Merge branch 'release_21.01' into release_21.05

client/src/components/Masthead/MastheadItem.vue

@@ -111,20 +111,13 @@ export default {
             return document.getElementById("galaxy_main");
         },
     },
-    updated() {
-        if (this.$refs.dropdown && this.galaxyIframe) {
-            this.galaxyIframe.addEventListener("load", this.iframeListener);
-        }
+    mounted() {
+        window.addEventListener("blur", this.hideDropdown);
     },
     destroyed() {
-        if (this.$refs.dropdown && this.galaxyIframe) {
-            this.galaxyIframe.removeEventListener("load", this.iframeListener);
-        }
+        window.removeEventListener("blur", this.hideDropdown);
     },
     methods: {
-        iframeListener() {
-            return this.galaxyIframe.contentDocument.addEventListener("click", this.hideDropdown);
-        },
         hideDropdown() {
             if (this.$refs.dropdown) {
                 this.$refs.dropdown.hide();

lib/galaxy/tool_util/cwl/util.py

@@ -172,7 +172,7 @@ def galactic_job_json(
 
     def replacement_file(value):
         if value.get('galaxy_id'):
-            return {"src": "hda", "id": value['galaxy_id']}
+            return {"src": "hda", "id": str(value['galaxy_id'])}
         file_path = value.get("location", None) or value.get("path", None)
         # format to match output definitions in tool, where did filetype come from?
         filetype = value.get("filetype", None) or value.get("format", None)
@@ -283,7 +283,7 @@ def galactic_job_json(
 
     def replacement_collection(value):
         if value.get('galaxy_id'):
-            return {"src": "hdca", "id": value['galaxy_id']}
+            return {"src": "hdca", "id": str(value['galaxy_id'])}
         assert "collection_type" in value
         collection_type = value["collection_type"]
         elements = to_elements(value, collection_type)

lib/galaxy/tool_util/deps/mulled/invfile.lua

@@ -60,7 +60,7 @@ end
 
 local destination_base_image = VAR.DEST_BASE_IMAGE
 if destination_base_image == '' then
-    destination_base_image = 'bgruening/busybox-bash:0.1'
+    destination_base_image = 'quay.io/bioconda/base-glibc-busybox-bash:latest'
 end
 
 local verbose = VAR.VERBOSE
@@ -101,11 +101,11 @@ inv.task('build')
 if VAR.SINGULARITY ~= '' then
     inv.task('singularity')
         .using(singularity_image)
-        .withHostConfig({binds = {"build:/data", "'" .. singularity_image_dir .. "':/import"}, privileged = true})
+        .withHostConfig({binds = {"build:/data", singularity_image_dir .. ":/import"}, privileged = true})
         .withConfig({entrypoint = {'/bin/sh', '-c'}})
-        .run('mkdir', '-p', '/usr/local/var/singularity/mnt/container')
-        .run('singularity', 'build', '/import/' .. VAR.SINGULARITY_IMAGE_NAME, '/import/Singularity.def')
-        .run('chown', VAR.USER_ID, '/import/' .. VAR.SINGULARITY_IMAGE_NAME)
+        .run('mkdir -p /usr/local/var/singularity/mnt/container && '
+            .. 'singularity build /import/' .. VAR.SINGULARITY_IMAGE_NAME .. ' /import/Singularity.def && '
+            .. 'chown ' .. VAR.USER_ID .. ' /import/' .. VAR.SINGULARITY_IMAGE_NAME)
 end
 
 inv.task('cleanup')

lib/galaxy/tool_util/deps/mulled/mulled_build.py

@@ -46,9 +46,12 @@ from ..conda_compat import MetaData
 log = logging.getLogger(__name__)
 
 DIRNAME = os.path.dirname(__file__)
-DEFAULT_BASE_IMAGE = "bgruening/busybox-bash:0.1"
-DEFAULT_EXTENDED_BASE_IMAGE = "bioconda/extended-base-image:latest"
-DEFAULT_CHANNELS = ["conda-forge", "bioconda"]
+DEFAULT_BASE_IMAGE = os.environ.get("DEFAULT_BASE_IMAGE", "quay.io/bioconda/base-glibc-busybox-bash:latest")
+DEFAULT_EXTENDED_BASE_IMAGE = os.environ.get("DEFAULT_EXTENDED_BASE_IMAGE", "quay.io/bioconda/base-glibc-debian-bash:latest")
+if 'DEFAULT_MULLED_CONDA_CHANNELS' in os.environ:
+    DEFAULT_CHANNELS = os.environ['DEFAULT_MULLED_CONDA_CHANNELS'].split(',')
+else:
+    DEFAULT_CHANNELS = ["conda-forge", "bioconda"]
 DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}"
 DEFAULT_BINDS = ["build/dist:/usr/local/"]
 DEFAULT_WORKING_DIR = '/source/'

test/unit/tool_util/mulled/test_mulled_build.py

@@ -5,6 +5,7 @@ from galaxy.tool_util.deps.mulled.mulled_build import (
     build_target,
     DEFAULT_BASE_IMAGE,
     DEFAULT_EXTENDED_BASE_IMAGE,
+    mull_targets,
 )
 from ..util import external_dependency_management
 
@@ -18,3 +19,11 @@ from ..util import external_dependency_management
 def test_base_image_for_targets(target, version, base_image):
     target = build_target(target, version=version)
     assert base_image_for_targets([target]) == base_image
+
+
+@external_dependency_management
+def test_mulled_build_files_cli(tmpdir):
+    singularity_image_dir = tmpdir.mkdir('singularity image dir')
+    target = build_target('zlib')
+    mull_targets([target], command='build-and-test', singularity=True, singularity_image_dir=singularity_image_dir)
+    assert singularity_image_dir.join('zlib').exists()