Snapshots refactor and mint incremental

docker-compose.dev.vector.yml

@@ -91,14 +91,11 @@ services:
       OIDC_RP_CLIENT_SECRET: ${OIDC_RP_CLIENT_SECRET}
       OIDC_RP_CLIENT_ID: 'fragalysis-local'
       OIDC_RENEW_ID_TOKEN_EXPIRY_MINUTES: 210
-      ISPYB_HOST: ispybdbproxy.diamond.ac.uk
+      # ISPYB_HOST: ispybdbproxy.diamond.ac.uk
       ISPYB_PORT: 4306
       ISPYB_USER: ${ISPYB_USER}
       ISPYB_PASSWORD: ${ISPYB_PASSWORD}
       SECURITY_CONNECTOR: ssh_ispyb
-      SSH_HOST: ssh.diamond.ac.uk
-      SSH_USER: ${SSH_USER}
-      SSH_PASSWORD: ${SSH_PASSWORD}
       LOGGING_FRAMEWORK_ROOT_LEVEL: DEBUG
       AUTHENTICATE_UPLOAD: 'False'
       CELERY_TASK_ALWAYS_EAGER: 'True'

js/components/datasets/customDatasetList.js

@@ -18,9 +18,9 @@ export const CustomDatasetList = memo(({ dataset, hideProjects, isActive }) => {
         dispatch(clearDatasetSettings(dataset.id));
       }
     }
-    return () => {
-      dispatch(clearDatasetSettings(dataset?.id));
-    };
+    // return () => {
+    //   dispatch(clearDatasetSettings(dataset?.id));
+    // };
   }, [dataset, dispatch, isActive, isLoadingMoleculeList]);
 
   const title = dataset && `${dataset.title} v.${dataset.version}`;

js/components/datasets/datasetMoleculeList.js

@@ -397,8 +397,6 @@ const DatasetMoleculeList = ({ title, datasetID, url }) => {
 
   const searchString = useSelector(state => state.datasetsReducers.searchString);
 
-  const currentActionList = useSelector(state => state.trackingReducers.current_actions_list);
-
   const isActiveFilter = !!(filterSettings || {}).active;
   const { getNglView } = useContext(NglContext);
 
@@ -494,12 +492,12 @@ const DatasetMoleculeList = ({ title, datasetID, url }) => {
   const isSelectedTypeOn = (typeList, isLHSReference) => {
     if (typeList) {
       if (!isLHSReference) {
-        return typeList.some(molId => allMolecules.some(mol => mol.id === molId));
+        return typeList.some(molId => allMolecules?.some(mol => mol.id === molId));
       } else {
-        const molsWithLHSReference = allMolecules.filter(mol => mol.site_observation_code);
+        const molsWithLHSReference = allMolecules?.filter(mol => mol.site_observation_code);
         return typeList.some(molId =>
           molsWithLHSReference.some(
-            mol => mol.site_observation_code === allMoleculesList.find(m => m.id === molId)?.code
+            mol => mol.site_observation_code === allMoleculesList?.find(m => m.id === molId)?.code
           )
         );
       }
@@ -563,7 +561,7 @@ const DatasetMoleculeList = ({ title, datasetID, url }) => {
         );
       } else {
         if (molecule.site_observation_code) {
-          const lhsMol = allMoleculesList.find(mol => mol.code === molecule.site_observation_code);
+          const lhsMol = allMoleculesList?.find(mol => mol.code === molecule.site_observation_code);
           if (lhsMol) {
             dispatch(removeLHSType[type](stage, lhsMol, colourList[molecule.id % colourList.length], skipTracking));
           }
@@ -597,7 +595,7 @@ const DatasetMoleculeList = ({ title, datasetID, url }) => {
             );
           } else {
             if (molecule.site_observation_code) {
-              const lhsMol = allMoleculesList.find(mol => mol.code === molecule.site_observation_code);
+              const lhsMol = allMoleculesList?.find(mol => mol.code === molecule.site_observation_code);
               if (lhsMol) {
                 if (type === 'protein') {
                   promises.push(
@@ -1479,7 +1477,7 @@ const DatasetMoleculeList = ({ title, datasetID, url }) => {
                         // #1249 dataset molecules currently could use side observation molecule for some renders
                         let idToFind = data.id;
                         if (data.site_observation_code) {
-                          const molecule = allMoleculesList.find(mol => mol.code === data.site_observation_code);
+                          const molecule = allMoleculesList?.find(mol => mol.code === data.site_observation_code);
                           if (molecule) {
                             idToFind = molecule.id;
                           }

js/components/datasets/inspirationDialog.js

@@ -156,7 +156,7 @@ export const InspirationDialog = memo(
       let rationale = '';
       if (datasetID && inspirationLists.hasOwnProperty(datasetID) && inspirationLists[datasetID][0]) {
         const moleculeID = inspirationLists[datasetID][0];
-        const molecule = moleculeLists[datasetID].find(molecule => molecule.id === moleculeID);
+        const molecule = moleculeLists[datasetID]?.find(molecule => molecule.id === moleculeID);
         if (molecule !== undefined) {
           rationale = molecule.text_scores.hasOwnProperty('rationale') ? molecule.text_scores.rationale : '';
         }
@@ -194,7 +194,7 @@ export const InspirationDialog = memo(
     }, [inspirationMoleculeDataList, searchString]);
 
     const allSelectedMolecules = inspirationMoleculeDataList.filter(
-      molecule => moleculesToEditIds.includes(molecule.id) /* || molForTagEditId.some(mid => molecule.id === mid)*/
+      molecule => moleculesToEditIds.includes(molecule?.id) /* || molForTagEditId.some(mid => molecule.id === mid)*/
     );
 
     // TODO: refactor from this line (duplicity in datasetMoleculeList.js)
@@ -451,6 +451,7 @@ export const InspirationDialog = memo(
               <div className={classes.content}>
                 {moleculeList.length > 0 &&
                   moleculeList.map((molecule, index, array) => {
+                    if (!molecule) return <> </>;
                     let data = molecule;
                     data.isInspiration = true;
                     let previousData = index > 0 && Object.assign({ isInspiration: true }, array[index - 1]);

js/components/datasets/redux/actions.js

@@ -623,3 +623,42 @@ export const setUpdatedDatasets = updatedDataset => ({
   type: constants.SET_UPDATED_DATASETS,
   payload: { updatedDataset }
 });
+
+export const setToBeDisplayedListForDataset = (datasetID, toBeDisplayedList) => {
+  return {
+    type: constants.SET_TO_BE_DISPLAYED_LIST_DATASET,
+    toBeDisplayedList: toBeDisplayedList,
+    datasetID: datasetID
+  };
+};
+
+export const appendToBeDisplayedListForDataset = (datasetID, item) => {
+  return {
+    type: constants.APPEND_TO_BE_DISPLAYED_LIST_DATASET,
+    item: item,
+    datasetID: datasetID
+  };
+};
+
+export const removeFromToBeDisplayedListForDataset = (datasetID, item) => {
+  return {
+    type: constants.REMOVE_FROM_TO_BE_DISPLAYED_LIST_DATASET,
+    item: item,
+    datasetID: datasetID
+  };
+};
+
+export const updateInToBeDisplayedListForDataset = (datasetID, item) => {
+  return {
+    type: constants.UPDATE_IN_TO_BE_DISPLAYED_LIST_DATASET,
+    item: item,
+    datasetID: datasetID
+  };
+};
+
+export const setToBeDisplayedLists = toBeDisplayedLists => {
+  return {
+    type: constants.SET_TO_BE_DISPLAYED_LISTS,
+    toBeDisplayedLists: toBeDisplayedLists
+  };
+};

js/components/datasets/redux/constants.js

@@ -122,7 +122,13 @@ export const constants = {
   SET_SELECTED_COMPOUNDS_ITERATOR: prefix + 'SET_SELECTED_COMPOUNDS_ITERATOR',
 
   SET_INSPIRATION_DIALOG_ACTION: prefix + 'SET_INSPIRATION_DIALOG_ACTION',
-  SET_INSPIRATION_DIALOG_OPENED_FOR_SELECTED_COMPOUND: prefix + 'SET_INSPIRATION_DIALOG_OPENED_FOR_SELECTED_COMPOUND'
+  SET_INSPIRATION_DIALOG_OPENED_FOR_SELECTED_COMPOUND: prefix + 'SET_INSPIRATION_DIALOG_OPENED_FOR_SELECTED_COMPOUND',
+
+  SET_TO_BE_DISPLAYED_LIST_DATASET: prefix + 'SET_TO_BE_DISPLAYED_LIST_DATASET',
+  APPEND_TO_BE_DISPLAYED_LIST_DATASET: prefix + 'APPEND_TO_BE_DISPLAYED_LIST_DATASET',
+  REMOVE_FROM_TO_BE_DISPLAYED_LIST_DATASET: prefix + 'REMOVE_FROM_TO_BE_DISPLAYED_LIST_DATASET',
+  UPDATE_IN_TO_BE_DISPLAYED_LIST_DATASET: prefix + 'UPDATE_IN_TO_BE_DISPLAYED_LIST_DATASET',
+  SET_TO_BE_DISPLAYED_LISTS: prefix + 'SET_TO_BE_DISPLAYED_LISTS'
 };
 
 export const COUNT_OF_VISIBLE_SCORES = 7;

js/components/datasets/redux/dispatchActions.js

@@ -37,7 +37,9 @@ import {
   removeDataset,
   appendCompoundToSelectedCompoundsByDataset,
   setDatasetIterator,
-  setSelectedCompoundsIterator
+  setSelectedCompoundsIterator,
+  appendToBeDisplayedListForDataset,
+  updateInToBeDisplayedListForDataset
 } from './actions';
 import { base_url } from '../../routes/constants';
 import {
@@ -75,11 +77,10 @@ import {
 } from '../../preview/molecule/redux/dispatchActions';
 import { OBJECT_TYPE } from '../../nglView/constants';
 import { getRepresentationsByType } from '../../nglView/generatingObjects';
-import { selectAllMoleculeList } from '../../preview/molecule/redux/selectors';
-import { getCompoundById } from '../../../reducers/tracking/dispatchActionsSwitchSnapshot';
 import { getRandomColor } from '../../preview/molecule/utils/color';
-import { BreakfastDiningOutlined } from '@mui/icons-material';
 import { isCompoundFromVectorSelector } from '../../preview/compounds/redux/dispatchActions';
+import { getCompoundById } from '../../../utils/genericDispatchActions';
+import { NGL_OBJECTS } from '../../../reducers/ngl/constants';
 
 export const initializeDatasetFilter = datasetID => (dispatch, getState) => {
   const state = getState();
@@ -106,34 +107,26 @@ export const addDatasetHitProtein = (
   skipTracking = false,
   representations = undefined
 ) => async dispatch => {
-  dispatch(appendProteinList(datasetID, generateMoleculeCompoundId(data), skipTracking));
-  return dispatch(
-    loadObject({
-      target: Object.assign(
-        { display_div: VIEWS.MAJOR_VIEW },
-        generateHitProteinObject(data, colourToggle, base_url, datasetID)
-      ),
-      stage,
-      previousRepresentations: representations,
-      orientationMatrix: null
+  dispatch(
+    appendToBeDisplayedListForDataset(datasetID, {
+      type: NGL_OBJECTS.PROTEIN,
+      id: data.id,
+      display: true,
+      representations: representations,
+      datasetID: datasetID
     })
-  ).finally(() => {
-    const currentOrientation = stage.viewerControls.getOrientation();
-    dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
-  });
+  );
 };
 
 export const removeDatasetHitProtein = (stage, data, colourToggle, datasetID, skipTracking = false) => dispatch => {
   dispatch(
-    deleteObject(
-      Object.assign(
-        { display_div: VIEWS.MAJOR_VIEW },
-        generateHitProteinObject(data, colourToggle, base_url, datasetID)
-      ),
-      stage
-    )
+    updateInToBeDisplayedListForDataset(datasetID, {
+      id: data.id,
+      display: false,
+      type: NGL_OBJECTS.PROTEIN,
+      datasetID: datasetID
+    })
   );
-  dispatch(removeFromProteinList(datasetID, generateMoleculeCompoundId(data), skipTracking));
 };
 
 export const addDatasetComplex = (
@@ -144,31 +137,26 @@ export const addDatasetComplex = (
   skipTracking = false,
   representations = undefined
 ) => async dispatch => {
-  dispatch(appendComplexList(datasetID, generateMoleculeCompoundId(data), skipTracking));
-  return dispatch(
-    loadObject({
-      target: Object.assign(
-        { display_div: VIEWS.MAJOR_VIEW },
-        generateComplexObject(data, colourToggle, base_url, datasetID)
-      ),
-      stage,
-      previousRepresentations: representations,
-      orientationMatrix: null
+  dispatch(
+    appendToBeDisplayedListForDataset(datasetID, {
+      type: NGL_OBJECTS.COMPLEX,
+      id: data.id,
+      display: true,
+      representations: representations,
+      datasetID: datasetID
     })
-  ).finally(() => {
-    const currentOrientation = stage.viewerControls.getOrientation();
-    dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
-  });
+  );
 };
 
 export const removeDatasetComplex = (stage, data, colourToggle, datasetID, skipTracking = false) => dispatch => {
   dispatch(
-    deleteObject(
-      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateComplexObject(data, colourToggle, base_url, datasetID)),
-      stage
-    )
+    updateInToBeDisplayedListForDataset(datasetID, {
+      id: data.id,
+      display: false,
+      type: NGL_OBJECTS.COMPLEX,
+      datasetID: datasetID
+    })
   );
-  dispatch(removeFromComplexList(datasetID, generateMoleculeCompoundId(data), skipTracking));
 };
 
 export const addDatasetSurface = (
@@ -178,31 +166,26 @@ export const addDatasetSurface = (
   datasetID,
   representations = undefined
 ) => async dispatch => {
-  dispatch(appendSurfaceList(datasetID, generateMoleculeCompoundId(data)));
-  return dispatch(
-    loadObject({
-      target: Object.assign(
-        { display_div: VIEWS.MAJOR_VIEW },
-        generateSurfaceObject(data, colourToggle, base_url, datasetID)
-      ),
-      stage,
-      previousRepresentations: representations,
-      orientationMatrix: null
+  dispatch(
+    appendToBeDisplayedListForDataset(datasetID, {
+      type: NGL_OBJECTS.SURFACE,
+      id: data.id,
+      display: true,
+      representations: representations,
+      datasetID: datasetID
     })
-  ).finally(() => {
-    const currentOrientation = stage.viewerControls.getOrientation();
-    dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
-  });
+  );
 };
 
 export const removeDatasetSurface = (stage, data, colourToggle, datasetID) => dispatch => {
   dispatch(
-    deleteObject(
-      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateSurfaceObject(data, colourToggle, base_url, datasetID)),
-      stage
-    )
+    updateInToBeDisplayedListForDataset(datasetID, {
+      id: data.id,
+      display: false,
+      type: NGL_OBJECTS.SURFACE,
+      datasetID: datasetID
+    })
   );
-  dispatch(removeFromSurfaceList(datasetID, generateMoleculeCompoundId(data)));
 };
 
 export const addDatasetLigand = (
@@ -213,43 +196,26 @@ export const addDatasetLigand = (
   skipTracking = false,
   representations = undefined
 ) => async (dispatch, getState) => {
-  dispatch(appendLigandList(datasetID, generateMoleculeCompoundId(data), skipTracking));
-  console.count(`Grabbed orientation before loading dataset ligand`);
-  const currentOrientation = stage.viewerControls.getOrientation();
-  return dispatch(
-    loadObject({
-      target: Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateMoleculeObject(data, colourToggle, datasetID)),
-      stage,
-      previousRepresentations: representations,
-      markAsRightSideLigand: true
+  dispatch(
+    appendToBeDisplayedListForDataset(datasetID, {
+      type: NGL_OBJECTS.LIGAND,
+      id: data.id,
+      display: true,
+      representations: representations,
+      datasetID: datasetID
     })
-  ).finally(() => {
-    const state = getState();
-    const skipOrientation = state.trackingReducers.skipOrientationChange;
-    if (!skipOrientation) {
-      const ligandOrientation = stage.viewerControls.getOrientation();
-      dispatch(setOrientation(VIEWS.MAJOR_VIEW, ligandOrientation));
-
-      dispatch(appendMoleculeOrientation(getDatasetMoleculeID(datasetID, data?.id), ligandOrientation));
-
-      // keep current orientation of NGL View
-      if (!skipOrientation) {
-        console.count(`Before applying orientation after loading dataset ligand.`);
-        stage.viewerControls.orient(currentOrientation);
-        console.count(`After applying orientation after loading dataset ligand.`);
-      }
-    }
-  });
+  );
 };
 
 export const removeDatasetLigand = (stage, data, colourToggle, datasetID, skipTracking = false) => dispatch => {
   dispatch(
-    deleteObject(
-      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateMoleculeObject(data, undefined, datasetID)),
-      stage
-    )
+    updateInToBeDisplayedListForDataset(datasetID, {
+      id: data.id,
+      display: false,
+      type: NGL_OBJECTS.LIGAND,
+      datasetID: datasetID
+    })
   );
-  dispatch(removeFromLigandList(datasetID, generateMoleculeCompoundId(data), skipTracking));
 };
 
 export const loadDataSets = targetId => async dispatch => {
@@ -553,7 +519,7 @@ export const autoHideDatasetDialogsOnScroll = ({ inspirationDialogRef, crossRefe
   const state = getState();
   const isOpenInspirationDialog = state.datasetsReducers.isOpenInspirationDialog;
   const isOpenCrossReferenceDialog = state.datasetsReducers.isOpenCrossReferenceDialog;
-  const isActionRestoring = state.trackingReducers.isActionRestoring;
+  const isActionRestoring = false; //state.trackingReducers.isActionRestoring;
 
   const currentBoundingClientRectInspiration =
     (inspirationDialogRef.current && inspirationDialogRef.current.getBoundingClientRect()) || null;