Implement upload warnings...

client/src/components/Upload/DefaultBox.vue

@@ -14,8 +14,8 @@ import { COLLECTION_TYPES, DEFAULT_FILE_NAME, hasBrowserSupport } from "./utils"
 
 import DefaultRow from "./DefaultRow.vue";
 import UploadBox from "./UploadBox.vue";
-import UploadExtension from "./UploadExtension.vue";
 import UploadSelect from "./UploadSelect.vue";
+import UploadSelectExtension from "./UploadSelectExtension.vue";
 
 library.add(faCopy, faEdit, faFolderOpen, faLaptop);
 
@@ -392,15 +392,13 @@ defineExpose({
                 placeholder="Select Type"
                 @input="updateCollectionType" />
             <span class="upload-footer-title">Type (set all):</span>
-            <UploadSelect
+            <UploadSelectExtension
                 class="upload-footer-extension"
                 :value="extension"
                 :disabled="isRunning"
-                :options="listExtensions"
-                what="file type"
-                placeholder="Select Type"
-                @input="updateExtension" />
-            <UploadExtension :extension="extension" :list-extensions="listExtensions" />
+                :list-extensions="listExtensions"
+                @input="updateExtension">
+            </UploadSelectExtension>
             <span class="upload-footer-title">Reference (set all):</span>
             <UploadSelect
                 class="upload-footer-genome"

client/src/components/Upload/UploadSelect.vue

@@ -33,6 +33,10 @@ const props = defineProps({
         type: Boolean,
         default: true,
     },
+    warn: {
+        type: Boolean,
+        default: false,
+    },
 });
 
 const emit = defineEmits(["input"]);
@@ -59,9 +63,10 @@ const currentValue = computed({
         select-label=""
         selected-label=""
         track-by="id">
-        <template
-            ><span slot="noResult" v-localize>No matching {{ what }}s found.</span></template
-        >
+        <span slot="noResult" v-localize>No matching {{ what }}s found.</span>
+        <span slot="singleLabel" slot-scope="{ option }" :class="{ 'selection-warning': warn }">
+            {{ option.text }}
+        </span>
     </Multiselect>
 </template>
 
@@ -71,6 +76,9 @@ const currentValue = computed({
     display: inline-block;
     min-height: unset;
     width: 150px;
+    .selection-warning {
+        color: $brand-warning;
+    }
     .multiselect__content-wrapper {
         .multiselect__content {
             width: inherit;

client/src/components/Upload/UploadSelectExtension.vue

@@ -0,0 +1,63 @@
+<script setup>
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faExclamationCircle } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { computed } from "vue";
+
+import { findExtension } from "./utils";
+
+import UploadExtension from "./UploadExtension.vue";
+import UploadSelect from "./UploadSelect.vue";
+import Popper from "@/components/Popper/Popper.vue";
+
+library.add(faExclamationCircle);
+
+const props = defineProps({
+    disabled: {
+        type: Boolean,
+        default: false,
+    },
+    listExtensions: {
+        type: Array,
+        required: true,
+    },
+    value: {
+        type: String,
+        default: null,
+    },
+});
+
+const emit = defineEmits(["input"]);
+
+const details = computed(() => findExtension(props.listExtensions, props.value));
+const warnText = computed(() => details.value.upload_warning);
+</script>
+
+<template>
+    <span title="">
+        <UploadSelect
+            :value="value"
+            :disabled="disabled"
+            :options="listExtensions"
+            what="file type"
+            placeholder="Select Type"
+            :warn="warnText ? true : false"
+            @input="(newValue) => emit('input', newValue)" />
+        <Popper v-if="warnText" placement="bottom" mode="light">
+            <template v-slot:reference>
+                <FontAwesomeIcon icon="fa-exclamation-circle" class="selection-warning" />
+            </template>
+            <div class="p-2">
+                {{ warnText }}
+            </div>
+        </Popper>
+        <UploadExtension :extension="value" :list-extensions="listExtensions" />
+    </span>
+</template>
+
+<style lang="scss" scoped>
+@import "theme/blue.scss";
+.selection-warning {
+    color: $brand-warning;
+}
+</style>

client/src/components/Upload/utils.js

@@ -74,6 +74,7 @@ async function loadUploadDatatypes() {
             description: datatypes[key].description,
             description_url: datatypes[key].description_url,
             composite_files: datatypes[key].composite_files,
+            upload_warning: datatypes[key].upload_warning,
         });
     }
     listExtensions.sort((a, b) => {

client/src/schema/schema.ts

@@ -3631,6 +3631,11 @@ export interface components {
              * @example bed
              */
             extension: string;
+            /**
+             * Upload warning
+             * @description End-user information regarding potential pitfalls with this upload type.
+             */
+            upload_warning?: string;
         };
         /** DatatypeEDAMDetails */
         DatatypeEDAMDetails: {

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -136,6 +136,9 @@
     </datatype>
     <datatype extension="fastg" type="galaxy.datatypes.sequence:Fastg" display_in_upload="true" description="fastg format faithfully represents genome assemblies in the face of allelic polymorphism and assembly uncertainty" description_url="http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf"/>
     <datatype extension="fastq" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq">
+      <upload_warning>
+        Generally a more specific fastq datatype should be specified, please consider selecting fastqsanger${auto_compressed_type} instead.
+      </upload_warning>
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
     </datatype>
     <datatype extension="fastqsanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true" description="Sanger variant of the FASTQ format: phred+33">
@@ -147,6 +150,9 @@
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
     </datatype>
     <datatype extension="fastqcssanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true" description="sequence in in color space phred scored quality values 0:93 represented by ASCII 33:126">
+      <upload_warning>
+        Color space data is rarely used in modern analyses, please consider selecting fastqsanger${auto_compressed_type} instead.
+      </upload_warning>
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
     </datatype>
     <datatype extension="fastqillumina" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true" description="Sanger variant of the FASTQ format: phred+64">

lib/galaxy/datatypes/_schema.py

@@ -47,6 +47,11 @@ class DatatypeDetails(BaseModel):
     composite_files: Optional[List[CompositeFileInfo]] = Field(
         default=None, title="Composite files", description="A collection of files composing this data type"
     )
+    upload_warning: Optional[str] = Field(
+        default=None,
+        title="Upload warning",
+        description="End-user information regarding potential pitfalls with this upload type.",
+    )
 
 
 class DatatypesMap(BaseModel):

lib/galaxy/datatypes/registry.py

@@ -250,6 +250,14 @@ def __import_module(full_path: str, datatype_module: str):
                         datatype_class.is_subclass = make_subclass
                         description = elem.get("description", None)
                         description_url = elem.get("description_url", None)
+
+                        # process as a list, in the future handle grabbing extensions here
+                        upload_warning_els = elem.findall("upload_warning")
+                        upload_warning_template = None
+                        for upload_warning_el in upload_warning_els:
+                            if upload_warning_template is not None:
+                                raise NotImplementedError("Multiple upload_warnings not implemented")
+                            upload_warning_template = Template(upload_warning_el.text)
                         datatype_instance = datatype_class()
                         self.datatypes_by_extension[extension] = datatype_instance
                         if mimetype is None:
@@ -303,6 +311,7 @@ def __import_module(full_path: str, datatype_module: str):
                             "extension": extension,
                             "description": description,
                             "description_url": description_url,
+                            "upload_warning": upload_warning(upload_warning_template),
                         }
                         composite_files = datatype_instance.get_composite_files()
                         if composite_files:
@@ -353,6 +362,7 @@ def __import_module(full_path: str, datatype_module: str):
                                     "extension": compressed_extension,
                                     "description": description,
                                     "description_url": description_url,
+                                    "upload_warning": upload_warning(upload_warning_template, auto_compressed_type),
                                 }
                             )
                             if auto_compressed_type == "gz":
@@ -965,6 +975,13 @@ def __getstate__(self):
         return state
 
 
+def upload_warning(template: Optional[Template], auto_compressed_type: Optional[str] = None) -> Optional[str]:
+    if template is None:
+        return None
+    template_args = {"auto_compressed_type": "" if auto_compressed_type is None else f".{auto_compressed_type}"}
+    return template.safe_substitute(template_args)
+
+
 def example_datatype_registry_for_sample(sniff_compressed_dynamic_datatypes_default=True):
     galaxy_dir = galaxy.util.galaxy_directory()
     sample_conf = os.path.join(galaxy_dir, "lib", "galaxy", "config", "sample", "datatypes_conf.xml.sample")