Unverified Commit 30af8fb6 authored by mvdbeek's avatar mvdbeek
Browse files

Merge branch 'release_25.0' into dev

parents dcd415a2 4225e4b0

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

+18 −0
Original line number Diff line number Diff line
@@ -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

+5 −1
Original line number Diff line number Diff line
@@ -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

+1 −1
Original line number Diff line number Diff line
@@ -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

+2 −0
Original line number Diff line number Diff line 
import pytest

from selenium.webdriver.support.ui import Select



from galaxy.util.unittest_utils import skip_if_site_down
@@ -12,6 +13,7 @@ from .framework import ( 
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

+12 −7
Original line number Diff line number Diff line
@@ -8,7 +8,10 @@ from urllib.parse import ( 
    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 @@ from galaxy.util import ( 
    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: