Merge pull request #1287 from PathwayCommons/iss1286_admin-flag-ungro…

…unded Admin: Flag entity-related issues
PathwayCommons · Jul 26, 2024 · a474cb6 · a474cb6
2 parents e7f2368 + e93728a
commit a474cb6
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Showing 4 changed files with 66 additions and 20 deletions.
diff --git a/src/client/components/document-management-components.js b/src/client/components/document-management-components.js
@@ -19,8 +19,11 @@ import {
 
 const DOCUMENT_STATUS_FIELDS = Document.statusFields();
 
-const hasIssues = doc => _.values( doc.issues() ).some( i => !_.isNull( i ) );
-const hasIssue = ( doc, key ) => _.has( doc.issues(), key ) && !_.isNull( _.get( doc.issues(), key ) );
+const issuesPresent = e => _.values( e.issues() ).some( i => !_.isNull( i ) );
+const hasEntityIssues = doc => doc.entities().some( issuesPresent );
+const hasDocIssues = doc => issuesPresent( doc );
+const hasIssues = doc => hasEntityIssues( doc ) || hasDocIssues( doc );
+const hasIssue = ( e, key ) => _.has( e.issues(), key ) && !_.isNull( _.get( e.issues(), key ) );
 
 /**
  * sendMail
@@ -315,20 +318,9 @@ class DocumentManagementDocumentComponent extends React.Component {
     // Document Header & Footer
     const getDocumentHeader = doc => {
       return h( 'div.document-management-document-section.meta', [
-        h( 'div.document-management-document-section-items', [
-          h( 'div', [
-            h( 'i.material-icons.hide-by-default.invalid', {
-              className: makeClassList({ 'show': hasIssues( doc ) })
-            }, 'warning' ),
-            // h( 'i.material-icons.hide-by-default.complete', {
-            //   className: makeClassList({ 'show': doc.submitted() || doc.isPublic() })
-            // }, 'check_circle' ),
-            h( 'i.material-icons.hide-by-default.mute', {
-              className: makeClassList({ 'show': doc.trashed() })
-            }, 'delete' )
-          ]),
-
-        ])
+        h( 'i.material-icons.hide-by-default.invalid', {
+          className: makeClassList({ 'show': hasIssues( doc ) })
+        }, 'warning' )
       ]);
     };
 
@@ -362,9 +354,7 @@ class DocumentManagementDocumentComponent extends React.Component {
 
       if( hasIssue( doc, 'paperId' ) ){
         const { paperId: paperIdIssue } = doc.issues();
-        const err = h( 'div', {
-          className: makeClassList({ 'issue': true })
-        }, `${paperIdIssue.error.name}: ${paperIdIssue.message}` );
+        const err = h( 'div', `${paperIdIssue.error.name}: ${paperIdIssue.message}` );
         items.push( err );
       }
 
@@ -401,6 +391,34 @@ class DocumentManagementDocumentComponent extends React.Component {
         ]);
     };
 
+    // Entities
+    const getEntityInfo = doc => {
+      const numEntities = doc.entities().length;
+      let items = [ h('div', { key: 'total' }, `Total: ${numEntities}`)];
+      const mixedOrganisms = doc.organisms().length > 1;
+      const hasIssue = hasEntityIssues( doc );
+      const hasWarning = mixedOrganisms; // orphaned nodes
+
+      if( hasIssue ){
+        const issues = doc.entities().filter( issuesPresent ).map( e =>  e.issues() );
+        const errors = _.flatten( issues ).map( i => i.error.name );
+        const errorTypes = _.toPairs( _.countBy( errors ) ).map( ([ error, count ], key) => h('div', { key }, `${error}: ${count}`) );
+        items.push( errorTypes );
+      }
+      if( hasWarning ){
+        if( mixedOrganisms ) items.push( h('div', { key: 'organism' }, 'Mixed organisms' ) );
+      }
+
+      return h( 'div.document-management-document-section', [
+        h( 'div.document-management-document-section-label', {
+          className: makeClassList({'issue': hasIssue, 'warning': hasWarning})
+        },[
+          h( 'div.document-management-document-section-label-text', 'Entities')
+        ]),
+        h( 'div.document-management-document-section-items', items )
+      ]);
+    };
+
     // Correspondence
     const getVerified = doc => {
       let radios = [];
@@ -477,7 +495,7 @@ class DocumentManagementDocumentComponent extends React.Component {
       return h( 'div.document-management-document-section', [
         h( 'div.document-management-document-section-label', {
           className: makeClassList({ 'issue': hasIssue( doc, 'authorEmail' ) })
-        }, 'Correspondence:' ),
+        }, 'Correspondence' ),
         content
       ]);
     };
@@ -540,6 +558,7 @@ class DocumentManagementDocumentComponent extends React.Component {
       getDocumentHeader( doc ),
       getDocumentArticle( doc ),
       getDocumentInfo( doc ),
+      getEntityInfo( doc ),
       getDocumentCorrespondence( doc ),
       getDocumentStats( doc )
     ]);

diff --git a/src/model/element/complex.js b/src/model/element/complex.js
@@ -92,6 +92,10 @@ class Complex extends Entity {
     return this.remove( ele, opts );
   }
 
+  normalized(){
+    return true;
+  }
+
   json(){
     return _.assign( {}, super.json(), _.pick( this.syncher.get(), _.keys(DEFAULTS) ) );
   }

diff --git a/src/model/element/entity.js b/src/model/element/entity.js
@@ -165,6 +165,25 @@ class Entity extends Element {
     return update;
   }
 
+  normalized(){
+    // normalized := has a name and is associated
+    const name = this.name();
+    return name && this.associated() && this.completed();
+  }
+
+  issues(){
+    const items = [];
+    if( !this.normalized() ){
+      items.push({
+        error: {
+          name: 'Normalization'
+        },
+        message: `Entity with name "${this.name()}" is not normalized`
+      });
+    }
+    return items;
+  }
+
   organism(){
     const assoc = this.association();
 

diff --git a/src/styles/document-management.css b/src/styles/document-management.css
@@ -29,6 +29,10 @@
   & .issue {
     color: var(--invalidColor);
   }
+
+  & .warning {
+    color: var(--brandColorDark);
+  }
 }
 
 .document-management-hidden {