#594 Electron Density - Settings read file

m2ms · Apr 13, 2021 · 5c1a7da · 5c1a7da
1 parent d6750de
commit 5c1a7da
Show file tree

Hide file tree

Showing 6 changed files with 141 additions and 43 deletions.
diff --git a/js/components/nglView/generatingObjects.js b/js/components/nglView/generatingObjects.js
@@ -154,7 +154,12 @@ export const generateSurfaceObject = (data, colourToggle, base_url, datasetID) =
 
 // Density
 export const generateDensityObject = (data, colourToggle, base_url, isWireframeStyle) => {
+  const proteinData = data && data.proteinData;
+
   let prot_url;
+  let sigmaa_url;
+  let diff_url;
+  let event_url;
 
   if (data && data.molecule_protein) {
     prot_url = base_url + data.molecule_protein;
@@ -166,16 +171,39 @@ export const generateDensityObject = (data, colourToggle, base_url, isWireframeS
     }
   }
 
+  if (proteinData && proteinData.event_info) {
+    if (location.protocol === 'https:') {
+      event_url = proteinData.event_info.replace('http://', 'https://');
+    } else {
+      event_url = proteinData.event_info;
+    }
+  }
+
+  if (proteinData && proteinData.sigmaa_info) {
+    if (location.protocol === 'https:') {
+      sigmaa_url = proteinData.sigmaa_info.replace('http://', 'https://');
+    } else {
+      sigmaa_url = proteinData.sigmaa_info;
+    }
+  }
+
+  if (proteinData && proteinData.diff_info) {
+    if (location.protocol === 'https:') {
+      diff_url = proteinData.diff_info.replace('http://', 'https://');
+    } else {
+      diff_url = proteinData.diff_info;
+    }
+  }
+
   return {
     name: `${data.protein_code || data.name}_${OBJECT_TYPE.DENSITY}`,
     OBJECT_TYPE: OBJECT_TYPE.DENSITY,
     sdf_info: data.sdf_info,
-    map_info: data.map_info,
-    event_info: data.event_info,
-    sigmaa_info: data.sigmaa_info,
-    diff_info: data.diff_info,
-    colour: colourToggle,
+    event_url,
+    sigmaa_url,
+    diff_url,
     prot_url,
+    colour: colourToggle,
     moleculeId: data.id,
     wireframe: isWireframeStyle,
     selectionType: SELECTION_TYPE.DENSITY

diff --git a/js/components/nglView/renderingObjects.js b/js/components/nglView/renderingObjects.js
@@ -387,7 +387,7 @@ const showHotspot = ({ stage, input_dict, object_name, representations }) => {
   }
 };
 
-const showDensity = ({ stage, input_dict, object_name, representations }) => {
+const showDensity = ({ stage, input_dict, object_name, representations, dispatch }) => {
   let densityParams = {
     color: input_dict.coluor,
     isolevel: input_dict.isoLevel || 3,
@@ -398,24 +398,29 @@ const showDensity = ({ stage, input_dict, object_name, representations }) => {
     opacity: input_dict.opacity || 1,
     opaqueBack: false
   };
-
   return Promise.all([
-    stage.loadFile(input_dict.sigmaa_info, { name: object_name, ext: 'map' }).then(comp => {
-      const repr = createRepresentationStructure(MOL_REPRESENTATION.surface, densityParams);
-      const reprArray = representations || createRepresentationsArray([repr]);
-      return assignRepresentationArrayToComp(reprArray, comp);
-    }),
-    stage.loadFile(input_dict.diff_info, { name: object_name, ext: 'map' }).then(comp => {
-      const repr = createRepresentationStructure(MOL_REPRESENTATION.surface, densityParams);
-      const reprArray = representations || createRepresentationsArray([repr]);
-      return assignRepresentationArrayToComp(reprArray, comp);
-    }),
-    stage.loadFile(input_dict.event_info, { name: object_name, ext: 'ccp4' }).then(comp => {
-      const repr = createRepresentationStructure(MOL_REPRESENTATION.surface, densityParams);
-      const reprArray = representations || createRepresentationsArray([repr]);
-      return assignRepresentationArrayToComp(reprArray, comp);
-    })
-  ]).then(values => [...values]);
+    input_dict.sigmaa_url &&
+      stage.loadFile(input_dict.sigmaa_url, { ext: 'map' }).then(comp => {
+        const repr = createRepresentationStructure(MOL_REPRESENTATION.surface, densityParams);
+        const reprArray = representations || createRepresentationsArray([repr]);
+        return assignRepresentationArrayToComp(reprArray, comp);
+      }),
+    input_dict.diff_url &&
+      stage.loadFile(input_dict.diff_url, { name: object_name, ext: 'map' }).then(comp => {
+        const repr = createRepresentationStructure(MOL_REPRESENTATION.surface, densityParams);
+        const reprArray = representations || createRepresentationsArray([repr]);
+        return assignRepresentationArrayToComp(reprArray, comp);
+      }),
+
+    input_dict.event_url &&
+      stage.loadFile(input_dict.event_url, { name: object_name, ext: 'ccp4' }).then(comp => {
+        const repr = createRepresentationStructure(MOL_REPRESENTATION.surface, densityParams);
+        const reprArray = representations || createRepresentationsArray([repr]);
+        return assignRepresentationArrayToComp(reprArray, comp);
+      })
+  ]).then(values => {
+    let val = [...values];
+  });
 };
 
 // Refactor this out into a utils directory

diff --git a/js/components/preview/molecule/redux/actions.js b/js/components/preview/molecule/redux/actions.js
@@ -12,5 +12,10 @@ export const reloadMoleculeReducer = newState => ({
 
 export const addImageToCache = (molId, image) => ({
   type: constants.ADD_IMAGE_TO_CACHE,
-  payload: {molId: molId, image: image}
+  payload: { molId: molId, image: image }
+});
+
+export const addProteindDataToCache = (molId, proteinData) => ({
+  type: constants.ADD_PROTEIN_DATA_TO_CACHE,
+  payload: { molId: molId, image: proteinData }
 });
diff --git a/js/components/preview/molecule/redux/constants.js b/js/components/preview/molecule/redux/constants.js
@@ -3,7 +3,8 @@ const prefix = 'PREVIEW_MOLECULE_';
 export const constants = {
   SET_SORT_DIALOG_OPEN: prefix + 'SET_SORT_DIALOG_OPEN',
   RELOAD_REDUCER: prefix + 'RELOAD_REDUCER',
-  ADD_IMAGE_TO_CACHE: prefix + 'ADD_IMAGE_TO_CACHE'
+  ADD_IMAGE_TO_CACHE: prefix + 'ADD_IMAGE_TO_CACHE',
+  ADD_PROTEIN_DATA_TO_CACHE: prefix + 'ADD_PROTEIN_DATA_TO_CACHE'
 };
 
 export const MOL_ATTR = {

diff --git a/js/components/preview/molecule/redux/dispatchActions.js b/js/components/preview/molecule/redux/dispatchActions.js
@@ -292,21 +292,28 @@ export const addDensity = (
   skipTracking = false,
   representations = undefined
 ) => dispatch => {
-  dispatch(
-    loadObject({
-      target: Object.assign(
-        { display_div: VIEWS.MAJOR_VIEW },
-        generateDensityObject(data, colourToggle, base_url, isWireframeStyle)
-      ),
-      stage,
-      previousRepresentations: representations,
-      orientationMatrix: null
-    })
-  ).finally(() => {
-    const currentOrientation = stage.viewerControls.getOrientation();
-    dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
+  dispatch(getProteinData(data)).then(i => {
+    if (i && i.length > 0) {
+      data.protein_data = i[0];
+
+      dispatch(
+        loadObject({
+          target: Object.assign(
+            { display_div: VIEWS.MAJOR_VIEW },
+            generateDensityObject(data, colourToggle, base_url, isWireframeStyle)
+          ),
+          stage,
+          previousRepresentations: representations,
+          orientationMatrix: null
+        })
+      ).finally(() => {
+        const currentOrientation = stage.viewerControls.getOrientation();
+        dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
+      });
+    }
+
+    dispatch(appendDensityList(generateMoleculeId(data), skipTracking));
   });
-  dispatch(appendDensityList(generateMoleculeId(data), skipTracking));
 };
 
 export const addDensityCustomView = (
@@ -773,6 +780,44 @@ export const getQualityInformation = (data, molType, width, height) => (dispatch
   }
 };
 
+export const getProteinData = molecule => (dispatch, getState) => {
+  const state = getState();
+
+  const proteindDataCache = state.previewReducers.molecule.proteinDataCache;
+
+  const code = molecule.protein_code;
+  const molId = molecule.id;
+  const molIdStr = molId.toString();
+  if (proteindDataCache.hasOwnProperty(molIdStr)) {
+    return new Promise((resolve, reject) => {
+      resolve(proteindDataCache[molIdStr]);
+    });
+  } else {
+    return loadProteinData(code).then(i => {
+      if (!proteindDataCache.hasOwnProperty(molIdStr)) {
+        dispatch(addImageToCache(molId.toString(), i));
+      }
+      return i;
+    });
+  }
+};
+
+const loadProteinData = code => {
+  if (code) {
+    let url = new URL(`${base_url}/api/proteins/?code=${code}`);
+    let onCancel = () => {};
+    return api({
+      url,
+      onCancel
+    }).then(response => {
+      return response.data.results;
+    });
+  } else {
+    console.error('Trying to load protein data for unknown molecule protein code.');
+    return Promise.resolve();
+  }
+};
+
 export const getMolImage = (molId, molType, width, height) => (dispatch, getState) => {
   const state = getState();
 

diff --git a/js/components/preview/molecule/redux/reducer.js b/js/components/preview/molecule/redux/reducer.js
@@ -2,7 +2,8 @@ import { constants } from './constants';
 
 export const INITIAL_STATE = {
   sortDialogOpen: false,
-  imageCache: {}
+  imageCache: {},
+  proteinDataCache: {}
 };
 
 export const molecule = (state = INITIAL_STATE, action = {}) => {
@@ -16,9 +17,22 @@ export const molecule = (state = INITIAL_STATE, action = {}) => {
       return Object.assign({}, state, { ...action.payload });
 
     case constants.ADD_IMAGE_TO_CACHE:
-      return {...state, imageCache: {
-        ...state.imageCache, [action.payload.molId]: action.payload.image
-      }};
+      return {
+        ...state,
+        imageCache: {
+          ...state.imageCache,
+          [action.payload.molId]: action.payload.image
+        }
+      };
+
+    case constants.ADD_PROTEIN_DATA_TO_CACHE:
+      return {
+        ...state,
+        proteinDataCache: {
+          ...state.proteinDataCache,
+          [action.payload.molId]: action.payload.proteinData
+        }
+      };
 
     default:
       return state;