xchem · mwinokan · Oct 14, 2024 · Jul 31, 2024 · Aug 22, 2024 · Aug 27, 2024
diff --git a/js/components/header/index.js b/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>

diff --git a/js/components/preview/molecule/moleculeView/moleculeView.js b/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

diff --git a/js/components/preview/molecule/observationCmpView/observationCmpView.js b/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

diff --git a/js/components/preview/molecule/observationsDialog.js b/js/components/preview/molecule/observationsDialog.js
@@ -53,6 +53,7 @@ import { updateLHSCompound, updateMoleculeInMolLists, updateMoleculeTag, updateT
 import { createPoseErrorMessage } from './api/poseApi';
 import { augumentTagObjectWithId, createMoleculeTagObject, DEFAULT_TAG_COLOR, getMoleculeTagForTag } from '../tags/utils/tagUtils';
 import { updateExistingTag } from '../tags/api/tagsApi';
+import { XCA_TAGS_CATEGORIES } from './moleculeView/moleculeView';
 
 const MIN_PANEL_HEIGHT = 250;
 
@@ -175,9 +176,12 @@ const useStyles = makeStyles(theme => ({
     // fontWeight: 'bold',
     paddingLeft: theme.spacing(1) / 4,
     paddingRight: theme.spacing(1) / 4,
-    '&:hover': {
+    '&:hover:not([disabled])': {
       cursor: 'pointer',
       backgroundColor: theme.palette.primary.light
+    },
+    '&:is([disabled])': {
+      color: theme.palette.dividerDark
     }
   },
   dropdownContentSide: {
@@ -277,13 +281,14 @@ export const ObservationsDialog = memo(
     const [tagEditorAnchorEl, setTagEditorAnchorEl] = useState(null);
     const [expandView, setExpandView] = useState(null);
     const [headerWidths, setHeaderWidths] = useState({
-      Quatassemblies: getCalculatedTagColumnWidth('Quatassemblies'),
+      CanonSites: getCalculatedTagColumnWidth('CanonSites'),
       ConformerSites: getCalculatedTagColumnWidth('ConformerSites'),
+      Quatassemblies: getCalculatedTagColumnWidth('Quatassemblies'),
       Crystalforms: getCalculatedTagColumnWidth('Crystalforms'),
       CrystalformSites: getCalculatedTagColumnWidth('CrystalformSites'),
-      CanonSites: getCalculatedTagColumnWidth('CanonSites'),
       CentroidRes: getCalculatedTagColumnWidth('CentroidRes'),
       LongCode: getCalculatedTagColumnWidth('LongCode'),
+      Path: getCalculatedTagColumnWidth('Path')
     });
 
     /**
@@ -292,7 +297,7 @@ export const ObservationsDialog = memo(
      * @param {*} tagCategory
      */
     const setHeaderWidthsHandler = (tagText, tagCategory) => {
-      const calculatedWidth = getCalculatedTagColumnWidth(tagText, '12px bold');
+      const calculatedWidth = getCalculatedTagColumnWidth(tagText, 'bold 12px');
       if (headerWidths[tagCategory] < calculatedWidth) {
         setHeaderWidths(old => {
           const newWidths = { ...old };
@@ -660,6 +665,16 @@ export const ObservationsDialog = memo(
       }
     };
 
+    /**
+     * Get observation list for un/tagging
+     *
+     * @returns {Object[]} observations
+     */
+    const observationsForTagOperations = useMemo(() => {
+      // observationsDataList - all observations, moleculeList - filtered, allSelectedMolecules - selected
+      return allSelectedMolecules.length > 0 ? allSelectedMolecules : moleculeList;
+    }, [allSelectedMolecules, moleculeList]);
+
     const tagObservations = async (tag, tagToExclude) => {
       try {
         // setTaggingInProgress(true);
@@ -675,7 +690,7 @@ export const ObservationsDialog = memo(
         }
 
         let molTagObjects = [];
-        observationsDataList.forEach(m => {
+        observationsForTagOperations.forEach(m => {
           if (!m.tags_set.some(id => id === tag.id)) {
             let newMol = { ...m };
             newMol.tags_set.push(tag.id);
@@ -743,7 +758,7 @@ export const ObservationsDialog = memo(
         }
 
         let molTagObjects = [];
-        observationsDataList.forEach(m => {
+        observationsForTagOperations.forEach(m => {
           let newMol = { ...m };
           newMol.tags_set = newMol.tags_set.filter(id => id !== tag.id);
 
@@ -837,6 +852,17 @@ export const ObservationsDialog = memo(
       toastInfo(`Tag for observations was changed from "${mainObservationTag.upload_name}" to "${tag.upload_name}". They could disappear based on your tag selection`, { autoHideDuration: 5000 });
     };
 
+    /**
+     * Decide if XCA tag change should not be allowed
+     *
+     * @param {string} category category of tag
+     * @returns {boolean}
+     */
+    const disableXCATagChange = useCallback(category => {
+      // #1522 CanonSite tags should not be allowed to change if there are selected only some observations
+      return category === 'CanonSites' && allSelectedMolecules.length > 0 && (allSelectedMolecules.length !== moleculeList.length);
+    }, [allSelectedMolecules, moleculeList]);
+
     return (
       <Popper id={id} open={open} anchorEl={anchorEl} placement="left-start" ref={ref}>
         <Panel
@@ -984,11 +1010,10 @@ export const ObservationsDialog = memo(
                             item
                             xs
                             container
-                            justifyContent="space-around"
-                            // adjust maxWidth if headers are a bit misplaced
-                            style={{ maxWidth: '74%', marginLeft: 95 }}
+                            alignItems="center"
+                            style={{ marginLeft: 95 }}
                           >
-                            {['Quatassemblies', 'ConformerSites', 'Crystalforms', 'CrystalformSites', 'CanonSites'].map(
+                            {XCA_TAGS_CATEGORIES.map(
                               (tagCategory, index) => (
                                 <Grid item align="center" key={index} className={classes.headerCell} style={{ minWidth: headerWidths[tagCategory] }}>
                                   {PLURAL_TO_SINGULAR[tagCategory]}
@@ -1001,6 +1026,9 @@ export const ObservationsDialog = memo(
                             <Grid item align="center" className={classes.headerCell} style={{ minWidth: headerWidths.LongCode }}>
                               LongCode
                             </Grid>
+                            <Grid item align="center" className={classes.headerCell} style={{ minWidth: headerWidths.Path }}>
+                              Path
+                            </Grid>
                           </Grid>
                         )}
                       </Grid>
@@ -1131,15 +1159,16 @@ export const ObservationsDialog = memo(
                       </Button>
                       <Grid container direction="row" className={classes.dropdownContent}>
                         {XCA_TAG_CATEGORIES.map(category =>
-                          <Grid key={category} item className={classNames(classes.dropdown, classes.dropdownItem)}>
+                          <Grid key={category} item className={classNames(classes.dropdown, classes.dropdownItem)} disabled={disableXCATagChange(category)}>
                             Change {PLURAL_TO_SINGULAR[category]}
-                            <Grid container direction="row" className={classNames(classes.dropdownContent, classes.dropdownContentSide)}>
-                              {getTagsForCategory(category)?.map(tag => (
-                                <Grid key={tag.id} item className={classes.dropdownItem} onClick={() => handleXCAtagChange(tag)}>
-                                  {tag.upload_name}
-                                </Grid>
-                              ))}
-                            </Grid>
+                            {!disableXCATagChange(category) &&
+                              <Grid container direction="row" className={classNames(classes.dropdownContent, classes.dropdownContentSide)}>
+                                {getTagsForCategory(category)?.map(tag => (
+                                  <Grid key={tag.id} item className={classes.dropdownItem} onClick={() => handleXCAtagChange(tag)}>
+                                    {tag.upload_name}
+                                  </Grid>
+                                ))}
+                              </Grid>}
                           </Grid>
                         )}
                       </Grid>