Merge branch 'alpha' into gh-actions-mergeback-v0.35.4-alpha

README.md

@@ -36,6 +36,7 @@ These instructions will get you a copy of the project and the API up and running
    *  [Database](#database)
 -  [Loading Data](#loading-data)
 -  [Submitting Data](#submitting-data)
+   *  [Load Order Dependencies](#load-order-dependencies)
 -  [Querying Data](#querying-data)
    *  [Elastic Search](#search)
    *  [Database Search](#find)
@@ -592,9 +593,8 @@ the new version of the application can function in a consistent state upon and a
 2. Reindex all data types by calling the `system/reindexeverything` endpoint with default arguments (found in the
    System Endpoints section in the swagger UI) and follow-up through the log server to check for progress and errors.
 3. Once reindexing completed, look at the dashboard page (where you deployed to)
-    and ensure that for each Entity and Ontology, the number in the `Database * count`  column matches the number in the `Search index * count` column (ignore the values for `Disease Annotations` and `Literature References`). If there is a mismatch for any row,
-    investigate what caused this and fix the issue first before continuing the deployment.
-4. If code to support new ontologies was added, create the respective new data loads through the Data loads page and load the new file.
+    and ensure that for each Entity and Ontology, the number in the `Database * count`  column matches the number in the `Search index * count` for all indexed datatypes. If there is a mismatch for any row, investigate what caused this and fix the issue first before continuing the deployment.
+4. If code to support new ontologies or datatypes was added, create the respective new data loads through the Data loads page (if not already done so via a database migration) and load the new files.  Attention should be paid to any [load order dependencies](#load-order-dependencies)
 5. After completing all above steps successfully, return to the code promoting section to complete the last step(s) ([alpha to beta](#promoting-code-from-alpha-to-beta) or [beta to production](#promoting-code-from-beta-to-production))
 
 
@@ -715,7 +715,7 @@ curl \
    -F "LoadType_SubType=@/full/path/to/file2.json"
 ```
 
-Valid values for LoadType, and SubType can be found in the examples below.
+Valid values for LoadType, and SubType can be found in the examples below.  Attention should be paid to any [load order dependencies](#load-order-dependencies).
 
 ### Curation System
 
@@ -769,6 +769,44 @@ The LinkML version for which the file is being submitted now needs to be added t
   "disease_agm_ingest_set" : [ {
 ```
 
+### Load Order Dependencies
+
+When loading data, whether it be via direct DQM submissions, FMS loads, or URL loads, there are a number of load order dependencies to take notice of.  The current list of loads and their dependencies (as of 16/12/2024) is given below.  As a general rule, entity loads should be run first.  Most loads will not remove the results of previous loads - the exception to this is the Gene load.  Running the Gene load will result of the removal of cross-references attached to the genes via the BioGrid-ORCS, ExpressionAtlas, and GEO CrossReference loads.  As such it is essential that these loads are rerun after a gene load.
+
+1. Entity loads
+   * AGM
+   * Allele
+   * Construct
+   * Gene
+   * HTP Dataset Annotation
+   * HTP Dataset Sample Annotation
+   * Molecule
+   * Sequence Targeting Reagent (dependent on: Gene)
+   * Variant
+2. Association loads
+   * Allele Association (dependent on: Allele, Gene)
+   * Construct Association (dependent on: AGM, Allele, Construct, Gene)
+   * Disease Annotation (dependent on: AGM, Allele, Gene)
+   * Expression (dependent on: Gene)
+   * GAF (dependent on: Gene)
+   * Interaction (dependent on: Gene)
+   * Phenotype Annotation (dependent on: AGM, Allele, Gene)
+3. CrossReference loads (all need to be rerun after Gene loads)
+   * BioGrid-ORCS (dependent on: Gene)
+   * ExpressionAtlas (dependent on: Gene)
+   * GEO CrossReference (dependent on: Gene)
+4. GFF loads
+   * GFF Gene (dependent on: Gene)
+   * GFF Transcript (dependent on: Gene)
+   * GFF CDS (dependent on: GFF Transcript)
+   * GFF Exon (dependent on: GFF Transcript)
+5. Orthology loads
+   * Orthology (dependent on: Gene)
+   * Paralogy (dependent on: Gene)
+6. VEP loads
+   * VEP Transcript (dependent on: Variant, GFF Transcript)
+   * VEP Gene (dependent on: VEP Transcript)
+
 ## Querying Data
 
 ### Search

src/main/cliapp/src/components/Actions/EntityDetailsAction.js

@@ -1,14 +1,18 @@
 import { Link } from 'react-router-dom/cjs/react-router-dom.min';
 import { Tooltip } from 'primereact/tooltip';
 
-export const EntityDetailsAction = ({ identifier, disabled }) => {
+export const EntityDetailsAction = ({ endpoint, identifier, disabled }) => {
 	const disabledClasses = disabled ? 'pointer-events-none opacity-50' : '';
 
 	if (!identifier) return null;
 
 	return (
 		<>
-			<Link to={`allele/${identifier}`} target="_blank" className={`${identifier.replace(':', '')} ${disabledClasses}`}>
+			<Link
+				to={`${endpoint}/${identifier}`}
+				target="_blank"
+				className={`${identifier.replace(':', '')} ${disabledClasses}`}
+			>
 				<i className="pi pi-info-circle"></i>
 			</Link>
 			<Tooltip target={`.${identifier.replace(':', '')}`} content={'Open Details'} />

src/main/cliapp/src/components/EntityCountsComponent.js

@@ -28,6 +28,8 @@ export const EntityCountsComponent = () => {
 					_tableData[type].push({
 						name: CLASSES[key].name,
 						link: CLASSES[key].link,
+						type: CLASSES[key].type,
+						isIndexed: CLASSES[key].isIndexed,
 						dbCount: res.entity[key]['dbCount'],
 						esCount: res.entity[key]['esCount'],
 					});
@@ -42,13 +44,15 @@ export const EntityCountsComponent = () => {
 	}, []);
 
 	const nameHyperlinkTemplate = (rowData) => {
+		if (!rowData.link) {
+			return rowData.name;
+		}
 		return <a href={rowData.link}>{rowData.name}</a>;
 	};
 
-	const ROW_HIGHLIGHT_IGNORE = ['Disease Annotations', 'Literature References', 'Bulk Loads / Failed Loads'];
-
 	const getRowClass = (rowData) => {
-		if (ROW_HIGHLIGHT_IGNORE.includes(rowData.name)) return;
+		console.log(rowData);
+		if (!rowData.isIndexed) return;
 
 		if (rowData?.dbCount !== rowData.esCount) {
 			return 'bg-gray-500 text-white';
@@ -58,7 +62,7 @@ export const EntityCountsComponent = () => {
 	return (
 		<>
 			<div className="grid nested dashboard">
-				<div className="col-4">
+				<div className="col-3">
 					<DataTable
 						header="Entities"
 						value={tableData.entity}
@@ -79,7 +83,7 @@ export const EntityCountsComponent = () => {
 						/>
 					</DataTable>
 				</div>
-				<div className="col-4">
+				<div className="col-3">
 					<DataTable
 						header="Ontologies"
 						value={tableData.ontology}
@@ -100,7 +104,23 @@ export const EntityCountsComponent = () => {
 						/>
 					</DataTable>
 				</div>
-				<div className="col-4">
+				<div className="col-3">
+					<DataTable
+						header="Associations"
+						value={tableData.association}
+						sortField="name"
+						sortOrder={1}
+						rowClassName={(rowData) => getRowClass(rowData)}
+					>
+						<Column field="name" header="Association Type" body={nameHyperlinkTemplate} />
+						<Column
+							field="dbCount"
+							header="Database Association Count"
+							body={(rowData) => <NumberTemplate number={rowData.dbCount} />}
+						/>
+					</DataTable>
+				</div>
+				<div className="col-3">
 					<DataTable
 						header="System"
 						value={tableData.system}

src/main/cliapp/src/components/GenericDataTable/GenericDataTable.js

@@ -370,8 +370,12 @@ export const GenericDataTable = (props) => {
 				{hasDetails && (
 					<Column
 						field="details"
-						editor={(props) => <EntityDetailsAction identifier={getIdentifier(props.rowData)} disabled={true} />}
-						body={(props) => <EntityDetailsAction identifier={getIdentifier(props)} disabled={isInEditMode} />}
+						editor={(props) => (
+							<EntityDetailsAction endpoint={endpoint} identifier={getIdentifier(props.rowData)} disabled={true} />
+						)}
+						body={(props) => (
+							<EntityDetailsAction endpoint={endpoint} identifier={getIdentifier(props)} disabled={isInEditMode} />
+						)}
 						showFilterMenu={false}
 						className={`text-center p-0 action-column ${isEditable ? 'visible' : 'hidden'}`}
 						bodyStyle={{ textAlign: 'center' }}

src/main/cliapp/src/components/Templates/dialog/ListDialogTemplate.js

@@ -9,7 +9,7 @@ export const ListDialogTemplate = ({ entities, handleOpen, getTextField, underli
 
 	const listTemplate = (item) => (
 		<div
-			className={`overflow-hidden text-overflow-ellipsis ${underline ? 'underline' : ''}`}
+			className={`overflow-hidden text-left text-overflow-ellipsis ${underline ? 'underline' : ''}`}
 			dangerouslySetInnerHTML={{ __html: item }}
 		/>
 	);