Merge branch 'release_20.09' into dev

galaxyproject · Nov 1, 2020 · c03cc3d · c03cc3d
2 parents a72cc38 + 31685ac
commit c03cc3d
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Showing 40 changed files with 987 additions and 240 deletions.
diff --git a/client/src/components/JobStates/CollectionJobStates.vue b/client/src/components/JobStates/CollectionJobStates.vue
@@ -36,7 +36,7 @@ export default {
     mixins: [mixin],
     computed: {
         loadingNote() {
-            return `Loading job data for ${this.collectionTypeDescription}}`;
+            return `Loading job data for ${this.collectionTypeDescription}`;
         },
         generatingNote() {
             return `${this.jobsStr} generating a ${this.collectionTypeDescription}`;

diff --git a/client/src/components/ProgressBar.vue b/client/src/components/ProgressBar.vue
@@ -1,6 +1,6 @@
 <template>
-    <div class="my-1">
-        <small class="position-absolute text-center w-100" v-if="note">
+    <div class="my-1 progressContainer">
+        <small v-if="note" class="progressNote">
             {{ note }}<span v-if="loading">.<span class="blinking">..</span></span>
         </small>
         <b-progress :max="total">
@@ -46,3 +46,13 @@ export default {
     },
 };
 </script>
+<style lang="css" scoped>
+.progressNote {
+    position: absolute;
+    text-align: center;
+    width: 100%;
+}
+.progressContainer {
+    position: relative;
+}
+</style>
diff --git a/client/src/components/User/ExternalIdentities/ExternalLogin.vue b/client/src/components/User/ExternalIdentities/ExternalLogin.vue
@@ -226,7 +226,10 @@ export default {
     },
     created() {
         this.rememberIdp = this.getIdpPreference() !== null;
-        this.getCILogonIdps();
+        /* Only fetch CILogonIDPs if custos/cilogon configured */
+        if (this.cilogonListShow) {
+            this.getCILogonIdps();
+        }
     },
 };
 </script>

diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
@@ -380,14 +380,14 @@ export default {
                     const markdown = report.markdown || reportDefault;
                     this.markdownText = markdown;
                     this.markdownConfig = report;
-                    showUpgradeMessage(data);
+                    const has_changes = showUpgradeMessage(data);
                     getVersions(this.id).then((versions) => {
                         this.versions = versions;
                     });
                     Vue.nextTick(() => {
                         this.canvasManager.drawOverview();
                         this.canvasManager.scrollToNodes();
-                        this.hasChanges = false;
+                        this.hasChanges = has_changes;
                     });
                 })
                 .catch((response) => {

diff --git a/client/src/components/Workflow/Editor/modules/utilities.js b/client/src/components/Workflow/Editor/modules/utilities.js
@@ -101,12 +101,14 @@ export function showForm(workflow, node, datatypes) {
 export function showUpgradeMessage(data) {
     // Determine if any parameters were 'upgraded' and provide message
     var upgrade_message = "";
+    let hasToolUpgrade = false;
     _.each(data.steps, (step, step_id) => {
         var details = "";
         if (step.errors) {
             details += `<li>${step.errors}</li>`;
         }
         _.each(data.upgrade_messages[step_id], (m) => {
+            hasToolUpgrade = true;
             details += `<li>${m}</li>`;
         });
         if (details) {
@@ -122,6 +124,7 @@ export function showUpgradeMessage(data) {
     } else {
         hide_modal();
     }
+    return hasToolUpgrade;
 }
 
 export function getWorkflowParameters(nodes) {

diff --git a/client/src/mvc/form/form-section.js b/client/src/mvc/form/form-section.js
@@ -89,9 +89,11 @@ var View = Backbone.View.extend({
                             break;
                         }
                     }
-                    if (i == selectedCase && nonhidden) {
+                    if (i == selectedCase) {
                         const selectedView = self.elements[input_def.id + "_" + i];
                         selectedView.renderOnce();
+                    }
+                    if (i == selectedCase && nonhidden) {
                         section_row.fadeIn("fast");
                     } else {
                         section_row.hide();
@@ -156,7 +158,7 @@ var View = Backbone.View.extend({
 
     /** Add a customized section */
     _addSection: function (input_def) {
-        const section = new View(this.app, { inputs: input_def.inputs, skip_render: true });
+        const section = new View(this.app, { inputs: input_def.inputs });
         var portlet = new Portlet.View({
             title: input_def.title || input_def.name,
             cls: "ui-portlet-section",

diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
@@ -56,6 +56,7 @@ def __init__(self, app, oidc_config_file, oidc_backends_config_file):
             file (e.g., oidc_backends_config.xml).
         """
         self.app = app
+        self.allowed_idps = None
         self._parse_oidc_config(oidc_config_file)
         self._parse_oidc_backends_config(oidc_backends_config_file)
 

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
@@ -938,6 +938,8 @@ class Anndata(H5):
     True
     >>> Anndata().sniff(get_test_fname('test.mz5'))
     False
+    >>> Anndata().sniff(get_test_fname('import.loom.krumsiek11.h5ad'))
+    True
     """
     file_ext = 'h5ad'
 
@@ -953,20 +955,20 @@ class Anndata(H5):
     MetadataElement(name="obs_names", desc="obs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
     MetadataElement(name="obs_layers", desc="obs_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
     MetadataElement(name="obs_count", default=0, desc="obs_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="obs_size", default=0, desc="obs_size", readonly=True, visible=True, no_value=0)
+    MetadataElement(name="obs_size", default=-1, desc="obs_size", readonly=True, visible=True, no_value=0)
     MetadataElement(name="obsm_layers", desc="obsm_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
     MetadataElement(name="obsm_count", default=0, desc="obsm_count", readonly=True, visible=True, no_value=0)
     MetadataElement(name="raw_var_layers", desc="raw_var_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
     MetadataElement(name="raw_var_count", default=0, desc="raw_var_count", readonly=True, visible=True, no_value=0)
     MetadataElement(name="raw_var_size", default=0, desc="raw_var_size", readonly=True, visible=True, no_value=0)
     MetadataElement(name="var_layers", desc="var_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
     MetadataElement(name="var_count", default=0, desc="var_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="var_size", default=0, desc="var_size", readonly=True, visible=True, no_value=0)
+    MetadataElement(name="var_size", default=-1, desc="var_size", readonly=True, visible=True, no_value=0)
     MetadataElement(name="varm_layers", desc="varm_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
     MetadataElement(name="varm_count", default=0, desc="varm_count", readonly=True, visible=True, no_value=0)
     MetadataElement(name="uns_layers", desc="uns_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
     MetadataElement(name="uns_count", default=0, desc="uns_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="shape", default=(), desc="shape", param=metadata.ListParameter, readonly=True, visible=True, no_value=(0, 0))
+    MetadataElement(name="shape", default=(-1, -1), desc="shape", param=metadata.ListParameter, readonly=True, visible=True, no_value=(0, 0))
 
     def sniff(self, filename):
         if super().sniff(filename):
@@ -979,79 +981,78 @@ def sniff(self, filename):
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
-        try:
-            with h5py.File(dataset.file_name, 'r') as anndata_file:
-                dataset.metadata.title = util.unicodify(anndata_file.attrs.get('title'))
-                dataset.metadata.description = util.unicodify(anndata_file.attrs.get('description'))
-                dataset.metadata.url = util.unicodify(anndata_file.attrs.get('url'))
-                dataset.metadata.doi = util.unicodify(anndata_file.attrs.get('doi'))
-                dataset.creation_date = util.unicodify(anndata_file.attrs.get('creation_date'))
-                # none of the above appear to work in any dataset tested, but could be useful for future
-                # AnnData datasets
-
-                # all possible keys
-                dataset.metadata.layers_count = len(anndata_file)
-                dataset.metadata.layers_names = list(anndata_file.keys())
-
-                def _layercountsize(tmp, lennames=0):
-                    "From TMP and LENNAMES, return layers, their number, and the length of one of the layers (all equal)."
-                    if hasattr(tmp, 'dtype'):
-                        layers = [util.unicodify(x) for x in tmp.dtype.names]
-                        count = len(tmp.dtype)
-                        size = int(tmp.size)
-                    else:
-                        layers = [util.unicodify(x) for x in tmp.keys()]
-                        count = len(layers)
-                        size = lennames
-                    return (layers, count, size)
-
-                if 'obs' in dataset.metadata.layers_names:
-                    tmp = anndata_file["obs"]
-                    dataset.metadata.obs_names = [util.unicodify(x) for x in tmp["index"]]
-                    dataset.metadata.obs_layers, \
-                        dataset.metadata.obs_count, \
-                        dataset.metadata.obs_size = _layercountsize(tmp, len(dataset.metadata.obs_names))
-
-                if 'obsm' in dataset.metadata.layers_names:
-                    tmp = anndata_file["obsm"]
-                    dataset.metadata.obsm_layers, dataset.metadata.obsm_count, _ = _layercountsize(tmp)
-
-                if 'raw.var' in dataset.metadata.layers_names:
-                    tmp = anndata_file["raw.var"]
-                    # full set of genes would never need to be previewed
-                    # dataset.metadata.raw_var_names = tmp["index"]
-                    dataset.metadata.raw_var_layers, \
-                        dataset.metadata.raw_var_count, \
-                        dataset.metadata.raw_var_size = _layercountsize(tmp, len(tmp["index"]))
-
-                if 'var' in dataset.metadata.layers_names:
-                    tmp = anndata_file["var"]
-                    # row names are never used in preview windows
-                    # dataset.metadata.var_names = tmp["index"]
-                    dataset.metadata.var_layers, \
-                        dataset.metadata.var_count, \
-                        dataset.metadata.var_size = _layercountsize(tmp, len(tmp["index"]))
-
-                if 'varm' in dataset.metadata.layers_names:
-                    tmp = anndata_file["varm"]
-                    dataset.metadata.varm_layers, dataset.metadata.varm_count, _ = _layercountsize(tmp)
-
-                if 'uns' in dataset.metadata.layers_names:
-                    tmp = anndata_file["uns"]
-                    dataset.metadata.uns_layers, dataset.metadata.uns_count, _ = _layercountsize(tmp)
-
-                if 'X' in dataset.metadata.layers_names:
-                    # Shape we determine here due to the non-standard representation of 'X' dimensions
-                    shape = anndata_file['X'].attrs.get("shape")
-                    if shape is not None:
-                        dataset.metadata.shape = tuple(shape)
-                    elif hasattr(anndata_file['X'], 'shape'):
-                        dataset.metadata.shape = tuple(anndata_file['X'].shape)
-                    else:
-                        dataset.metadata.shape = (int(dataset.metadata.obs_size), int(dataset.metadata.var_size))
-
-        except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+        with h5py.File(dataset.file_name, 'r') as anndata_file:
+            dataset.metadata.title = util.unicodify(anndata_file.attrs.get('title'))
+            dataset.metadata.description = util.unicodify(anndata_file.attrs.get('description'))
+            dataset.metadata.url = util.unicodify(anndata_file.attrs.get('url'))
+            dataset.metadata.doi = util.unicodify(anndata_file.attrs.get('doi'))
+            dataset.creation_date = util.unicodify(anndata_file.attrs.get('creation_date'))
+            dataset.metadata.shape = anndata_file.attrs.get('shape') or dataset.metadata.shape
+            # none of the above appear to work in any dataset tested, but could be useful for future
+            # AnnData datasets
+
+            # all possible keys
+            dataset.metadata.layers_count = len(anndata_file)
+            dataset.metadata.layers_names = list(anndata_file.keys())
+
+            def _layercountsize(tmp, lennames=0):
+                "From TMP and LENNAMES, return layers, their number, and the length of one of the layers (all equal)."
+                if hasattr(tmp, 'dtype'):
+                    layers = [util.unicodify(x) for x in tmp.dtype.names]
+                    count = len(tmp.dtype)
+                    size = int(tmp.size)
+                else:
+                    layers = [util.unicodify(x) for x in list(tmp.keys())]
+                    count = len(layers)
+                    size = lennames
+                return (layers, count, size)
+
+            if 'obs' in dataset.metadata.layers_names:
+                tmp = anndata_file["obs"]
+                dataset.metadata.obs_names = [util.unicodify(x) for x in tmp["index"]]
+                dataset.metadata.obs_layers, \
+                    dataset.metadata.obs_count, \
+                    dataset.metadata.obs_size = _layercountsize(tmp, len(dataset.metadata.obs_names))
+
+            if 'obsm' in dataset.metadata.layers_names:
+                tmp = anndata_file["obsm"]
+                dataset.metadata.obsm_layers, dataset.metadata.obsm_count, _ = _layercountsize(tmp)
+
+            if 'raw.var' in dataset.metadata.layers_names:
+                tmp = anndata_file["raw.var"]
+                # full set of genes would never need to be previewed
+                # dataset.metadata.raw_var_names = tmp["index"]
+                dataset.metadata.raw_var_layers, \
+                    dataset.metadata.raw_var_count, \
+                    dataset.metadata.raw_var_size = _layercountsize(tmp, len(tmp["index"]))
+
+            if 'var' in dataset.metadata.layers_names:
+                tmp = anndata_file["var"]
+                # row names are never used in preview windows
+                # dataset.metadata.var_names = tmp["index"]
+                dataset.metadata.var_layers, \
+                    dataset.metadata.var_count, \
+                    dataset.metadata.var_size = _layercountsize(tmp, len(tmp["index"]))
+
+            if 'varm' in dataset.metadata.layers_names:
+                tmp = anndata_file["varm"]
+                dataset.metadata.varm_layers, dataset.metadata.varm_count, _ = _layercountsize(tmp)
+
+            if 'uns' in dataset.metadata.layers_names:
+                tmp = anndata_file["uns"]
+                dataset.metadata.uns_layers, dataset.metadata.uns_count, _ = _layercountsize(tmp)
+
+            # Resolving the problematic shape parameter
+            if 'X' in dataset.metadata.layers_names:
+                # Shape we determine here due to the non-standard representation of 'X' dimensions
+                shape = anndata_file['X'].attrs.get("shape")
+                if shape is not None:
+                    dataset.metadata.shape = tuple(shape)
+                elif hasattr(anndata_file['X'], 'shape'):
+                    dataset.metadata.shape = tuple(anndata_file['X'].shape)
+
+            if dataset.metadata.shape is None:
+                dataset.metadata.shape = (int(dataset.metadata.obs_size), int(dataset.metadata.var_size))
 
     def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:

diff --git a/lib/galaxy/datatypes/test/import.loom.krumsiek11.h5ad b/lib/galaxy/datatypes/test/import.loom.krumsiek11.h5ad