- RC of #1190

xchem · Dec 13, 2023 · 3b4e7a7 · 3b4e7a7
1 parent 1debb80
commit 3b4e7a7
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Showing 7 changed files with 104 additions and 92 deletions.
diff --git a/docker-compose.dev.vector.yml b/docker-compose.dev.vector.yml
@@ -103,6 +103,7 @@ services:
       AUTHENTICATE_UPLOAD: 'False'
       CELERY_TASK_ALWAYS_EAGER: 'True'
       DEBUG_FRAGALYSIS: 'True'
+      PROXY_FORWARDED_PROTO_HEADER: 'http'
     depends_on:
       database:
         condition: service_healthy

diff --git a/js/components/preview/molecule/moleculeList.js b/js/components/preview/molecule/moleculeList.js
@@ -483,7 +483,7 @@ export const MoleculeList = memo(({ hideProjects }) => {
         categories.length > 0
       ) {
         dispatch(initializeFilter(object_selection, joinedMoleculeLists));
-        dispatch(initializeMolecules(majorViewStage));
+        // dispatch(initializeMolecules(majorViewStage));
         wereMoleculesInitialized.current = true;
       }
       if (
@@ -494,7 +494,7 @@ export const MoleculeList = memo(({ hideProjects }) => {
         noTagsReceived
       ) {
         dispatch(initializeFilter(object_selection, joinedMoleculeLists));
-        dispatch(initializeMolecules(majorViewStage));
+        // dispatch(initializeMolecules(majorViewStage));
         wereMoleculesInitialized.current = true;
       }
     }
@@ -1157,11 +1157,11 @@ export const MoleculeList = memo(({ hideProjects }) => {
             wrap="nowrap"
           >
             <Grid item container justifyContent="flex-start" direction="row">
-              {Object.keys(moleculeProperty).map(key => (
+              {/* {Object.keys(moleculeProperty).map(key => (
                 <Grid item key={key} className={classes.rightBorder}>
                   {moleculeProperty[key]}
                 </Grid>
-              ))}
+              ))} */}
             </Grid>
           </Grid>
         </Grid>

diff --git a/js/components/preview/molecule/moleculeView/moleculeView.js b/js/components/preview/molecule/moleculeView/moleculeView.js
@@ -388,15 +388,15 @@ const MoleculeView = memo(
 
     const getCalculatedProps = useCallback(
       () => [
-        { name: moleculeProperty.mw, value: data.mw ?? 0 },
-        { name: moleculeProperty.logP, value: data.logp ?? 0 },
-        { name: moleculeProperty.tpsa, value: data.tpsa ?? 0 },
-        { name: moleculeProperty.ha, value: data.ha ?? 0 },
-        { name: moleculeProperty.hacc, value: data.hacc ?? 0 },
-        { name: moleculeProperty.hdon, value: data.hdon ?? 0 },
-        { name: moleculeProperty.rots, value: data.rots ?? 0 },
-        { name: moleculeProperty.rings, value: data.rings ?? 0 },
-        { name: moleculeProperty.velec, value: data.velec ?? 0 }
+        // { name: moleculeProperty.mw, value: data.mw ?? 0 },
+        // { name: moleculeProperty.logP, value: data.logp ?? 0 },
+        // { name: moleculeProperty.tpsa, value: data.tpsa ?? 0 },
+        // { name: moleculeProperty.ha, value: data.ha ?? 0 },
+        // { name: moleculeProperty.hacc, value: data.hacc ?? 0 },
+        // { name: moleculeProperty.hdon, value: data.hdon ?? 0 },
+        // { name: moleculeProperty.rots, value: data.rots ?? 0 },
+        // { name: moleculeProperty.rings, value: data.rings ?? 0 },
+        // { name: moleculeProperty.velec, value: data.velec ?? 0 }
         //   { name: moleculeProperty.vectors, value: countOfVectors },
         //   { name: moleculeProperty.cpd, value: cmpds }
       ],

diff --git a/js/components/preview/molecule/observationCmpList.js b/js/components/preview/molecule/observationCmpList.js
@@ -304,6 +304,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
   const categories = useSelector(state => state.apiReducers.categoryList);
 
   const lhsCompoundsList = useSelector(state => getLHSCompoundsList(state));
+  const visibleObservations = useSelector(state => selectJoinedMoleculeList(state));
 
   const proteinsHasLoaded = useSelector(state => state.nglReducers.proteinsHasLoaded);
 
@@ -330,29 +331,6 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
       // setCurrentPage(0);
     }, [object_selection]);*/
 
-  let filteredLHSCompoundsList = useMemo(() => {
-    return lhsCompoundsList;
-  }, [lhsCompoundsList]);
-
-  let compoundMolecules = useMemo(() => {
-    const compoundMolecules = {};
-
-    filteredLHSCompoundsList.forEach(compound => {
-      const molsForCmp = allMoleculesList.filter(molecule => molecule.cmpd === compound.id);
-      compoundMolecules[compound.id] = molsForCmp.sort((a, b) => {
-        if (a.code < b.code) {
-          return -1;
-        }
-        if (a.code > b.code) {
-          return 1;
-        }
-        return 0;
-      });
-    });
-
-    return compoundMolecules;
-  }, [filteredLHSCompoundsList, allMoleculesList]);
-
   let joinedMoleculeLists = useMemo(() => {
     // const searchedString = currentActionList.find(action => action.type === 'SEARCH_STRING_HIT_NAVIGATOR');
     if (searchString) {
@@ -499,7 +477,11 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
   const wereMoleculesInitialized = useRef(false);
 
   useEffect(() => {
-    if ((proteinsHasLoaded === true || proteinsHasLoaded === null) && all_mol_lists.length > 0) {
+    if (
+      (proteinsHasLoaded === true || proteinsHasLoaded === null) &&
+      all_mol_lists?.length > 0 &&
+      lhsCompoundsList?.length > 0
+    ) {
       if (!directAccessProcessed && directDisplay && directDisplay.molecules && directDisplay.molecules.length > 0) {
         dispatch(applyDirectSelection(majorViewStage));
         wereMoleculesInitialized.current = true;
@@ -533,6 +515,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
     }
   }, [
     list_type,
+    lhsCompoundsList,
     majorViewStage,
     dispatch,
     hideProjects,
@@ -735,6 +718,36 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
     return null;
   };
 
+  let filteredLHSCompoundsList = useMemo(() => {
+    const compounds = [];
+    lhsCompoundsList.forEach(compound => {
+      const molsForCmp = joinedMoleculeLists.filter(molecule => molecule.cmpd === compound.id);
+      if (molsForCmp.length > 0) {
+        compounds.push(compound);
+      }
+    });
+    return compounds;
+  }, [lhsCompoundsList, joinedMoleculeLists]);
+
+  let compoundMolecules = useMemo(() => {
+    const compoundMolecules = {};
+
+    filteredLHSCompoundsList.forEach(compound => {
+      const molsForCmp = allMoleculesList.filter(molecule => molecule.cmpd === compound.id);
+      compoundMolecules[compound.id] = molsForCmp.sort((a, b) => {
+        if (a.code < b.code) {
+          return -1;
+        }
+        if (a.code > b.code) {
+          return 1;
+        }
+        return 0;
+      });
+    });
+
+    return compoundMolecules;
+  }, [filteredLHSCompoundsList, allMoleculesList]);
+
   const isLigandOn = changeButtonClassname(fragmentDisplayList, joinedLigandMatchLength);
   const isProteinOn = changeButtonClassname(proteinList, joinedProteinMatchLength);
   const isComplexOn = changeButtonClassname(complexList, joinedComplexMatchLength);
@@ -935,7 +948,8 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
         }
       }}
       color={'inherit'}
-      disabled={/*!joinedMoleculeListsCopy.length || */ predefinedFilter !== 'none'}
+      // disabled={predefinedFilter !== 'none'}
+      disabled={true}
     >
       <Tooltip title="Filter/Sort">
         <FilterList />
@@ -1178,11 +1192,11 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
             wrap="nowrap"
           >
             <Grid item container justifyContent="flex-start" direction="row">
-              {Object.keys(moleculeProperty).map(key => (
+              {/* {Object.keys(moleculeProperty).map(key => (
                 <Grid item key={key} className={classes.rightBorder}>
                   {moleculeProperty[key]}
                 </Grid>
-              ))}
+              ))} */}
             </Grid>
           </Grid>
         </Grid>
@@ -1216,44 +1230,6 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
                 }
                 useWindow={false}
               >
-                {/* <GroupNglControlButtonsContext.Provider value={groupNglControlButtonsDisabledState}>
-                  {currentMolecules.map((data, index, array) => {
-                    const selected = allSelectedMolecules.some(molecule => molecule.id === data.id);
-                    const isTagEditorInvokedByMolecule = data.id === molForTagEditId;
-
-                    return (
-                      <MoleculeView
-                        key={data.id}
-                        index={index}
-                        imageHeight={imgHeight}
-                        imageWidth={imgWidth}
-                        data={data}
-                        previousItemData={index > 0 && array[index - 1]}
-                        nextItemData={index < array?.length && array[index + 1]}
-                        setRef={setTagEditorAnchorEl}
-                        removeSelectedTypes={removeSelectedTypes}
-                        L={fragmentDisplayList.includes(data.id)}
-                        P={proteinList.includes(data.id)}
-                        C={complexList.includes(data.id)}
-                        S={surfaceList.includes(data.id)}
-                        D={densityList.includes(data.id)}
-                        D_C={densityListCustom.includes(data.id)}
-                        Q={qualityList.includes(data.id)}
-                        V={vectorOnList.includes(data.id)}
-                        I={informationList.includes(data.id)}
-                        eventInfo={data?.proteinData?.event_info || null}
-                        sigmaaInfo={data?.proteinData?.sigmaa_info || null}
-                        diffInfo={data?.proteinData?.diff_info || null}
-                        isTagEditorInvokedByMolecule={isTagEditorInvokedByMolecule}
-                        isTagEditorOpen={isTagEditorInvokedByMolecule && isTagEditorOpen}
-                        selected={selected}
-                        disableL={selected && groupNglControlButtonsDisabledState.ligand}
-                        disableP={selected && groupNglControlButtonsDisabledState.protein}
-                        disableC={selected && groupNglControlButtonsDisabledState.complex}
-                      />
-                    );
-                  })}
-                </GroupNglControlButtonsContext.Provider> */}
                 {filteredLHSCompoundsList.map((data, index, array) => {
                   const molsForCmp = compoundMolecules[data.id];
                   const selected = allSelectedLHSCmps.some(molecule => molecule.id === data.id);

diff --git a/js/components/preview/molecule/observationCmpView/observationCmpView.js b/js/components/preview/molecule/observationCmpView/observationCmpView.js
@@ -359,15 +359,15 @@ const ObservationCmpView = memo(
     const { getNglView } = useContext(NglContext);
     const stage = getNglView(VIEWS.MAJOR_VIEW) && getNglView(VIEWS.MAJOR_VIEW).stage;
 
-    const getFirstObservation = () => {
+    const getFirstObservation = useCallback(() => {
       let result = null;
 
       if (observations && observations.length > 0) {
         result = observations[0];
       }
 
       return result;
-    };
+    }, [observations]);
 
     const getAllObservationsSelectedInList = list => {
       let result = [];
@@ -436,15 +436,15 @@ const ObservationCmpView = memo(
 
     const getCalculatedProps = useCallback(
       () => [
-        { name: moleculeProperty.mw, value: data.mw ?? 0 },
-        { name: moleculeProperty.logP, value: data.logp ?? 0 },
-        { name: moleculeProperty.tpsa, value: data.tpsa ?? 0 },
-        { name: moleculeProperty.ha, value: data.ha ?? 0 },
-        { name: moleculeProperty.hacc, value: data.hacc ?? 0 },
-        { name: moleculeProperty.hdon, value: data.hdon ?? 0 },
-        { name: moleculeProperty.rots, value: data.rots ?? 0 },
-        { name: moleculeProperty.rings, value: data.rings ?? 0 },
-        { name: moleculeProperty.velec, value: data.velec ?? 0 }
+        // { name: moleculeProperty.mw, value: data.mw ?? 0 },
+        // { name: moleculeProperty.logP, value: data.logp ?? 0 },
+        // { name: moleculeProperty.tpsa, value: data.tpsa ?? 0 },
+        // { name: moleculeProperty.ha, value: data.ha ?? 0 },
+        // { name: moleculeProperty.hacc, value: data.hacc ?? 0 },
+        // { name: moleculeProperty.hdon, value: data.hdon ?? 0 },
+        // { name: moleculeProperty.rots, value: data.rots ?? 0 },
+        // { name: moleculeProperty.rings, value: data.rings ?? 0 },
+        // { name: moleculeProperty.velec, value: data.velec ?? 0 }
         //   { name: moleculeProperty.vectors, value: countOfVectors },
         //   { name: moleculeProperty.cpd, value: cmpds }
       ],

diff --git a/js/components/preview/molecule/redux/dispatchActions.js b/js/components/preview/molecule/redux/dispatchActions.js
@@ -70,6 +70,7 @@ import { readQualityInformation } from '../../../nglView/renderingHelpers';
 import { addSelectedTag } from '../../tags/redux/dispatchActions';
 import { CATEGORY_TYPE } from '../../../../constants/constants';
 import { selectJoinedMoleculeList } from './selectors';
+import { compareTagsAsc } from '../../tags/utils/tagUtils';
 // import { molFile, pdbApo } from './testData';
 
 /**
@@ -657,14 +658,15 @@ export const initializeMolecules = majorView => (dispatch, getState) => {
     const isSnapshot = state.apiReducers.isSnapshot;
 
     if (!isSnapshot) {
-      const firstTag = dispatch(getFirstTag());
+      const firstTag = dispatch(getFirstTagAlphabetically());
       let firstMolecule = null;
       if (firstTag) {
         dispatch(addSelectedTag(firstTag));
-        firstMolecule = dispatch(getFirstMoleculeForTag(firstTag.id));
+        // firstMolecule = dispatch(getFirstMoleculeForTag(firstTag.id));
       } else if (noTagsReceived) {
-        firstMolecule = dispatch(getFirstMolecule());
+        // firstMolecule = dispatch(getFirstMolecule());
       }
+      firstMolecule = dispatch(getFirstMolOfFirstCompound());
       if (firstMolecule) {
         dispatch(addHitProtein(majorView, firstMolecule, colourList[firstMolecule.id % colourList.length], true)).then(
           () => {
@@ -688,6 +690,30 @@ export const getFirstTag = () => (dispatch, getState) => {
   }
 };
 
+export const getFirstTagAlphabetically = () => (dispatch, getState) => {
+  const state = getState();
+  const tagsList = state.apiReducers.tagList;
+  const sortedTags = tagsList.sort(compareTagsAsc);
+  return sortedTags && sortedTags.length > 0 ? sortedTags[0] : null;
+};
+
+export const getFirstMolOfFirstCompound = () => (dispatch, getState) => {
+  const state = getState();
+  const compoundsList = state.apiReducers.lhs_compounds_list;
+  const firstCompound = compoundsList[0];
+  if (firstCompound) {
+    const molList = state.apiReducers.all_mol_lists;
+    const firstMols = molList?.filter(m => m.cmpd === firstCompound.id);
+    if (firstMols && firstMols.length > 0) {
+      return firstMols[0];
+    } else {
+      return null;
+    }
+  } else {
+    return null;
+  }
+};
+
 export const getFirstMoleculeForTag = tagId => (dispatch, getState) => {
   const state = getState();
   const molList = state.apiReducers.all_mol_lists;

diff --git a/js/components/preview/tags/redux/dispatchActions.js b/js/components/preview/tags/redux/dispatchActions.js
@@ -218,6 +218,15 @@ export const loadMoleculesAndTagsNew = targetId => async (dispatch, getState) =>
       const siteObs = allMolecules.find(m => m.cmpd === c.id);
       c['smiles'] = siteObs ? siteObs.smiles : '';
     });
+    compounds.sort((a, b) => {
+      if (a.smiles < b.smiles) {
+        return -1;
+      }
+      if (a.smiles > b.smiles) {
+        return 1;
+      }
+      return 0;
+    });
     dispatch(setLHSCompoundsLIst([...compounds]));
   });
 };