Merge remote-tracking branch 'remotes/origin/allfunctionality' into p…

…erfMerge1
m2ms · Dec 17, 2020 · f28d5e7 · f28d5e7
2 parents c7d89b5 + 14b1e61
commit f28d5e7
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Showing 9 changed files with 151 additions and 31 deletions.
diff --git a/js/components/preview/molecule/moleculeListSortFilterDialog.js b/js/components/preview/molecule/moleculeListSortFilterDialog.js
@@ -173,6 +173,9 @@ export const MoleculeListSortFilterDialog = memo(
     }, [joinedMoleculeLists]);
 
     const [initState, setInitState] = useState(initialize());
+
+    filter = filter || initState;
+
     const [filteredCount, setFilteredCount] = useState(getFilteredMoleculesCount(joinedMoleculeLists, filter));
     const [predefinedFilter, setPredefinedFilter] = useState(filter.predefined);
 

diff --git a/js/components/preview/molecule/moleculeView.js b/js/components/preview/molecule/moleculeView.js
@@ -612,7 +612,7 @@ const MoleculeView = memo(
                       )}
                       onClick={() => {
                         // always deselect all if are selected only some of options
-                        selectedAll.current = hasSomeValuesOn ? false : !selectedAll.current;
+                        selectedAll.current = hasSomeValuesOn || hasAllValuesOn ? false : !selectedAll.current;
 
                         setCalledFromAll();
                         onLigand(true);

diff --git a/js/components/preview/moleculeGroups/redux/dispatchActions.js b/js/components/preview/moleculeGroups/redux/dispatchActions.js
@@ -1,4 +1,7 @@
 import {
+  complexObjectTypes,
+  generateComplex,
+  generateMolecule,
   generateSphere
 } from '../../molecule/molecules_helpers';
 import { VIEWS } from '../../../../constants/constants';
@@ -8,28 +11,111 @@ import {
   loadObject
 } from '../../../../reducers/ngl/dispatchActions';
 import {
+  removeFromComplexList,
+  removeFromProteinList,
+  removeFromSurfaceList,
+  removeFromFragmentDisplayList,
+  removeFromVectorOnList,
   resetSelectionState,
   setComplexList,
   setFilter,
   setFragmentDisplayList,
   setMolGroupSelection,
+  setObjectSelection,
   setVectorList,
   setVectorOnList
 } from '../../../../reducers/selection/actions';
 import { setCountOfRemainingMoleculeGroups, setMoleculeOrientations } from '../../../../reducers/ngl/actions';
-import { setMolGroupList, setMolGroupOn } from '../../../../reducers/api/actions';
+import { setMolGroupList, setMolGroupOn, setMolGroupOff } from '../../../../reducers/api/actions';
 import { getUrl, loadFromServer } from '../../../../utils/genericList';
 import { OBJECT_TYPE } from '../../../nglView/constants';
 import { setSortDialogOpen } from '../../molecule/redux/actions';
 import { resetCurrentCompoundsSettings } from '../../compounds/redux/actions';
 import { reloadSession } from '../../../snapshot/redux/dispatchActions';
 import { resetRestoringState } from '../../../../reducers/tracking/dispatchActions';
+import { selectJoinedMoleculeList } from '../../molecule/redux/selectors';
 
-export const clearAfterDeselectingMoleculeGroup = () => (
-  dispatch
+export const clearAfterDeselectingMoleculeGroup = ({ molGroupId, currentMolGroup, majorViewStage }) => (
+  dispatch,
+  getState
 ) => {
+  dispatch(setObjectSelection([molGroupId]));
+
+  let site;
+  const state = getState();
+  const { fragmentDisplayList, complexList, proteinList, surfaceList, vectorOnList, vector_list } = state.selectionReducers;
+
+  const actionFragmentDisplayList = [];
+  const actionComplexList = [];
+  const actionProteinList = [];
+  const actionSurfaceList = [];
+  const actionVectorOnList = [];
+
+  // loop through all molecules
+  selectJoinedMoleculeList(state).forEach(mol => {
+    site = mol.site;
+
+    // remove Ligand
+    dispatch(
+      deleteObject(
+        Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateMolecule(mol.protein_code, mol.sdf_info)),
+        majorViewStage
+      )
+    );
+
+    // remove Complex, Protein, Surface
+    Object.keys(complexObjectTypes).forEach(type => {
+      dispatch(
+        deleteObject(
+          Object.assign(
+            { display_div: VIEWS.MAJOR_VIEW },
+            generateComplex(mol.protein_code, mol.sdf_info, mol.molecule_protein, type)
+          ),
+          majorViewStage
+        )
+      );
+    });
+
+    if (fragmentDisplayList.find(ligand => ligand === mol.id)) actionFragmentDisplayList.push(mol);
+    if (complexList.find(ligand => ligand === mol.id)) actionComplexList.push(mol);
+    if (proteinList.find(ligand => ligand === mol.id)) actionProteinList.push(mol);
+    if (surfaceList.find(ligand => ligand === mol.id)) actionSurfaceList.push(mol);
+    if (vectorOnList.find(ligand => ligand === mol.id)) actionVectorOnList.push(mol);
+  });
+  dispatch(setMolGroupOff(molGroupId, {
+    ligand: actionFragmentDisplayList,
+    protein: actionProteinList,
+    complex: actionComplexList,
+    surface: actionSurfaceList,
+    vector: actionVectorOnList
+  }));
+
+  // remove all Vectors
+  vector_list
+    .filter(v => v.site === site)
+    .forEach(item => {
+      dispatch(deleteObject(Object.assign({ display_div: VIEWS.MAJOR_VIEW }, item), majorViewStage));
+    });
+
+  dispatch(setObjectSelection(undefined));
+
   // remove all molecule orientations
   dispatch(setMoleculeOrientations({}));
+
+  // remove all selected ALCV of given site
+  currentMolGroup.mol_id.forEach(moleculeID => {
+    // remove Ligand, Complex, Vectors from selection
+    //Ligand
+    dispatch(removeFromFragmentDisplayList({ id: moleculeID }, true));
+    // Complex
+    dispatch(removeFromComplexList({ id: moleculeID }, true));
+    // Protein
+    dispatch(removeFromProteinList({ id: moleculeID }, true));
+    // Surface
+    dispatch(removeFromSurfaceList({ id: moleculeID }, true));
+    // Vectors
+    dispatch(removeFromVectorOnList({ id: moleculeID }, true));
+  });
 };
 
 export const saveMoleculeGroupsToNglView = (molGroupList, stage, projectId) => dispatch => {
@@ -200,7 +286,11 @@ export const onDeselectMoleculeGroup = ({ moleculeGroup, stageSummaryView, major
   const selectionCopy = mol_group_selection.slice();
   const objIdx = mol_group_selection.indexOf(moleculeGroup.id);
   dispatch(
-    clearAfterDeselectingMoleculeGroup()
+    clearAfterDeselectingMoleculeGroup({
+      molGroupId: moleculeGroup.id,
+      currentMolGroup,
+      majorViewStage
+    })
   );
   selectionCopy.splice(objIdx, 1);
   dispatch(

diff --git a/js/reducers/api/actions.js b/js/reducers/api/actions.js
@@ -59,6 +59,14 @@ export const setMolGroupOn = function(mol_group_id) {
   };
 };
 
+export const setMolGroupOff = function(mol_group_id, selectionGroups) {
+  return {
+    type: constants.SET_MOL_GROUP_OFF,
+    mol_group_off: mol_group_id,
+    selectionGroups
+  };
+};
+
 export const setMolGroupList = function(mol_group_list) {
   return {
     type: constants.SET_MOL_GROUP_LIST,

diff --git a/js/reducers/api/constants.js b/js/reducers/api/constants.js
@@ -11,6 +11,7 @@ export const constants = {
   SET_PANNDA_EVENT_ON: prefix + 'SET_PANNDA_EVENT_ON',
 
   SET_MOL_GROUP_ON: prefix + 'SET_MOL_GROUP_ON',
+  SET_MOL_GROUP_OFF: prefix + 'SET_MOL_GROUP_OFF',
   SET_MOL_GROUP_LIST: prefix + 'SET_MOL_GROUP_LIST',
   SET_MOLECULE_LIST: prefix + 'SET_MOLECULE_LIST',
   SET_CACHED_MOL_LISTS: prefix + 'SET_CACHED_MOL_LISTS',

diff --git a/js/reducers/selection/actions.js b/js/reducers/selection/actions.js
@@ -39,10 +39,11 @@ export const setCurrentVector = vectorSmile => {
   };
 };
 
-export const setFragmentDisplayList = function(fragmentDisplayList) {
+export const setFragmentDisplayList = function(fragmentDisplayList, skipTracking = false) {
   return {
     type: constants.SET_FRAGMENT_DISPLAY_LIST,
-    fragmentDisplayList: fragmentDisplayList
+    fragmentDisplayList: fragmentDisplayList,
+    skipTracking
   };
 };
 
@@ -62,10 +63,11 @@ export const removeFromFragmentDisplayList = function(item, skipTracking = false
   };
 };
 
-export const setProteinList = function(proteinList) {
+export const setProteinList = function(proteinList, skipTracking = false) {
   return {
     type: constants.SET_PROTEIN_LIST,
-    proteinList: proteinList
+    proteinList: proteinList,
+    skipTracking
   };
 };
 
@@ -84,10 +86,11 @@ export const removeFromProteinList = function(item, skipTracking = false) {
     skipTracking: skipTracking
   };
 };
-export const setComplexList = function(complexList) {
+export const setComplexList = function(complexList, skipTracking = false) {
   return {
     type: constants.SET_COMPLEX_LIST,
-    complexList: complexList
+    complexList: complexList,
+    skipTracking
   };
 };
 
@@ -107,10 +110,11 @@ export const removeFromComplexList = function(item, skipTracking = false) {
   };
 };
 
-export const setSurfaceList = function(surfaceList) {
+export const setSurfaceList = function(surfaceList, skipTracking = false) {
   return {
     type: constants.SET_SURFACE_LIST,
-    surfaceList: surfaceList
+    surfaceList: surfaceList,
+    skipTracking
   };
 };
 
@@ -151,10 +155,11 @@ export const removeFromDensityList = function(item) {
   };
 };
 
-export const setVectorOnList = function(vectorOnList) {
+export const setVectorOnList = function(vectorOnList, skipTracking = false) {
   return {
     type: constants.SET_VECTOR_ON_LIST,
-    vectorOnList: vectorOnList
+    vectorOnList: vectorOnList,
+    skipTracking
   };
 };
 

diff --git a/js/reducers/tracking/dispatchActions.js b/js/reducers/tracking/dispatchActions.js
@@ -1513,10 +1513,24 @@ const removeRepresentation = (parentKey, representation, nglView) => (dispatch,
 const handleMoleculeGroupAction = (action, isSelected, stageSummaryView, majorViewStage) => (dispatch, getState) => {
   const state = getState();
   if (action) {
-    let moleculeGroup = getMolGroup(action.object_name, state);
+    const { selectionGroups, object_name } = action;
+    let moleculeGroup = getMolGroup(object_name, state);
     if (moleculeGroup) {
       if (isSelected === true) {
         dispatch(selectMoleculeGroup(moleculeGroup, stageSummaryView));
+
+        for (const type in selectionGroups) {
+          if (selectionGroups.hasOwnProperty(type)) {
+            const typeGroup = selectionGroups[type];
+            for (const mol of typeGroup) {
+              if (type === 'ligand') {
+                dispatch(addType[type](majorViewStage, mol, colourList[mol.id % colourList.length], true, true));
+              } else {
+                dispatch(addType[type](majorViewStage, mol, colourList[mol.id % colourList.length], true));
+              }
+            }
+          }
+        }
       } else {
         dispatch(onDeselectMoleculeGroup({ moleculeGroup, stageSummaryView, majorViewStage }));
       }

diff --git a/js/reducers/tracking/trackingActions.js b/js/reducers/tracking/trackingActions.js
@@ -42,20 +42,19 @@ export const findTrackAction = (action, state) => {
           };
         }
       }
-    } else if (action.type.includes(selectionConstants.SET_OBJECT_SELECTION)) {
-      let objectId = action.payload && action.payload[0];
-      if (objectId) {
-        let molGroupName = getMolGroupName(objectId, state);
-        trackAction = {
-          type: actionType.SITE_TURNED_OFF,
-          timestamp: Date.now(),
-          username: username,
-          object_type: actionObjectType.SITE,
-          object_name: molGroupName,
-          object_id: objectId,
-          text: `${actionDescription.SITE} ${molGroupName} ${actionDescription.TURNED_OFF}`
-        };
-      }
+    } else if (action.type.includes(apiConstants.SET_MOL_GROUP_OFF)) {
+      const { mol_group_off, selectionGroups } = action;
+      let molGroupName = getMolGroupName(mol_group_off, state);
+      trackAction = {
+        type: actionType.SITE_TURNED_OFF,
+        timestamp: Date.now(),
+        username: username,
+        object_type: actionObjectType.SITE,
+        object_name: molGroupName,
+        object_id: mol_group_off,
+        selectionGroups,
+        text: `${actionDescription.SITE} ${molGroupName} ${actionDescription.TURNED_OFF}`
+      };
     } else if (action.type === selectionConstants.SET_HIDE_ALL) {
       if (action.data) {
         let objectType = actionObjectType.MOLECULE;

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "fragalysis-frontend",
-  "version": "0.9.37",
+  "version": "0.9.40",
   "description": "Frontend for fragalysis",
   "main": "webpack.config.js",
   "scripts": {