#1522, #1518

js/components/header/index.js

@@ -68,6 +68,7 @@ import { AddProjectDetail } from '../projects/addProjectDetail';
 import { ServicesStatusWrapper } from '../services';
 import { COMPANIES, get_logo } from '../funders/constants';
 import { setEditTargetDialogOpen } from '../target/redux/actions';
+import { Upload } from '@mui/icons-material';
 
 const useStyles = makeStyles(theme => ({
   padding: {
@@ -272,8 +273,8 @@ export default memo(
                   targetName !== undefined ? (
                     <>
                       {currentProject.authorID === null ||
-                      currentProject.projectID === null ||
-                      currentProject.authorID === userId ? (
+                        currentProject.projectID === null ||
+                        currentProject.authorID === userId ? (
                         <Button
                           onClick={() => {
                             isProjectModalLoading === false
@@ -574,6 +575,29 @@ export default memo(
                 </ListItemIcon>
                 <ListItemText primary="Contributors" />
               </ListItem>
+              {DJANGO_CONTEXT.pk &&
+                <>
+                  <Divider />
+                  <ListItem button onClick={() => openLink(URLS.lhsUpload)}>
+                    <ListItemIcon>
+                      <Upload />
+                    </ListItemIcon>
+                    <ListItemText primary="LHS upload" />
+                  </ListItem>
+                  <ListItem button onClick={() => openLink(URLS.rhsUpload)}>
+                    <ListItemIcon>
+                      <Upload />
+                    </ListItemIcon>
+                    <ListItemText primary="RHS upload" />
+                  </ListItem>
+                  <ListItem button onClick={() => openLink(URLS.metadataUpload)}>
+                    <ListItemIcon>
+                      <Upload />
+                    </ListItemIcon>
+                    <ListItemText primary="Metadata upload" />
+                  </ListItem>
+                </>
+              }
               <Divider />
               {authListItem}
             </Grid>

js/components/preview/molecule/moleculeView/moleculeView.js

@@ -58,6 +58,8 @@ import { DJANGO_CONTEXT } from '../../../../utils/djangoContext';
 import { getFontColorByBackgroundColor } from '../../../../utils/colors';
 import { api, METHOD } from '../../../../utils/api';
 import { base_url } from '../../../routes/constants';
+import { ContentCopyRounded } from '@mui/icons-material';
+import { ToastContext } from '../../../toast';
 
 const useStyles = makeStyles(theme => ({
   container: {
@@ -358,6 +360,8 @@ export const img_data_init = `<svg xmlns="http://www.w3.org/2000/svg" version="1
     <animateTransform attributeName="transform" type="rotate" repeatCount="indefinite" dur="0.689655172413793s" values="0 50 50;360 50 50" keyTimes="0;1"></animateTransform>
   </circle>  '</svg>`;
 
+export const XCA_TAGS_CATEGORIES = ['CanonSites', 'ConformerSites', 'Quatassemblies', 'Crystalforms', 'CrystalformSites'];
+
 const MoleculeView = memo(
   ({
     imageHeight,
@@ -409,6 +413,7 @@ const MoleculeView = memo(
     const [tagEditModalOpenNew, setTagEditModalOpenNew] = useState(tagEditorOpenObs);
 
     const { getNglView } = useContext(NglContext);
+    const { toastInfo } = useContext(ToastContext);
     const stage = getNglView(VIEWS.MAJOR_VIEW) && getNglView(VIEWS.MAJOR_VIEW).stage;
 
     const isLigandOn = L;
@@ -463,6 +468,7 @@ const MoleculeView = memo(
     const [moleculeTooltipOpen, setMoleculeTooltipOpen] = useState(false);
     const [tagPopoverOpen, setTagPopoverOpen] = useState(null);
     const [centroidRes, setCentroidRes] = useState('');
+    const [experimentalPath, setExperimentalPath] = useState('');
 
     const moleculeImgRef = useRef(null);
 
@@ -476,9 +482,6 @@ const MoleculeView = memo(
       setTagEditModalOpenNew(tagEditorOpenObs);
     }, [tagEditorOpenObs]);
 
-    const XCA_TAGS_CATEGORIES = ['CanonSites', 'ConformerSites', 'Quatassemblies', 'Crystalforms', 'CrystalformSites'];
-    const XCA_TAGS_CATEGORIES_EXPANDED = ['Quatassemblies', 'ConformerSites', 'Crystalforms', 'CrystalformSites', 'CanonSites'];
-
     useEffect(() => {
       api({
         url: `${base_url}/api/canon_site_confs/`,
@@ -515,6 +518,26 @@ const MoleculeView = memo(
         });
     }, [data.canon_site_conf]);
 
+    useEffect(() => {
+      api({
+        url: `${base_url}/api/experiments/`,
+        method: METHOD.GET
+      })
+        .then(resp => {
+          const experiment = resp.data.results.find(experiment => experiment.id === data.experiment);
+          if (experiment) {
+            setExperimentalPath(experiment.pdb_info_source_file ?? '');
+          } else {
+            console.log('there is not any matching canonSiteConf object with ' + data.experiment + ' id');
+            setExperimentalPath('');
+          }
+        })
+        .catch(err => {
+          console.log('error fetching experiment from experiments api', err);
+          setExperimentalPath('');
+        });
+    }, [data.experiment]);
+
     useEffect(() => {
       if (showExpandedView) {
         setHeaderWidthsHandler(centroidRes, 'CentroidRes');
@@ -523,7 +546,7 @@ const MoleculeView = memo(
           setHeaderWidthsHandler(getTagLabel(tagCategory), tagCategory);
         })
       }
-    }, [showExpandedView, getTagType, getTagLabel, centroidRes, data.longcode, setHeaderWidthsHandler, XCA_TAGS_CATEGORIES]);
+    }, [showExpandedView, getTagType, getTagLabel, centroidRes, data.longcode, setHeaderWidthsHandler]);
 
     const handlePopoverOpen = event => {
       setTagPopoverOpen(event.currentTarget);
@@ -1135,6 +1158,11 @@ const MoleculeView = memo(
       return tagTooltip;
     }, [getTagType]);
 
+    const copyExperimentalPaths = async () => {
+      await navigator.clipboard.writeText(experimentalPath);
+      toastInfo('Link was copied to the clipboard', { autoHideDuration: 5000 });
+    };
+
     return (
       <>
         <Grid
@@ -1428,7 +1456,6 @@ const MoleculeView = memo(
                   xs={5}
                   container
                   direction="row"
-                  justifyContent="center"
                   alignItems="center"
                   // wrap="nowrap"
                   style={{ height: "100%" }}
@@ -1488,7 +1515,7 @@ const MoleculeView = memo(
               </div>}
           </Grid>
           {showExpandedView && <Grid item container alignItems='center' wrap="nowrap">
-            {XCA_TAGS_CATEGORIES_EXPANDED.map((tagCategory, index) => {
+            {XCA_TAGS_CATEGORIES.map((tagCategory, index) => {
               return <Tooltip title={`${PLURAL_TO_SINGULAR[tagCategory]} - ${getTagTooltip(tagCategory)}`} key={index}>
                 <Grid item align="center" className={classes.categoryCell} style={{ minWidth: headerWidths[tagCategory] }}>
                   {getTagLabel(tagCategory)}
@@ -1505,6 +1532,13 @@ const MoleculeView = memo(
                 {data.longcode}
               </Grid>
             </Tooltip>
+            <Tooltip title={experimentalPath.length > 0 ? experimentalPath : 'empty path'}>
+              <Grid item align="center" style={{ minWidth: headerWidths.Path }}>
+                <IconButton color="inherit" onClick={copyExperimentalPaths} size="small">
+                  <ContentCopyRounded fontSize="small" />
+                </IconButton>
+              </Grid>
+            </Tooltip>
           </Grid>}
         </Grid >
         <SvgTooltip

js/components/preview/molecule/observationCmpList.js

@@ -10,7 +10,10 @@ import {
   Divider,
   Typography,
   IconButton,
-  ButtonGroup
+  ButtonGroup,
+  Select,
+  MenuItem,
+  Checkbox
 } from '@material-ui/core';
 import React, { useState, useEffect, useCallback, memo, useRef, useContext, useMemo } from 'react';
 import { useDispatch, useSelector } from 'react-redux';
@@ -321,6 +324,89 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
 
   const [predefinedFilter, setPredefinedFilter] = useState(filter !== undefined ? filter.predefined : DEFAULT_FILTER);
 
+  const [ascending, setAscending] = useState(true);
+  const handleAscendingChecked = (event) => setAscending(event.target.checked);
+  const SORT_OPTIONS = [
+    'POSE_NAME',
+    'COMPOUND_CODE',
+    'CANONSITE_NUMBER',
+    'CONFORMERSITE_NUMBER',
+    'OBSERVATION_COUNT'
+  ];
+  const sortOptions = {
+    POSE_NAME: {
+      title: 'Pose name',
+      handler: (a, b, asc) => compareByPoseName(a, b, asc)
+    },
+    COMPOUND_CODE: {
+      title: 'Compound code',
+      handler: (a, b, asc) => compareByCompoundCode(a, b, asc)
+    },
+    CANONSITE_NUMBER: {
+      title: 'CanonSite number',
+      handler: (a, b, asc) => compareByCanonSiteNumber(a, b, asc)
+    },
+    CONFORMERSITE_NUMBER: {
+      title: 'ConformerSite number',
+      handler: (a, b, asc) => compareByConformerSiteNumber(a, b, asc)
+    },
+    OBSERVATION_COUNT: {
+      title: 'Observation count',
+      handler: (a, b, asc) => compareByObservationCount(a, b, asc)
+    }
+  };
+  const [sortOption, setSortOption] = useState(SORT_OPTIONS[0]);
+
+  const compareByPoseName = (a, b, asc) => {
+    const aName = a.code;
+    const bName = b.code;
+    return asc ? aName.localeCompare(bName, undefined, { numeric: true, sensitivity: 'base' })
+      : bName.localeCompare(aName, undefined, { numeric: true, sensitivity: 'base' });
+  };
+  const compareByCompoundCode = (a, b, asc) => {
+    const aName = a.main_site_observation_cmpd_code;
+    const bName = b.main_site_observation_cmpd_code;
+    return asc ? aName.localeCompare(bName, undefined, { numeric: true, sensitivity: 'base' })
+      : bName.localeCompare(aName, undefined, { numeric: true, sensitivity: 'base' });
+  };
+  const compareByCanonSiteNumber = (a, b, asc) => {
+    const aName = getCanonSiteTagPrefix(a);
+    const bName = getCanonSiteTagPrefix(b);
+    return asc ? aName.localeCompare(bName, undefined, { numeric: true, sensitivity: 'base' })
+      : bName.localeCompare(aName, undefined, { numeric: true, sensitivity: 'base' });
+  };
+  const compareByConformerSiteNumber = (a, b, asc) => {
+    const aName = getConformerSiteTagPrefix(a);
+    const bName = getConformerSiteTagPrefix(b);
+    return asc ? aName.localeCompare(bName, undefined, { numeric: true, sensitivity: 'base' })
+      : bName.localeCompare(aName, undefined, { numeric: true, sensitivity: 'base' });
+  };
+  const compareByObservationCount = (a, b, asc) => {
+    const aCount = a.site_observations.length;
+    const bCount = b.site_observations.length;
+    return asc ? aCount - bCount : bCount - aCount;
+  };
+
+  /**
+   * Get CanonSites tag for sorting
+   */
+  const getCanonSiteTagPrefix = useCallback(pose => {
+    const mainObservation = pose.associatedObs.find(observation => observation.id === pose.main_site_observation);
+    const canonSitesTag = categories.find(tagCategory => tagCategory.category === 'CanonSites');
+    const canonSite = tags.find(tag => tag.category === canonSitesTag.id && tag.site_observations.includes(mainObservation.id));
+    return canonSite !== undefined ? canonSite.tag_prefix : '';
+  }, [categories, tags]);
+
+  /**
+   * Get ConformerSites tag for sorting
+   */
+  const getConformerSiteTagPrefix = useCallback(pose => {
+    const mainObservation = pose.associatedObs.find(observation => observation.id === pose.main_site_observation);
+    const conformerSitesTag = categories.find(tagCategory => tagCategory.category === 'ConformerSites');
+    const conformerSite = tags.find(tag => tag.category === conformerSitesTag.id && tag.site_observations.includes(mainObservation.id));
+    return conformerSite !== undefined ? conformerSite.tag_prefix : '';
+  }, [categories, tags]);
+
   const isActiveFilter = !!(filter || {}).active;
 
   const { getNglView } = useContext(NglContext);
@@ -718,8 +804,9 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
         compounds.push(compound);
       }
     });
+    compounds.sort((a, b) => sortOptions[sortOption].handler(a, b, ascending));
     return compounds;
-  }, [joinedMoleculeLists, lhsCompoundsList]);
+  }, [joinedMoleculeLists, lhsCompoundsList, sortOptions, sortOption, ascending]);
 
   useEffect(() => {
     if (isObservationDialogOpen && observationsForLHSCmp?.length > 0) {
@@ -1113,7 +1200,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
 
         {
           <Tooltip title={selectAllHitsPressed ? 'Unselect all hits' : 'Select all hits'}>
-            <Grid item style={{ marginLeft: '20px' }}>
+            <Grid item style={{ marginLeft: '5px' }}>
               <Button
                 variant="outlined"
                 className={classNames(classes.contColButton, {
@@ -1133,7 +1220,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
         }
         {selectedDisplayHits === true ? (
           <Tooltip title={'Unselect displayed hits'}>
-            <Grid item style={{ marginLeft: '20px' }}>
+            <Grid item style={{ marginLeft: '5px' }}>
               <Button
                 variant="outlined"
                 className={classNames(classes.contColButton, {
@@ -1152,7 +1239,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
           </Tooltip>
         ) : (
           <Tooltip title={'Select displayed hits'}>
-            <Grid item style={{ marginLeft: '20px' }}>
+            <Grid item style={{ marginLeft: '5px' }}>
               <Button
                 variant="outlined"
                 className={classNames(classes.contColButton, {
@@ -1174,6 +1261,32 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
           <Typography variant="caption" className={classes.noOfSelectedHits}>{`Selected: ${allSelectedMolecules ? allSelectedMolecules.length : 0
             }`}</Typography>
         </Grid>
+        <Grid style={{ marginTop: '4px' }}>
+          <Typography variant="caption" className={classes.noOfSelectedHits}>Sort by</Typography>
+        </Grid>
+        <Grid style={{ marginTop: '4px', marginLeft: '4px' }}>
+          <Tooltip title={sortOption ? sortOptions[sortOption].title : "Sort by"}>
+            <Select
+              value={sortOption}
+              onChange={(event) => setSortOption(event.target.value)}
+              // fullWidth
+              size="small"
+              style={{ fontSize: 10, width: 75 }}
+            >
+              {SORT_OPTIONS.map((option, index) => (
+                <MenuItem key={`${index}-${option}`} value={option} style={{ fontSize: 12, padding: '3px 7px' }}>
+                  {sortOptions[option].title}
+                </MenuItem>
+              ))}
+            </Select>
+          </Tooltip>
+        </Grid>
+        <Tooltip title={ascending ? "Ascending" : "Descending"}>
+          <Grid style={{ marginTop: '4px' }}>
+            <Checkbox checked={ascending} onChange={handleAscendingChecked} size="small" style={{ padding: 3 }} />
+            <Typography variant="caption" className={classes.noOfSelectedHits}>ASC</Typography>
+          </Grid>
+        </Tooltip>
       </Grid>
       <Grid container spacing={1} direction="column" justifyContent="flex-start" className={classes.container}>
         <Grid item>

js/components/preview/molecule/observationCmpView/observationCmpView.js

@@ -1611,7 +1611,7 @@ const ObservationCmpView = memo(
             {/* CanonSites */}
             <Grid item xs container direction="column" justifyContent="center" alignItems="stretch" wrap="nowrap">
               <Tooltip
-                title={<div style={{ whiteSpace: 'pre-line' }}>CanonSite - {getCanonSitesTag().upload_name}</div>}
+                title={<div style={{ whiteSpace: 'pre-line' }}>CanonSite - {getCanonSitesTag().tag}</div>}
               >
                 <Grid
                   item
@@ -1631,7 +1631,7 @@ const ObservationCmpView = memo(
               {getConformerSites().map((conformerSite, i, sites) => (
                 <Tooltip
                   key={conformerSite.id + i}
-                  title={<div style={{ whiteSpace: 'pre-line' }}>ConformerSite - {conformerSite.upload_name}</div>}
+                  title={<div style={{ whiteSpace: 'pre-line' }}>ConformerSite - {conformerSite.tag}</div>}
                 >
                   <Grid
                     item