Merge remote-tracking branch 'origin/feature/#267-Tabs' into feature/#…

…267-Tabs # Conflicts: # js/components/datasets/redux/actions.js # js/components/datasets/redux/constants.js # js/components/datasets/redux/dispatchActions.js # js/components/datasets/redux/reducer.js # js/components/preview/Preview.js
m2ms · May 11, 2020 · 16f776b · 16f776b
2 parents ea8a158 + d0276f7
commit 16f776b
Show file tree

Hide file tree

Showing 34 changed files with 631 additions and 595 deletions.
diff --git a/js/components/common/Surfaces/Panel/index.js b/js/components/common/Surfaces/Panel/index.js
@@ -1,5 +1,5 @@
 import React, { forwardRef, memo, useEffect, useState } from 'react';
-import { Paper as MaterialPaper, makeStyles, Grid, IconButton, Typography } from '@material-ui/core';
+import { Paper as MaterialPaper, makeStyles, Grid, IconButton, Typography, CircularProgress } from '@material-ui/core';
 import ExpandMore from '@material-ui/icons/ExpandMore';
 import ExpandLess from '@material-ui/icons/ExpandLess';
 
@@ -44,6 +44,9 @@ const useStyles = makeStyles(theme => ({
   hidden: {
     height: 0,
     display: 'none'
+  },
+  loading: {
+    paddingTop: theme.spacing(2)
   }
 }));
 
@@ -60,6 +63,7 @@ export const Panel = memo(
         onExpandChange,
         children,
         bodyOverflow,
+        isLoading,
         ...rest
       },
       ref
@@ -132,6 +136,13 @@ export const Panel = memo(
               </Grid>
             </div>
           )}
+          {isLoading && (
+            <Grid container alignItems="center" justify="center" className={classes.loading}>
+              <Grid item>
+                <CircularProgress />
+              </Grid>
+            </Grid>
+          )}
           {hasExpansion && <div className={expanded === true ? bodyClass : classes.hidden}>{children}</div>}
           {!hasExpansion && <div className={bodyClass}>{children}</div>}
         </MaterialPaper>

diff --git a/js/components/datasets/redux/dispatchActions.js b/js/components/datasets/redux/dispatchActions.js
@@ -1,4 +1,215 @@
 import { deleteObject, loadObject, setOrientation } from '../../../reducers/ngl/dispatchActions';
+import {
+  setFilter,
+  appendLigandList,
+  appendProteinList,
+  appendComplexList,
+  appendSurfaceList,
+  removeFromLigandList,
+  removeFromProteinList,
+  removeFromComplexList,
+  removeFromSurfaceList
+} from './actions';
+import { base_url } from '../../routes/constants';
+import {
+  generateMoleculeId,
+  generateHitProteinObject,
+  generateComplexObject,
+  generateSurfaceObject,
+  generateMoleculeObject
+} from '../../nglView/generatingObjects';
+import { VIEWS } from '../../../constants/constants';
+import { MOL_ATTRIBUTES } from '../../preview/molecule/redux/constants';
+
+import { addMoleculeList } from './actions';
+
+export const initializeDatasetMoleculeLists = moleculeList => (dispatch, getState) => {
+  console.log('initializing testing datasets');
+  const state = getState();
+  const customDatasets = state.datasetsReducers.datasets;
+  const testingMoleculeList = moleculeList.slice(0, 6);
+  // TODO temporarily, just adding testing data
+  customDatasets.forEach(dataset => {
+    dispatch(
+      addMoleculeList(
+        dataset.id,
+        (testingMoleculeList => {
+          const newList = [];
+          testingMoleculeList.forEach(molecule => {
+            // molecule.protein_code is used as prefix for element names in display controls
+            newList.push(Object.assign({}, molecule, { protein_code: dataset.id + '_' + molecule.id }));
+          });
+          return newList;
+        })(testingMoleculeList)
+      )
+    );
+  });
+};
+
+export const getListedMolecules = (object_selection, cached_mol_lists) => {
+  let molecules = [];
+  if ((object_selection || []).length) {
+    for (let molgroupId of object_selection) {
+      // Selected molecule groups
+      const molGroup = cached_mol_lists[molgroupId];
+      if (molGroup) {
+        molecules = molecules.concat(molGroup);
+      } else {
+        console.log(`Molecule group ${molgroupId} not found in cached list`);
+      }
+    }
+  }
+
+  return molecules;
+};
+
+export const initializeFilter = (object_selection, cached_mol_lists) => (dispatch, getState) => {
+  const state = getState();
+  if (!object_selection || !cached_mol_lists) {
+    object_selection = (() => {
+      let tmp = [];
+      state.datasetsReducers.datasets.forEach(dataset => {
+        tmp.push(dataset.id);
+      });
+      return tmp;
+    })(state.datasetsReducers.datasets);
+    cached_mol_lists = state.datasetsReducers.moleculeLists;
+  }
+
+  let initObject = state.selectionReducers.filter;
+
+  if (initObject === undefined) {
+    initObject = {
+      active: false,
+      predefined: 'none',
+      filter: {},
+      priorityOrder: MOL_ATTRIBUTES.map(molecule => molecule.key)
+    };
+  } else {
+    initObject = Object.assign({}, initObject);
+    console.log('using saved filter');
+  }
+
+  for (let attr of MOL_ATTRIBUTES) {
+    const lowAttr = attr.key.toLowerCase();
+    let minValue = -999999;
+    let maxValue = 0;
+    for (let molecule of getListedMolecules(object_selection, cached_mol_lists)) {
+      const attrValue = molecule[lowAttr];
+      if (attrValue > maxValue) maxValue = attrValue;
+      if (minValue === -999999) minValue = maxValue;
+      if (attrValue < minValue) minValue = attrValue;
+    }
+
+    initObject.filter[attr.key] = {
+      priority: 0,
+      order: 1,
+      minValue: minValue,
+      maxValue: maxValue,
+      isFloat: attr.isFloat
+    };
+  }
+  dispatch(setFilter(initObject));
+  return initObject;
+};
+
+/* ----------------------------------------------- */
+
+export const addProtein = (stage, data, colourToggle, datasetID) => dispatch => {
+  dispatch(
+    loadObject(
+      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateHitProteinObject(data, colourToggle, base_url)),
+      stage,
+      undefined,
+      null
+    )
+  ).finally(() => {
+    const currentOrientation = stage.viewerControls.getOrientation();
+    dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
+  });
+  dispatch(appendProteinList(datasetID, generateMoleculeId(data)));
+};
+
+export const removeProtein = (stage, data, colourToggle, datasetID) => dispatch => {
+  dispatch(
+    deleteObject(
+      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateHitProteinObject(data, colourToggle, base_url)),
+      stage
+    )
+  );
+  dispatch(removeFromProteinList(datasetID, generateMoleculeId(data)));
+};
+
+export const addComplex = (stage, data, colourToggle, datasetID) => dispatch => {
+  dispatch(
+    loadObject(
+      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateComplexObject(data, colourToggle, base_url)),
+      stage,
+      undefined,
+      null
+    )
+  ).finally(() => {
+    const currentOrientation = stage.viewerControls.getOrientation();
+    dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
+  });
+  dispatch(appendComplexList(datasetID, generateMoleculeId(data)));
+};
+
+export const removeComplex = (stage, data, colourToggle, datasetID) => dispatch => {
+  dispatch(
+    deleteObject(
+      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateComplexObject(data, colourToggle, base_url)),
+      stage
+    )
+  );
+  dispatch(removeFromComplexList(datasetID, generateMoleculeId(data)));
+};
+
+export const addSurface = (stage, data, colourToggle, datasetID) => dispatch => {
+  dispatch(
+    loadObject(
+      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateSurfaceObject(data, colourToggle, base_url)),
+      stage,
+      undefined,
+      null
+    )
+  ).finally(() => {
+    const currentOrientation = stage.viewerControls.getOrientation();
+    dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
+  });
+  dispatch(appendSurfaceList(datasetID, generateMoleculeId(data)));
+};
+
+export const removeSurface = (stage, data, colourToggle, datasetID) => dispatch => {
+  dispatch(
+    deleteObject(
+      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateSurfaceObject(data, colourToggle, base_url)),
+      stage
+    )
+  );
+  dispatch(removeFromSurfaceList(datasetID, generateMoleculeId(data)));
+};
+
+export const addLigand = (stage, data, colourToggle, datasetID) => dispatch => {
+  dispatch(
+    loadObject(
+      Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateMoleculeObject(data, colourToggle)),
+      stage,
+      undefined,
+      null
+    )
+  ).finally(() => {
+    const currentOrientation = stage.viewerControls.getOrientation();
+    dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
+  });
+  dispatch(appendLigandList(datasetID, generateMoleculeId(data)));
+};
+
+export const removeLigand = (stage, data, colourToggle, datasetID) => dispatch => {
+  dispatch(deleteObject(Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateMoleculeObject(data)), stage));
+  dispatch(removeFromLigandList(datasetID, generateMoleculeId(data)));
+};
+import { deleteObject, loadObject, setOrientation } from '../../../reducers/ngl/dispatchActions';
 import {
   setFilter,
   appendLigandList,

diff --git a/js/components/landing/Landing.js b/js/components/landing/Landing.js
@@ -3,8 +3,7 @@
  */
 import { Grid, Link } from '@material-ui/core';
 import React, { memo, useContext, useEffect, useState } from 'react';
-import TargetList from '../target/targetList';
-//import SessionList from '../session/sessionList';
+import { TargetList } from '../target/targetList';
 import { connect } from 'react-redux';
 import * as apiActions from '../../reducers/api/actions';
 import * as selectionActions from '../../reducers/selection/actions';
@@ -50,10 +49,9 @@ const Landing = memo(
     return (
       <Grid container spacing={2}>
         <Grid item xs={4}>
-          <TargetList key="TARGLIST" />
+          <TargetList />
         </Grid>
         <Grid item xs={8}>
-          {/*<SessionList />*/}
           <Projects />
         </Grid>
       </Grid>