Merge pull request #442 from alliance-genome/release/v0.4.0-rc4

Release/v0.4.0 rc4

.github/workflows/alpha-build-and-deploy.yml

@@ -1,15 +1,12 @@
 name: Alpha branch Build and Deployment
 on:
-  push:
+  pull_request:
+    types: [closed]
     branches:
       - alpha
-    paths-ignore:
-      - '**.md'
-      - .gitignore
-      - .github/workflows/github-actions-PR-validation.yml
-      - .github/workflows/github-release-build-and-deploy.yml
 jobs:
   build-and-push-docker-image:
+    if: github.event.pull_request.merged == true && !contains(github.event.pull_request.labels.*.name, 'no-deploy')
     runs-on: ubuntu-20.04
     steps:
     - name: Check out repository code
@@ -43,6 +40,7 @@ jobs:
         docker push $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG
         docker push $ECR_REGISTRY/$ECR_REPOSITORY:${GITHUB_REF#refs/heads/}
   deploy-to-alpha:
+    if: github.event.pull_request.merged == true && !contains(github.event.pull_request.labels.*.name, 'no-deploy')
     needs: [build-and-push-docker-image]
     runs-on: ubuntu-20.04
     steps:

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Alliance of Genome Resources
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

docker/run_es

@@ -1 +1 @@
-docker run -d --net curation -p 9200:9200 -p 9300:9300 -e "discovery.type=single-node" --name elasticsearch docker.elastic.co/elasticsearch/elasticsearch:7.10.2
+docker run -d --net curation -p 9200:9200 -p 9300:9300 -e "discovery.type=single-node" -e "ES_JAVA_OPTS=-Xmx4g -Xms4g" --name elasticsearch docker.elastic.co/elasticsearch/elasticsearch:7.10.2

src/main/cliapp/src/App.js

@@ -7,7 +7,7 @@ import { oktaAuthConfig } from './oktaAuthConfig';
 import { SiteLayout } from './containers/layout'
 
 import routes from './routes';
-
+import './App.scss';
 
 const App = () => {
 

src/main/cliapp/src/App.scss

@@ -1 +1,7 @@
+.p-frozen-column{
+	z-index : 1
+}
 
+.p-datatable-scrollable .p-datatable-thead{
+	z-index : 2
+}

src/main/cliapp/src/components/ErrorMessageComponent.js

@@ -5,11 +5,11 @@ import { Message }  from "primereact/message";
 export function ErrorMessageComponent({ errorField, errorMessages: errorMessagesRow }) {
     if(errorMessagesRow){
         return (
-            <div>
+            <div style={{position:"absolute", paddingTop:"25px"}}>
                 <Message
                     severity={errorMessagesRow[errorField] ? errorMessagesRow[errorField].severity : ""}
                     text={errorMessagesRow[errorField] ? errorMessagesRow[errorField].message : ""}
-                    style={{position:"absolute"}}
+                    style={{position:"absolute", display: "inline-table", zIndex: "5"}}
                 />
             </div>
         );

src/main/cliapp/src/containers/controlledVocabularyPage/ControlledVocabularyComponent.js

@@ -405,9 +405,9 @@ export const ControlledVocabularyComponent = () => {
           filter={col.filter}
           showFilterMenu={false}
           filterElement={col.filterElement}
-          style={{whiteSpace: 'normal', 
-              display: 'inline-block', 
-              minWidth:`${columnWidths[col.field]}vw`, 
+          style={{whiteSpace: 'normal',
+              display: 'inline-block',
+              minWidth:`${columnWidths[col.field]}vw`,
               maxWidth: `${columnWidths[col.field]}vw`
           }}
           headerClassName='surface-0'
@@ -512,7 +512,7 @@ export const ControlledVocabularyComponent = () => {
 
     const onRowEditCVCChange = (event) => {
         setEditingCVCRows(event.data);
-    };                             
+    };
 
     const handleColumnResizeEnd = (event) => {
         const currentWidth = event.element.clientWidth;
@@ -545,8 +545,8 @@ export const ControlledVocabularyComponent = () => {
           currentPageReportTemplate="Showing {first} to {last} of {totalRecords}" rows={tableState.rows} rowsPerPageOptions={[10, 20, 50, 100, 250, 1000]}
           resizableColumns columnResizeMode="expand" showGridlines onColumnResizeEnd={handleColumnResizeEnd}
         >
+        <Column rowEditor style={{maxWidth: '7rem'}} headerStyle={{ width: '7rem', position: 'sticky' }} bodyStyle={{textAlign: 'center'}} frozen headerClassName='surface-0'/>
           {columnList}
-          <Column rowEditor style={{'maxWidth': '7rem'}} headerStyle={{ width: '7rem' }} bodyStyle={{textAlign: 'center'}}/>
         </DataTable>
         <NewTermForm
             newTermDialog = {newTermDialog}

src/main/cliapp/src/containers/dashboardPage/Dashboard.js

@@ -47,6 +47,10 @@ export const Dashboard = () => {
       setTermCounts((list) => [...list, { name: "CHEBI", count: results.totalResults, link: '/#/ontology/chebi' }]);
     });
 
+    searchService.search('xsmoterm', 0, 0).then(results => {
+      setTermCounts((list) => [...list, { name: "XSMO", count: results.totalResults, link: '/#/ontology/xsmo' }]);
+    });
+
     searchService.search('ecoterm', 0, 0).then(results => {
       setTermCounts((list) => [...list, { name: "ECO", count: results.totalResults, link: '/#/ontology/eco' }]);
     });
@@ -87,6 +91,15 @@ export const Dashboard = () => {
       setTermCounts((list) => [...list, { name: "WBbt", count: results.totalResults, link: '/#/ontology/wbbt' }]);
     });
 
+    searchService.search('xbaterm', 0, 0).then(results => {
+      setTermCounts((list) => [...list, { name: "XBA", count: results.totalResults, link: '/#/ontology/xba' }]);
+    });
+
+
+    searchService.search('xbsterm', 0, 0).then(results => {
+      setTermCounts((list) => [...list, { name: "XBS", count: results.totalResults, link: '/#/ontology/xbs' }]);
+    });
+
     searchService.search('xcoterm', 0, 0).then(results => {
       setTermCounts((list) => [...list, { name: "XCO", count: results.totalResults, link: '/#/ontology/xco' }]);
     });
@@ -114,6 +127,14 @@ export const Dashboard = () => {
     searchService.search('zfsterm', 0, 0).then(results => {
       setTermCounts((list) => [...list, { name: "ZFS", count: results.totalResults, link: '/#/ontology/zfs' }]);
     });
+
+    searchService.search('xpoterm', 0, 0).then(results => {
+      setTermCounts((list) => [...list, { name: "XPO", count: results.totalResults, link: '/#/ontology/xpo' }]);
+    });
+
+    searchService.search('xbedterm', 0, 0).then(results => {
+      setTermCounts((list) => [...list, { name: "XBED", count: results.totalResults, link: '/#/ontology/xbed' }]);
+    });
   }, []);
 
   const nameHyperlinkTemplate = (rowData) => {

src/main/cliapp/src/containers/dataLoadsPage/DataLoadsComponent.js

@@ -137,10 +137,10 @@ export const DataLoadsComponent = () => {
   const loadFileActionBodyTemplate = (rowData) => {
     let ret = [];
 
-    if(!rowData.status || rowData.status === "FINISHED" || rowData.status === "FAILED") {
+    if(!rowData.status || rowData.status === "FINISHED" || rowData.status === "FAILED" || rowData.status === "STOPPED") {
       ret.push(<Button key="run" icon="pi pi-play" className="p-button-rounded p-button-success mr-2" onClick={() => runLoadFile(rowData)} />);
     }
-    if(!rowData.status || rowData.status === "FINISHED" || rowData.status === "FAILED") {
+    if(!rowData.status || rowData.status === "FINISHED" || rowData.status === "FAILED" || rowData.status === "STOPPED") {
       ret.push(<Button key="delete" icon="pi pi-trash" className="p-button-rounded p-button-danger mr-2" onClick={() => deleteLoadFile(rowData)} />);
     }
 
@@ -153,7 +153,7 @@ export const DataLoadsComponent = () => {
 
     ret.push(<Button key="edit" icon="pi pi-pencil" className="p-button-rounded p-button-warning mr-2" onClick={() => editLoad(rowData)} />);
 
-    if (!rowData.status || rowData.status === "FINISHED" || rowData.status === "FAILED") {
+    if (!rowData.status || rowData.status === "FINISHED" || rowData.status === "FAILED" || rowData.status === "STOPPED") {
       ret.push(<Button key="run" icon="pi pi-play" className="p-button-rounded p-button-success mr-2" onClick={() => runLoad(rowData)} />);
     }
 
@@ -241,9 +241,11 @@ export const DataLoadsComponent = () => {
   const statusTemplate = (rowData) => {
     let styleClass = 'p-button-text p-button-plain';
     if (rowData.status === 'FAILED') { styleClass = "p-button-danger"; }
-    if (rowData.status && (rowData.status.endsWith('STARTED') || 
-      rowData.status.endsWith('RUNNING') ||
-      rowData.status.endsWith('PENDING'))) { styleClass = "p-button-success"; }
+    if (rowData.status && (
+        rowData.status.endsWith('STARTED') ||
+        rowData.status.endsWith('RUNNING') ||
+        rowData.status.endsWith('PENDING')
+      )) { styleClass = "p-button-success"; }
 
     return (
       <Button label={rowData.status} tooltip={rowData.errorMessage} className={`p-button-rounded ${styleClass}`} />
@@ -254,7 +256,7 @@ export const DataLoadsComponent = () => {
     return (
       <div className="card">
         <DataTable key="historyTable" value={file.history} responsiveLayout="scroll">
-          
+
           <Column field="loadStarted" header="Load Started" />
           <Column field="loadFinished" header="Load Finished" />
           <Column field="completedRecords" header="Records Completed" />

src/main/cliapp/src/containers/diseaseAnnotationsPage/DiseaseAnnotationsTable.js

@@ -1,4 +1,4 @@
-import React, { useRef, useState, useEffect } from 'react'
+import React, { useRef, useState, useEffect } from 'react';
 import { useSessionStorage } from '../../service/useSessionStorage';
 import { useSetDefaultColumnOrder } from '../../utils/useSetDefaultColumnOrder';
 import { DataTable } from 'primereact/datatable';
@@ -280,7 +280,7 @@ export const DiseaseAnnotationsTable = () => {
         </Button>
       )
     }
-  }; 
+  };
 
   const conditionRelationsTemplate = (rowData) => {
     if (rowData.conditionRelations) {
@@ -1127,10 +1127,8 @@ export const DiseaseAnnotationsTable = () => {
           paginatorTemplate="CurrentPageReport FirstPageLink PrevPageLink PageLinks NextPageLink LastPageLink RowsPerPageDropdown"
           currentPageReportTemplate="Showing {first} to {last} of {totalRecords}" rows={tableState.rows} rowsPerPageOptions={[1, 10, 20, 50, 100, 250, 1000]}
         >
-
+          <Column field='rowEditor' rowEditor style={{maxWidth: '7rem'}} headerStyle={{ width: '7rem', position: 'sticky' }} bodyStyle={{ textAlign: 'center' }} frozen headerClassName='surface-0'/>
           {columnList}
-          <Column field='rowEditor' rowEditor style={{'maxWidth': '7rem'}} headerStyle={{ width: '7rem' }} bodyStyle={{ textAlign: 'center' }} />
-
         </DataTable>
       </div>
       <RelatedNotesDialog

src/main/cliapp/src/containers/experimentalConditionsPage/ExperimentalConditionsTable.js

@@ -584,8 +584,8 @@ export const ExperimentalConditionsTable = () => {
           paginatorTemplate="CurrentPageReport FirstPageLink PrevPageLink PageLinks NextPageLink LastPageLink RowsPerPageDropdown"
           currentPageReportTemplate="Showing {first} to {last} of {totalRecords}" rows={tableState.rows} rowsPerPageOptions={[10, 20, 50, 100, 250, 1000]}
         >
+        <Column rowEditor style={{ maxWidth: '7rem' }} headerStyle={{ maxWidth: '7rem', position: 'sticky' }} bodyStyle={{ textAlign: 'center' }} frozen headerClassName='surface-0'/>
           {columnList}
-          <Column rowEditor style={{ maxWidth: '7rem' }} headerStyle={{ maxWidth: '7rem' }} bodyStyle={{ textAlign: 'center' }}></Column>
         </DataTable>
       </div>
   )

src/main/cliapp/src/containers/layout/SiteLayout.js

@@ -220,6 +220,11 @@ export const SiteLayout = (props) => {
                         { label: 'FlyBase Developmental Ontology (FBdv)', icon: 'pi pi-fw pi-home', to: '/ontology/fbdv' },
                         { label: 'Mouse Developmental Stages (MmusDv)', icon: 'pi pi-fw pi-home', to: '/ontology/mmusdv' },
                         { label: 'Zebrafish Developmental Stages Ontology (ZFS)', icon: 'pi pi-fw pi-home', to: '/ontology/zfs' },
+                        { label: 'Xenopus Anatomy Ontology (XBA)', icon: 'pi pi-fw pi-home', to: '/ontology/xba' },
+                        { label: 'Xenopus Developmental Stage Ontology (XBS)', icon: 'pi pi-fw pi-home', to: '/ontology/xbs' },
+                        { label: 'Xenopus Phenotype Ontology (XPO)', icon: 'pi pi-fw pi-home', to: '/ontology/xpo' },
+                        { label: 'Xenbase Experimantal Data Ontology (XBED)', icon: 'pi pi-fw pi-home', to: '/ontology/xbed' },
+                        { label: 'Xenopus Small Molecule Ontology (XSMO)', icon: 'pi pi-fw pi-home', to: '/ontology/xsmo' },
                         { label: 'NCBI Organismal Classification (NCBITaxon)', icon: 'pi pi-fw pi-home', to: '/ontology/ncbitaxon' }
                     ]
                 },

src/main/cliapp/src/containers/ontologies/XBAOntologyComponent.js

@@ -0,0 +1,20 @@
+import React from 'react'
+import { OntologyTable } from './OntologyTable';
+
+export const XBAOntologyComponent = () => {
+  const columns = [
+    { field: "curie", header: "Curie" },
+    { field: "name", header: "Name" },
+    { field: "definition", header: "Definition" },
+    { field: "obsolete", header: "Obsolete" }
+  ]
+
+  return (
+    < OntologyTable
+      endpoint={"xbaterm"}
+      ontologyAbbreviation={"XBA"}
+      columns={columns}
+    />
+  )
+
+}

src/main/cliapp/src/containers/ontologies/XBEDOntologyComponent.js

@@ -0,0 +1,20 @@
+import React from 'react'
+import { OntologyTable } from './OntologyTable';
+
+export const XBEDOntologyComponent = () => {
+  const columns = [
+    { field: "curie", header: "Curie" },
+    { field: "name", header: "Name" },
+    { field: "definition", header: "Definition" },
+    { field: "obsolete", header: "Obsolete" }
+  ]
+
+  return (
+    < OntologyTable
+      endpoint={"xbedterm"}
+      ontologyAbbreviation={"XBED"}
+      columns={columns}
+    />
+  )
+
+}

src/main/cliapp/src/containers/ontologies/XBSOntologyComponent.js

@@ -0,0 +1,20 @@
+import React from 'react'
+import { OntologyTable } from './OntologyTable';
+
+export const XBSOntologyComponent = () => {
+  const columns = [
+    { field: "curie", header: "Curie" },
+    { field: "name", header: "Name" },
+    { field: "definition", header: "Definition" },
+    { field: "obsolete", header: "Obsolete" }
+  ]
+
+  return (
+    < OntologyTable
+      endpoint={"xbsterm"}
+      ontologyAbbreviation={"XBS"}
+      columns={columns}
+    />
+  )
+
+}

src/main/cliapp/src/containers/ontologies/XPOOntologyComponent.js

@@ -0,0 +1,20 @@
+import React from 'react'
+import { OntologyTable } from './OntologyTable';
+
+export const XPOOntologyComponent = () => {
+  const columns = [
+    { field: "curie", header: "Curie" },
+    { field: "name", header: "Name" },
+    { field: "definition", header: "Definition" },
+    { field: "obsolete", header: "Obsolete" }
+  ]
+
+  return (
+    < OntologyTable
+      endpoint={"xpoterm"}
+      ontologyAbbreviation={"XPO"}
+      columns={columns}
+    />
+  )
+
+}

src/main/cliapp/src/containers/ontologies/XSMOOntologyComponent.js

@@ -0,0 +1,20 @@
+import React from 'react'
+import { OntologyTable } from './OntologyTable';
+
+export const XSMOOntologyComponent = () => {
+  const columns = [
+    { field: "curie", header: "Curie" },
+    { field: "name", header: "Name" },
+    { field: "definition", header: "Definition" },
+    { field: "obsolete", header: "Obsolete" }
+  ]
+
+  return (
+    < OntologyTable
+      endpoint={"xsmoterm"}
+      ontologyAbbreviation={"XSMO"}
+      columns={columns}
+    />
+  )
+
+}

src/main/cliapp/src/routes.js

@@ -37,6 +37,11 @@ import { WBlsOntologyComponent } from './containers/ontologies/WBlsOntologyCompo
 import { FBdvOntologyComponent } from './containers/ontologies/FBdvOntologyComponent';
 import { MmusDvOntologyComponent } from './containers/ontologies/MmusDvOntologyComponent';
 import { ZFSOntologyComponent } from './containers/ontologies/ZFSOntologyComponent';
+import { XBAOntologyComponent } from './containers/ontologies/XBAOntologyComponent';
+import { XBSOntologyComponent } from './containers/ontologies/XBSOntologyComponent';
+import { XPOOntologyComponent } from './containers/ontologies/XPOOntologyComponent';
+import { XBEDOntologyComponent } from './containers/ontologies/XBEDOntologyComponent';
+import { XSMOOntologyComponent } from './containers/ontologies/XSMOOntologyComponent';
 import { NCBITaxonOntologyComponent } from './containers/ontologies/NCBITaxonOntologyComponent';
 
 
@@ -69,6 +74,11 @@ export default (
     <SecureRoute path="/ontology/fbdv" component={FBdvOntologyComponent} />
     <SecureRoute path="/ontology/mmusdv" component={MmusDvOntologyComponent} />
     <SecureRoute path="/ontology/zfs" component={ZFSOntologyComponent} />
+    <SecureRoute path="/ontology/xba" component={XBAOntologyComponent} />
+    <SecureRoute path="/ontology/xbs" component={XBSOntologyComponent} />
+    <SecureRoute path="/ontology/xpo" component={XPOOntologyComponent} />
+    <SecureRoute path="/ontology/xbed" component={XBEDOntologyComponent} />
+    <SecureRoute path="/ontology/xsmo" component={XSMOOntologyComponent} />
     <SecureRoute path="/ontology/ncbitaxon" component={NCBITaxonOntologyComponent} />
     <SecureRoute path="/fmspage" component={FMSComponent} />
     <SecureRoute path="/metricspage" component={MetricsComponent} />

src/main/cliapp/src/service/DataLoadService.js

@@ -84,7 +84,7 @@ export class DataLoadService extends BaseAuthService {
 
     getOntologyTypes() {
         return [
-            "ECO", "ZFA", "DO", "MA", "CHEBI", "XCO", "MP", "DAO", "ZECO", "WBBT", "EMAPA", "GO", "SO", "WBLS", "FBDV", "MMUSDV", "ZFS"
+            "ECO", "ZFA", "DO", "MA", "CHEBI", "XCO", "MP", "DAO", "ZECO", "WBBT", "EMAPA", "GO", "SO", "WBLS", "FBDV", "MMUSDV", "ZFS", "XBA_XBS", "XPO", "XBED", "XSMO"
         ];
     }