Merge staging changes into production for 2024.11.1 (#458)

* Squashed commit of the following: commit e613216 Author: Boris Kovar <[email protected]> Date: Wed Jul 31 13:57:02 2024 +0200 - implemented #1251 * #1482 added TagName and CentroidRes columns for expanded view of observation dialog * #1489 show warning toast message if is defined on target load * #1322 added longcode column * updated general function for tag comparison * #1505 adjusted getting of centroid_res * #1458 allow to tag XCA sites, temp commit # Conflicts: # js/components/preview/molecule/observationsDialog.js * #1458 adjusted functionality and styling to proper change tag * #1508 removed TagName column in expanded observation dialog, changed order of columns, adjusted labels and tooltips, show observation dialog in its full height * #1508 adjusted column order and width calculation * #1501 added upload links to menu * #1501 (#451) * Squashed commit of the following: commit e613216 Author: Boris Kovar <[email protected]> Date: Wed Jul 31 13:57:02 2024 +0200 - implemented #1251 * #1482 added TagName and CentroidRes columns for expanded view of observation dialog * #1489 show warning toast message if is defined on target load * #1322 added longcode column * updated general function for tag comparison * #1505 adjusted getting of centroid_res * #1458 allow to tag XCA sites, temp commit # Conflicts: # js/components/preview/molecule/observationsDialog.js * #1458 adjusted functionality and styling to proper change tag * #1508 removed TagName column in expanded observation dialog, changed order of columns, adjusted labels and tooltips, show observation dialog in its full height * #1508 adjusted column order and width calculation * #1501 added upload links to menu --------- Co-authored-by: Boris Kovar <[email protected]> * #1520 show tag alias instead of upload_name on hit navigator CanonSites & ConformerSites box tooltip * #1519 keep tag in edit window after save * #1519 and #1520 (#453) * Squashed commit of the following: commit e613216 Author: Boris Kovar <[email protected]> Date: Wed Jul 31 13:57:02 2024 +0200 - implemented #1251 * #1482 added TagName and CentroidRes columns for expanded view of observation dialog * #1489 show warning toast message if is defined on target load * #1322 added longcode column * updated general function for tag comparison * #1505 adjusted getting of centroid_res * #1458 allow to tag XCA sites, temp commit # Conflicts: # js/components/preview/molecule/observationsDialog.js * #1458 adjusted functionality and styling to proper change tag * #1508 removed TagName column in expanded observation dialog, changed order of columns, adjusted labels and tooltips, show observation dialog in its full height * #1508 adjusted column order and width calculation * #1501 added upload links to menu * #1520 show tag alias instead of upload_name on hit navigator CanonSites & ConformerSites box tooltip * #1519 keep tag in edit window after save --------- Co-authored-by: Boris Kovar <[email protected]> * #1497 added Path column for extended view of observations * #1497 (#454) * Squashed commit of the following: commit e613216 Author: Boris Kovar <[email protected]> Date: Wed Jul 31 13:57:02 2024 +0200 - implemented #1251 * #1482 added TagName and CentroidRes columns for expanded view of observation dialog * #1489 show warning toast message if is defined on target load * #1322 added longcode column * updated general function for tag comparison * #1505 adjusted getting of centroid_res * #1458 allow to tag XCA sites, temp commit # Conflicts: # js/components/preview/molecule/observationsDialog.js * #1458 adjusted functionality and styling to proper change tag * #1508 removed TagName column in expanded observation dialog, changed order of columns, adjusted labels and tooltips, show observation dialog in its full height * #1508 adjusted column order and width calculation * #1501 added upload links to menu * #1520 show tag alias instead of upload_name on hit navigator CanonSites & ConformerSites box tooltip * #1519 keep tag in edit window after save * #1497 added Path column for extended view of observations --------- Co-authored-by: Boris Kovar <[email protected]> * #1518 properly remove tag from list after updating its object * #1522 allow to change XCA tags for selections but not for CanonSite * #1463 initial implementation of new sort options for hit navigator * #1514 (#456) * #1514 replaced project_id occurrences with project and adjusted functionality with current B/E * #1514 added target_access_string to /api/download_structures, replaced /api/molgroup with /api/siteobservationgroup, minor fixes * #1523 #1463 (#457) * #1514 replaced project_id occurrences with project and adjusted functionality with current B/E * #1514 added target_access_string to /api/download_structures, replaced /api/molgroup with /api/siteobservationgroup, minor fixes * #1523 adjusted inspiration dialog layout and removed molecular properties headers from it too * #1463 show "Ascending" instead of "ASC" when there is a possible space for it * removed unnecessary setter and comments --------- Co-authored-by: Boris Kovar <[email protected]> Co-authored-by: matej <[email protected]> Co-authored-by: matej <[email protected]>
xchem · Nov 4, 2024 · a4ecd71 · a4ecd71
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diff --git a/js/components/datasets/inspirationDialog.js b/js/components/datasets/inspirationDialog.js
@@ -32,8 +32,8 @@ import GroupNglControlButtonsContext from '../preview/molecule/groupNglControlBu
 
 const useStyles = makeStyles(theme => ({
   paper: {
-    width: 472,
-    height: 294,
+    width: 505,
+    // height: 294,
     overflowY: 'hidden'
   },
   molHeader: {
@@ -382,11 +382,11 @@ export const InspirationDialog = memo(
             <>
               <Grid container justifyContent="flex-start" direction="row" className={classes.molHeader} wrap="nowrap">
                 <Grid item container justifyContent="flex-start" direction="row">
-                  {Object.keys(moleculeProperty).map(key => (
+                  {/* {Object.keys(moleculeProperty).map(key => (
                     <Grid item key={key} className={classes.rightBorder}>
                       {moleculeProperty[key]}
                     </Grid>
-                  ))}
+                  ))} */}
                   {allSelectedMolecules.length > 0 && (
                     <Grid item>
                       <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: {
@@ -145,7 +147,7 @@ const useStyles = makeStyles(theme => ({
   image: {
     border: 'solid 1px',
     borderColor: theme.palette.background.divider,
-    borderStyle: 'solid solid solid none',
+    borderStyle: 'none none none solid',
     position: 'relative'
   },
   imageMargin: {
@@ -411,6 +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;
@@ -465,6 +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);
 
@@ -514,6 +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');
@@ -1134,6 +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
@@ -1174,7 +1203,7 @@ const MoleculeView = memo(
           </Grid>
           <Grid item container className={classes.detailsCol} justifyContent="space-between" direction="row">
             <Grid item container direction="column" alignItems="center" xs>
-              <Grid item container justifyContent="flex-start" alignItems="center" direction="row">
+              <Grid item container justifyContent="flex-start" alignItems="center" direction="row" xs>
                 <Grid item container justifyContent="space-between" direction="column" xs={3}>
                   {/* Title label */}
                   <Tooltip title={data.prefix_tooltip ?? '-' + (data.id === pose?.main_site_observation ? " - main observation" : "")} placement="bottom-start">
@@ -1503,6 +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/observationCmpList.js b/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';
@@ -222,6 +225,9 @@ const useStyles = makeStyles(theme => ({
       //color: theme.palette.black
     }
   },
+  selectButton: {
+    padding: '4px 2px !important'
+  },
   formControl: {
     color: 'inherit',
     margin: theme.spacing(1),
@@ -321,6 +327,89 @@ 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);
@@ -330,10 +419,29 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
   const filterRef = useRef();
   const tagEditorRef = useRef();
   const scrollBarRef = useRef();
+  const hitNavigatorRef = useRef();
   const [tagEditorAnchorEl, setTagEditorAnchorEl] = useState(null);
+  const [hitNavigatorWidth, setHitNavigatorWidth] = useState(0);
 
   const areLSHCompoundsInitialized = useSelector(state => state.selectionReducers.areLSHCompoundsInitialized);
 
+  useEffect(() => {
+    if (hitNavigatorRef && hitNavigatorRef.current) {
+
+      const resizeObserver = new ResizeObserver(() => {
+        if (hitNavigatorRef.current.offsetWidth !== hitNavigatorWidth) {
+          setHitNavigatorWidth(hitNavigatorRef.current.offsetWidth);
+        }
+      });
+
+      resizeObserver.observe(hitNavigatorRef.current);
+
+      return function cleanup() {
+        resizeObserver.disconnect();
+      }
+    }
+  }, [hitNavigatorRef, hitNavigatorWidth]);
+
   if (directDisplay && directDisplay.target) {
     target = directDisplay.target;
   }
@@ -718,8 +826,9 @@ 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) {
@@ -973,7 +1082,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
   };
 
   return (
-    <Panel hasHeader title="Hit navigator" headerActions={actions}>
+    <Panel hasHeader title="Hit navigator" headerActions={actions} ref={hitNavigatorRef}>
       <AlertModal
         title="Are you sure?"
         description={`Loading of ${joinedMoleculeLists?.length} may take a long time`}
@@ -1113,7 +1222,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
 
         {
           <Tooltip title={selectAllHitsPressed ? 'Unselect all hits' : 'Select all hits'}>
-            <Grid item style={{ marginLeft: '20px' }}>
+            <Grid item style={{ marginLeft: '2px' }} className={classes.selectButton}>
               <Button
                 variant="outlined"
                 className={classNames(classes.contColButton, {
@@ -1133,7 +1242,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
         }
         {selectedDisplayHits === true ? (
           <Tooltip title={'Unselect displayed hits'}>
-            <Grid item style={{ marginLeft: '20px' }}>
+            <Grid item className={classes.selectButton}>
               <Button
                 variant="outlined"
                 className={classNames(classes.contColButton, {
@@ -1152,7 +1261,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
           </Tooltip>
         ) : (
           <Tooltip title={'Select displayed hits'}>
-            <Grid item style={{ marginLeft: '20px' }}>
+            <Grid item className={classes.selectButton}>
               <Button
                 variant="outlined"
                 className={classNames(classes.contColButton, {
@@ -1171,9 +1280,35 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
           </Tooltip>
         )}
         <Grid style={{ marginTop: '4px' }}>
-          <Typography variant="caption" className={classes.noOfSelectedHits}>{`Selected: ${allSelectedMolecules ? allSelectedMolecules.length : 0
+          <Typography variant="caption">{`Selected: ${allSelectedMolecules ? allSelectedMolecules.length : 0
             }`}</Typography>
         </Grid>
+        <Grid style={{ marginTop: '4px' }}>
+          <Typography variant="caption" style={{ paddingLeft: 3 }}>Sort by</Typography>
+        </Grid>
+        <Grid style={{ marginTop: '4px', marginLeft: '4px' }}>
+          <Tooltip title={sortOption ? sortOptions[sortOption].title : "Sort by"}>
+            <Select
+              value={sortOption}
+              onChange={(event) => setSortOption(event.target.value)}
+              // fullWidth
+              size="small"
+              style={{ fontSize: 10, width: 75 }}
+            >
+              {SORT_OPTIONS.map((option, index) => (
+                <MenuItem key={`${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: 0 }} />
+            <Typography variant="caption">{(selectAllHitsPressed && hitNavigatorWidth > 508) || (!selectAllHitsPressed && hitNavigatorWidth > 491) ? 'Ascending' : 'ASC'}</Typography>
+          </Grid>
+        </Tooltip>
       </Grid>
       <Grid container spacing={1} direction="column" justifyContent="flex-start" className={classes.container}>
         <Grid item>

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