflows[args.workflow_id]['license']" />
             </div>
+            <InstanceUrl
+                v-else-if="name == 'instance_citation_link'"
+                :href="config.citation_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl v-else-if="name == 'instance_terms_link'" :href="config.terms_url" :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_support_link'"
+                :href="config.support_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_help_link'"
+                :href="config.helpsite_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_resources_link'"
+                :href="config.instance_resource_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_access_link'"
+                :href="config.instance_access_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_organization_link'"
+                :href="config.ga4gh_service_organization_url"
+                :title="config.ga4gh_service_organization_name"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
             <HistoryLink v-else-if="name == 'history_link'" :args="args" :histories="histories" />
             <HistoryDatasetAsImage v-else-if="name == 'history_dataset_as_image'" :args="args" />
             <HistoryDatasetLink v-else-if="name == 'history_dataset_link'" :args="args" />

client/src/components/Markdown/MarkdownToolBox.vue

@@ -19,6 +19,7 @@
                     :expanded="true"
                     @onClick="onClick" />
                 <ToolSection v-else :category="workflowSection" :expanded="true" @onClick="onClick" />
+                <ToolSection :category="linksSection" :expanded="false" @onClick="onClick" />
                 <ToolSection :category="otherSection" :expanded="true" @onClick="onClick" />
                 <ToolSection
                     v-if="hasVisualizations"
@@ -250,6 +251,48 @@ export default {
                     },
                 ],
             },
+            linksSection: {
+                title: "Galaxy Instance Links",
+                name: "links",
+                elems: [
+                    {
+                        id: "instance_access_link",
+                        name: "Access",
+                        description: "(link used to access this Galaxy)",
+                    },
+                    {
+                        id: "instance_resources_link",
+                        name: "Resources",
+                        description: "(link for more information about this Galaxy)",
+                    },
+                    {
+                        id: "instance_help_link",
+                        name: "Help",
+                        description: "(link for finding help content for this Galaxy)",
+                    },
+                    {
+                        id: "instance_support_link",
+                        name: "Support",
+                        description: "(link for support for this Galaxy)",
+                    },
+                    {
+                        id: "instance_citation_link",
+                        name: "Citation",
+                        description: "(link describing how to cite this Galaxy instance)",
+                    },
+                    {
+                        id: "instance_terms_link",
+                        name: "Terms and Conditions",
+                        description: "(link describing terms and conditions for using this Galaxy instance)",
+                    },
+                    {
+                        id: "instance_organization_link",
+                        name: "Organization",
+                        description: "(link describing organization that runs this Galaxy instance)",
+                    },
+                ],
+            },
+
             visualizationSection: {
                 title: "Visualizations",
                 name: "visualizations",

client/src/components/PageDisplay/PageDisplay.vue

@@ -12,7 +12,7 @@
                     @onEdit="onEdit" />
                 <PageHtml v-else :page="page" />
             </div>
-            <b-alert v-else variant="info" show>Unsupported page format.</b-alert>
+            <LoadingSpan v-else message="Loading Galaxy configuration" />
         </template>
     </PublishedItem>
 </template>
@@ -27,10 +27,12 @@ import { urlData } from "@/utils/url";
 
 import PageHtml from "./PageHtml.vue";
 import PublishedItem from "@/components/Common/PublishedItem.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
 import Markdown from "@/components/Markdown/Markdown.vue";
 
 export default {
     components: {
+        LoadingSpan,
         Markdown,
         PageHtml,
         PublishedItem,

doc/source/admin/galaxy_options.rst

@@ -1650,13 +1650,26 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    URL of the support resource for the galaxy instance.  Used in
-    activation emails.
+    URL of the support resource for the galaxy instance.  Used outside
+    of web contexts such as in activation emails and in Galaxy
+    markdown report generation.
     Example value 'https://galaxyproject.org/'
 :Default: ``None``
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~
+``instance_access_url``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    URL used to access this Galaxy server. Used outside of web
+    contexts such as in Galaxy markdown report generation.
+    Example value 'https://usegalaxy.org'
+:Default: ``None``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``email_domain_blocklist_file``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -4036,54 +4049,59 @@
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~
-``ga4gh_service_id``
-~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~
+``organization_name``
+~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Service ID for GA4GH services (exposed via the service-info
-    endpoint for the Galaxy DRS API). If unset, one will be generated
-    using the URL the target API requests are made against.
+    The name of the organization that operates this Galaxy instance.
+    Serves as the default for the GA4GH service organization name and
+    can be exposed through Galaxy markdown for reports and such. For
+    instance, "Not Evil Corporation".
+    For GA4GH APIs, this is exposed via the service-info endpoint for
+    the Galaxy DRS API. If unset, one will be generated using
+    ga4gh_service_id (but only in the context of GA4GH APIs).
     For more information on GA4GH service definitions - check out
     https://github.com/ga4gh-discovery/ga4gh-service-registry and
     https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
-    This value should likely reflect your service's URL. For instance
-    for usegalaxy.org this value should be org.usegalaxy. Particular
-    Galaxy implementations will treat this value as a prefix and
-    append the service type to this ID. For instance for the DRS
-    service "id" (available via the DRS API) for the above
-    configuration value would be org.usegalaxy.drs.
 :Default: ``None``
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``ga4gh_service_organization_name``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~
+``organization_url``
+~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Service name for host organization (exposed via the service-info
-    endpoint for the Galaxy DRS API). If unset, one will be generated
-    using ga4gh_service_id.
+    The URL of the organization that operates this Galaxy instance.
+    Serves as the default for the GA4GH service organization name and
+    can be exposed through Galaxy markdown for reports and such. For
+    instance, "notevilcorp.com".
+    For GA4GH APIs, this is exposed via the service-info endpoint.
     For more information on GA4GH service definitions - check out
     https://github.com/ga4gh-discovery/ga4gh-service-registry and
     https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
 :Default: ``None``
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``ga4gh_service_organization_url``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~
+``ga4gh_service_id``
+~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Organization URL for host organization (exposed via the
-    service-info endpoint for the Galaxy DRS API). If unset, one will
-    be generated using the URL the target API requests are made
-    against.
+    Service ID for GA4GH services (exposed via the service-info
+    endpoint for the Galaxy DRS API). If unset, one will be generated
+    using the URL the target API requests are made against.
     For more information on GA4GH service definitions - check out
     https://github.com/ga4gh-discovery/ga4gh-service-registry and
     https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
+    This value should likely reflect your service's URL. For instance
+    for usegalaxy.org this value should be org.usegalaxy. Particular
+    Galaxy implementations will treat this value as a prefix and
+    append the service type to this ID. For instance for the DRS
+    service "id" (available via the DRS API) for the above
+    configuration value would be org.usegalaxy.drs.
 :Default: ``None``
 :Type: str
 

lib/galaxy/config/__init__.py

@@ -637,6 +637,8 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         "fetch_url_whitelist": "fetch_url_allowlist",
         "containers_resolvers_config_file": "container_resolvers_config_file",
         "activation_email": "email_from",
+        "ga4gh_service_organization_name": "organization_name",
+        "ga4gh_service_organization_url": "organization_url",
     }
 
     deprecated_options = list(renamed_options.keys()) + [

lib/galaxy/config/config_manage.py

@@ -203,6 +203,8 @@ def lint(self, args, app_desc, key, value) -> None:
     "legacy_eager_objectstore_initialization": _DeprecatedAndDroppedAction(),
     "enable_openid": _DeprecatedAndDroppedAction(),
     "openid_consumer_cache_path": _DeprecatedAndDroppedAction(),
+    "ga4gh_service_organization_name": _RenameAction("organization_name"),
+    "ga4gh_service_organization_url": _RenameAction("organization_url"),
 }
 
 

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1116,11 +1116,17 @@ galaxy:
   # message, before the 'Your Galaxy Team' signature.
   #custom_activation_email_message: null
 
-  # URL of the support resource for the galaxy instance.  Used in
-  # activation emails.
+  # URL of the support resource for the galaxy instance.  Used outside
+  # of web contexts such as in activation emails and in Galaxy markdown
+  # report generation.
   # Example value 'https://galaxyproject.org/'
   #instance_resource_url: null
 
+  # URL used to access this Galaxy server. Used outside of web contexts
+  # such as in Galaxy markdown report generation.
+  # Example value 'https://usegalaxy.org'
+  #instance_access_url: null
+
   # E-mail domains blocklist is used for filtering out users that are
   # using disposable email addresses at registration.  If their
   # address's base domain matches any domain on the list, they are
@@ -2187,6 +2193,28 @@ galaxy:
   # production server.
   #bootstrap_admin_api_key: null
 
+  # The name of the organization that operates this Galaxy instance.
+  # Serves as the default for the GA4GH service organization name and
+  # can be exposed through Galaxy markdown for reports and such. For
+  # instance, "Not Evil Corporation".
+  # For GA4GH APIs, this is exposed via the service-info endpoint for
+  # the Galaxy DRS API. If unset, one will be generated using
+  # ga4gh_service_id (but only in the context of GA4GH APIs).
+  # For more information on GA4GH service definitions - check out
+  # https://github.com/ga4gh-discovery/ga4gh-service-registry and
+  # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
+  #organization_name: null
+
+  # The URL of the organization that operates this Galaxy instance.
+  # Serves as the default for the GA4GH service organization name and
+  # can be exposed through Galaxy markdown for reports and such. For
+  # instance, "notevilcorp.com".
+  # For GA4GH APIs, this is exposed via the service-info endpoint.
+  # For more information on GA4GH service definitions - check out
+  # https://github.com/ga4gh-discovery/ga4gh-service-registry and
+  # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
+  #organization_url: null
+
   # Service ID for GA4GH services (exposed via the service-info endpoint
   # for the Galaxy DRS API). If unset, one will be generated using the
   # URL the target API requests are made against.
@@ -2201,22 +2229,6 @@ galaxy:
   # be org.usegalaxy.drs.
   #ga4gh_service_id: null
 
-  # Service name for host organization (exposed via the service-info
-  # endpoint for the Galaxy DRS API). If unset, one will be generated
-  # using ga4gh_service_id.
-  # For more information on GA4GH service definitions - check out
-  # https://github.com/ga4gh-discovery/ga4gh-service-registry and
-  # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
-  #ga4gh_service_organization_name: null
-
-  # Organization URL for host organization (exposed via the service-info
-  # endpoint for the Galaxy DRS API). If unset, one will be generated
-  # using the URL the target API requests are made against.
-  # For more information on GA4GH service definitions - check out
-  # https://github.com/ga4gh-discovery/ga4gh-service-registry and
-  # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
-  #ga4gh_service_organization_url: null
-
   # Service environment (exposed via the service-info endpoint for the
   # Galaxy DRS API) for implemented GA4GH services.
   # Suggested values are prod, test, dev, staging.