Merge branch 'release_25.0' into dev

Author: mvdbeek

client/src/components/Workflow/Import/TrsSearch.vue

@@ -9,6 +9,7 @@ import { useRouter } from "vue-router/composables";
 
 import { getRedirectOnImportPath } from "@/components/Workflow/redirectPath";
 import { Services } from "@/components/Workflow/services";
+import { useMarkdown } from "@/composables/markdown";
 import { withPrefix } from "@/utils/redirect";
 
 import type { TrsSelection } from "./types";
@@ -26,6 +27,8 @@ type TrsSearchData = {
     [key: string]: unknown;
 };
 
+const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
+
 const fields = [
     { key: "name", label: "Name" },
     { key: "description", label: "Description" },
@@ -195,7 +198,22 @@ async function importVersion(trsId?: string, toolIdToImport?: string, version?:
                             @onImport="(versionId) => importVersion(trsSelection?.id, row.item.data.id, versionId)" />
                     </BCard>
                 </template>
+
+                <template v-slot:cell(description)="row">
+                    <span class="trs-description" v-html="renderMarkdown(row.item.data.description)" />
+                </template>
             </BTable>
         </div>
     </BCard>
 </template>
+
+<style>
+.trs-description {
+    position: relative;
+    overflow: hidden;
+    display: -webkit-box;
+    -webkit-box-orient: vertical;
+    -webkit-line-clamp: 3;
+    line-clamp: 3;
+}
+</style>

client/src/components/Workflow/Import/TrsTool.vue

@@ -4,6 +4,8 @@ import { faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
 
+import { useMarkdown } from "@/composables/markdown";
+
 import type { TrsTool, TrsToolVersion } from "./types";
 
 library.add(faUpload);
@@ -18,6 +20,8 @@ const emit = defineEmits<{
     (e: "onImport", versionId: string): void;
 }>();
 
+const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
+
 function importVersion(version: TrsToolVersion) {
     const version_id = version.id.includes(`:${version.name}`) ? version.name : version.id;
     emit("onImport", version_id);
@@ -34,7 +38,7 @@ function importVersion(version: TrsToolVersion) {
         <div>
             <b>Description:</b>
 
-            <span>{{ props.trsTool.description }}</span>
+            <span v-html="renderMarkdown(props.trsTool.description)" />
         </div>
         <div>
             <b>Organization</b>

client/src/utils/navigation/navigation.yml

@@ -691,7 +691,7 @@ trs_search:
     search: "#trs-search-query"
     search_result:
       type: xpath
-      selector: "//td[contains(text(), '${workflow_name}')]"
+      selector: "//td[contains(., '${workflow_name}')]"
     import_button: ".workflow-import"
     select_server_button: "#dropdownTrsServer"
     import_version: '[data-version-name*="${version}"]'

lib/galaxy_test/selenium/test_data_source_tools.py

@@ -1,3 +1,4 @@
+import pytest
 from selenium.webdriver.support.ui import Select
 
 from galaxy.util.unittest_utils import skip_if_site_down
@@ -12,6 +13,7 @@
 class TestDataSource(SeleniumTestCase, UsesHistoryItemAssertions):
     ensure_registered = True
 
+    @pytest.mark.skip("Skipping UCSC table direct1 data source test, chromedriver fails captcha")
     @selenium_test
     @managed_history
     @skip_if_site_down("https://genome.ucsc.edu/cgi-bin/hgTables")

tools/data_source/data_source.py

@@ -8,7 +8,10 @@
     urlencode,
     urlparse,
 )
-from urllib.request import urlopen
+from urllib.request import (
+    Request,
+    urlopen,
+)
 
 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
@@ -17,6 +20,7 @@
     get_charset_from_http_headers,
     stream_to_open_named_file,
 )
+from galaxy.util.user_agent import get_default_headers
 
 GALAXY_PARAM_PREFIX = "GALAXY"
 GALAXY_ROOT_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
@@ -51,15 +55,16 @@ def __main__():
             sys.exit("The remote data source application has not sent back a URL parameter in the request.")
 
         # The following calls to urlopen() will use the above default timeout
+        headers = get_default_headers()
         try:
             if URL_method == "get":
-                page = urlopen(cur_URL, timeout=DEFAULT_SOCKET_TIMEOUT)
+                req = Request(cur_URL, headers=headers)
             elif URL_method == "post":
-                page = urlopen(
-                    cur_URL,
-                    urlencode(params["param_dict"]["incoming_request_params"]).encode("utf-8"),
-                    timeout=DEFAULT_SOCKET_TIMEOUT,
-                )
+                data = urlencode(params["param_dict"]["incoming_request_params"]).encode("utf-8")
+                req = Request(cur_URL, data=data, headers=headers)
+            else:
+                raise Exception("Unknown URL_method specified: %s" % URL_method)
+            page = urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT)
         except Exception as e:
             sys.exit("The remote data source application may be off line, please try again later. Error: %s" % str(e))
         if max_file_size: