Remove some subscription / reactivity / caching bugs and the unnecessary PatientLocations collection

2016-02-10 16:38:49 +01:00
1 parent 7d42456f57
commit 9cde04bcfe
@@ -1,4 +1,5 @@
 LesionLocations = new Meteor.Collection(null);
+LesionLocations._debugName = 'LesionLocations';

 var organGroups = [
    'Abdominal/Chest Wall',
@@ -1,4 +1,5 @@
 LocationResponses = new Meteor.Collection(null);
+LocationResponses._debugName = 'LocationResponses';

 LocationResponses.insert({
    text: 'Complete response',
@@ -1 +0,0 @@
-PatientLocations = new Meteor.Collection(null);
@@ -194,11 +194,10 @@
                    y: mouseEventData.currentPoints.image.y - 70,
                    pointNearHandle: pointNearTextBox,
                    active: false,
-                    movesIndependently: true,
+                    movesIndependently: false,
                    drawnIndependently: true,
                    allowedOutsideImage: true
                },
-
                perpendicularStart: {
                    x: mouseEventData.currentPoints.image.x,
                    y: mouseEventData.currentPoints.image.y,
@@ -208,7 +207,6 @@
                    drawnIndependently: true,
                    index: 2
                },
-
                perpendicularEnd: {
                    x: mouseEventData.currentPoints.image.x,
                    y: mouseEventData.currentPoints.image.y,
@@ -217,7 +215,6 @@
                    drawnIndependently: true,
                    index: 3
                }
-
            },
            imageId: imageId,
            seriesInstanceUid: seriesInstanceUid,
@@ -141,7 +141,7 @@
                    y: mouseEventData.currentPoints.image.y - 50,
                    pointNearHandle: pointNearTextBox,
                    active: false,
-                    movesIndependently: true,
+                    movesIndependently: false,
                    drawnIndependently: true,
                    allowedOutsideImage: true
                }
@@ -59,18 +59,53 @@ Template.associationModal.events({
            // Sort the study dates, so we can get a range for these values
            studyDates = studyDates.sort();

-            // Create a new timepoint to represent the (baseline or follow-up) studies
-            var timepoint = {
-                timepointType: timepointType,
-                timepointId: uuid.new(),
-                studyInstanceUids: studyInstanceUids,
-                patientId: relatedStudies[0].patientId, // TODO: Revisit this (Should timepoints be related to patientId?)
-                earliestDate: studyDates[0].format('YYYYMMDD'),
-                latestDate: studyDates[studyDates.length - 1].format('YYYYMMDD')
-            };
+            // Check if these studies are already associated with an existing Timepoint
+            var existingTimepoint;
+            if (timepointType === 'baseline') {
+                // If we're trying to associate them to the Baseline, we don't need to
+                // check if the studyInstanceUids are already associated with anything else
+                existingTimepoint = Timepoints.findOne({
+                    patientId: relatedStudies[0].patientId,
+                    timepointType: 'baseline'
+                });
+            } else {
+                // If we're trying to associate them to a Follow-up, we should check if any
+                // of them are already part of a Follow-up (e.g. Follow-up 1), so that
+                // the rest will also be associated with Follow-up 1.
+                existingTimepoint = Timepoints.findOne({
+                    patientId: relatedStudies[0].patientId,
+                    studyInstanceUids: {
+                        $in: studyInstanceUids
+                    }
+                });
+            }

-            // Insert this timepoint into the Timepoints Collection
-            Timepoints.insert(timepoint);
+            var timepointId;
+            if (existingTimepoint) {
+                // If these studies are already associated with an existing Timepoint,
+                // and the desired timepoint type is the same (e.g. Follow-up), update
+                // this Timepoint instead of creating a new one
+                Timepoints.update(existingTimepoint._id, {
+                    $set: {
+                        studyInstanceUids: studyInstanceUids
+                    }
+                });
+                timepointId = existingTimepoint.timepointId;
+            } else {
+                // Create a new timepoint to represent the (baseline or follow-up) studies
+                var timepoint = {
+                    timepointType: timepointType,
+                    timepointId: uuid.new(),
+                    studyInstanceUids: studyInstanceUids,
+                    patientId: relatedStudies[0].patientId,
+                    earliestDate: studyDates[0].format('YYYYMMDD'),
+                    latestDate: studyDates[studyDates.length - 1].format('YYYYMMDD')
+                };
+
+                // Insert this timepoint into the Timepoints Collection
+                Timepoints.insert(timepoint);
+                timepointId = timepoint.timepointId;
+            }

            // Loop through these studies to associate them with the newly created timepoint
            relatedStudies.forEach(function(study) {
@@ -83,7 +118,7 @@ Template.associationModal.events({
                    // If a study already exists, update the entry with the new timepointId
                    Studies.update(existingStudy._id, {
                        $set: {
-                            timepointId: timepoint.timepointId
+                            timepointId: timepointId
                        }
                    });
                } else {
@@ -93,7 +128,7 @@ Template.associationModal.events({
                    delete study._id;

                    // Attach the timepointId and insert it into the Studies Collection
-                    study.timepointId = timepoint.timepointId;
+                    study.timepointId = timepointId;
                    Studies.insert(study);
                }
            });
@@ -205,20 +205,6 @@ Template.lesionLocationDialog.events({
            _id: selectedOptionId
        });

-        var id;
-        var existingLocation = PatientLocations.findOne({
-            location: locationObj.location
-        });
-        if (existingLocation) {
-            id = existingLocation._id;
-        } else {
-            // Adds location data to PatientLocation and retrieve the location ID
-            id = PatientLocations.insert({
-                location: locationObj.location,
-                locationId: locationObj._id
-            });
-        }
-
        // Add an ID value to the tool data to link it to the Measurements collection
        if (!measurementData.id) {
            measurementData.id = 'notready';
@@ -226,7 +212,6 @@ Template.lesionLocationDialog.events({
            // Link locationUID with active lesion measurementData
            measurementData.location = locationObj.location;
            measurementData.locationId = locationObj.id;
-            measurementData.locationUID = id;

            /// Set the isTarget value to true, since this is the target-lesion dialog callback
            measurementData.isTarget = true;
@@ -241,8 +226,7 @@ Template.lesionLocationDialog.events({
                $set: {
                    location: locationObj.location,
                    locationId: locationObj.id,
-                    isNodal: locationObj.isNodal,
-                    locationUID: id
+                    isNodal: locationObj.isNodal
                }
            });
        }
@@ -31,10 +31,10 @@ function removeTimepointAssociations() {
            return;
        }

-        // Update the Studies Collection to remove the link to this Timepoint
-        Studies.update(study._id, {
-            unset: {
-                timepointId: ''
+        // Remove this entry from the Studies Collection
+        Meteor.call('removeAssociatedStudy', study._id, function(error) {
+            if (error) {
+                log.warn(error);
            }
        });

@@ -70,27 +70,28 @@ function getLesionLocationCallback(measurementData, eventData) {

    // Find out if this lesion number is already added in the lesion manager for another timepoint
    // If it is, disable selector location
-    var locationUID = LesionManager.lesionNumberExists(measurementData);
-    if (locationUID) {
+    var locationId = LesionManager.lesionNumberExists(measurementData);
+    if (locationId) {
        // Add an ID value to the tool data to link it to the Measurements collection
        measurementData.id = 'notready';

-        measurementData.locationUID = locationUID;
+        measurementData.locationId = locationId;

        // Disable the selection of a new location
-        disableLocationSelection(measurementData.locationUID);
+        disableLocationSelection(measurementData.locationId);
    }

    // Disable selector location to prevent selecting a new location
-    function disableLocationSelection(locationUID) {
-        var locationName = LesionManager.getLocationName(locationUID);
-        selectorLocation.find('option').each(function() {
-            if ($(this).text() === locationName) {
-                // Select location in locations dropdown list
-                selectorLocation.find('option').eq($(this).index()).prop('selected', true);
-            }
-        });
-
+    function disableLocationSelection(locationId) {
+        var locationObject = LesionLocations.findOne({
+                id: locationId
+            });
+        
+        if (!locationObject) {
+            return;
+        }
+        
+        selectorLocation.find('option[value="' + locationObject._id + '"]').prop('selected', true);
        selectorLocation.prop('disabled', true);
    }

@@ -273,26 +274,12 @@ Template.nonTargetLesionDialog.events({
            _id: selectedOptionId
        });

-        var id;
-        var existingLocation = PatientLocations.findOne({
-            location: locationObj.location
-        });
-        if (existingLocation) {
-            id = existingLocation._id;
-        } else {
-            // Adds location data to PatientLocation and retrieve the location ID
-            id = PatientLocations.insert({
-                location: locationObj.location
-            });
-        }
-
        if (measurementData.id) {
            // Update the location data
            Measurements.update(measurementData.id, {
                $set: {
                    location: locationObj.location,
                    locationId: locationObj.id,
-                    locationUID: id
                }
            });
        } else {
@@ -300,9 +287,6 @@ Template.nonTargetLesionDialog.events({
            measurementData.id = 'notready';
        }

-        // Link locationUID with active lesion measurementData
-        measurementData.locationUID = id;
-
        /// Set the isTarget value to true, since this is the target-lesion dialog callback
        measurementData.isTarget = false;

@@ -76,12 +76,7 @@ Template.studyDateList.events({
        var loadingIndicator = selectBox.siblings('.loading');
        loadingIndicator.css('display', 'block');

-        Meteor.call('GetStudyMetadata', studyInstanceUid, function(error, study) {
-            if (error) {
-                log.warn(error);
-                return;
-            }
-
+        getStudyMetadata(studyInstanceUid, function(study) {
            sortStudy(study);

            // Hide the loading indicator
@@ -1,12 +0,0 @@
-<template name="timepointTextDialog">
-    <div id="timepointTextDialog">
-        <div class="timepointDialogContentWrapper">
-            <div class="dialogContent">
-                <div class="timepointContent">
-                    <input type="checkbox" id="checkBoxBaseline" value="ok">
-                    <label for="checkBoxBaseline">Baseline</label>
-                </div>
-            </div>
-        </div>
-    </div>
-</template>
@@ -1,25 +0,0 @@
-#timepointTextDialog
-  display: none
-  position: absolute
-  z-index: 99
-
-  .timepointDialogContentWrapper
-    position: absolute
-    width: 100px
-    height: 30px
-    padding: 5px
-    background-color: rgba(255,255,255,1)
-    border-top-left-radius: 5px
-    border-top-right-radius: 5px
-
-    .dialogContent
-      margin: 0 auto
-      float: none
-      padding: 0
-
-    .timepointContent
-      font-size: 16px
-
-    #checkBoxBaseline
-      height: 16px
-      width: 16px
@@ -1,20 +1,3 @@
-/**
- * Retrieve a location name (e.g. Liver Right) from the
- * PatientLocations Collection by id, if it exists. Otherwise,
- * return an empty string.
- *
- * @param id
- * @returns {*|string}
- */
-function getLocationName(id) {
-    var locationObject = PatientLocations.findOne(id);
-    if (!locationObject || !locationObject.location) {
-        return '';
-    }
-
-    return locationObject.location;
-}
-
 /**
 * Update the Timepoint object for a specific Measurement.
 * If no measurement exists yet, one will be created.
@@ -33,7 +16,6 @@ function updateLesionData(lesionData) {
        return;
    }

-
    var timepoint = Timepoints.findOne({
        timepointId: study.timepointId
    });
@@ -84,7 +66,7 @@ function updateLesionData(lesionData) {

        // Retrieve the location name given the locationUID
        if (lesionData.locationUID !== undefined) {
-            var locationObj = PatientLocations.findOne({
+            var locationObj = LesionLocations.findOne({
                locationUID: lesionData.locationUID
            });

@@ -191,12 +173,11 @@ function lesionNumberExists(lesionData) {
        return;
    }

-    return measurement.locationUID;
+    return measurement.locationId;
 }

 LesionManager = {
    updateLesionData: updateLesionData,
    getNewLesionNumber: getNewLesionNumber,
-    lesionNumberExists: lesionNumberExists,
-    getLocationName: getLocationName
+    lesionNumberExists: lesionNumberExists
 };
@@ -50,7 +50,7 @@ function RECIST(image) {
            shortestDiameter: {
                numericality: {
                    greaterThanOrEqualTo: 15,
-                    message: '^Nodal target lesions must be >= %{count} mm short axis'
+                    //message: '^Nodal target lesions must be >= %{count} mm short axis'
                }
            }
        };
@@ -72,7 +72,7 @@ function RECIST(image) {
        totalLesionBurden: {
            numericality: {
                greaterThanOrEqualTo: 2, // TODO: Check this, the value wasn't specified!
-                message: '^Total lesion burden (SPD target lesions + SPD new lesions) should be greater than %{count}.'
+                //message: '^Total lesion burden (SPD target lesions + SPD new lesions) should be greater than %{count}.'
            }
        }
    };
@@ -126,7 +126,7 @@ function RECIST(image) {
            longestDiameter: {
                numericality: {
                    greaterThanOrEqualTo: 20,
-                    message: '^Extranodal lesions must be >= %{count} mm on chest X-ray'
+                    //message: '^Extranodal lesions must be >= %{count} mm on chest X-ray'
                }
            }
        };
@@ -135,7 +135,7 @@ function RECIST(image) {
            longestDiameter: {
                numericality: {
                    greaterThanOrEqualTo: 10,
-                    message: '^Extranodal target lesions must be >= %{count} mm long axis'
+                    //message: '^Extranodal target lesions must be >= %{count} mm long axis'
                }
            }
        };
@@ -340,6 +340,9 @@ getTrialCriteriaConstraints = function(criteriaType, imageId) {

    // Otherwise, retrieve the series metaData to identify the modality of the image
    var seriesMetaData = cornerstoneTools.metaData.get('series', imageId);
+    if (!seriesMetaData) {
+        return;
+    }

    // TODO: Get the rest of the metaData that has already been loaded by Cornerstone
    var image = {};
@@ -363,7 +366,6 @@ getTrialCriteriaConstraints = function(criteriaType, imageId) {
    });

    if (!study) {
-        log.warn('No study/timepoint association.');
        return;
    }

@@ -1,5 +1,6 @@
 // Create a client-only Collection to store our Validation Errors
 ValidationErrors = new Meteor.Collection(null);
+ValidationErrors._debugName = 'ValidationErrors';

 // Set Validate.js Library's default options
 validate.options = {
@@ -216,8 +217,8 @@ function validateSingleMeasurement(measurementData) {
    var criteriaType = Session.get('TrialResponseAssessmentCriteria');
    var currentConstraints = getTrialCriteriaConstraints(criteriaType, measurementData.imageId);

+    // If we have no relevant constraints, stop here
    if (!currentConstraints) {
-        log.warn('No relevant contraints could be applied');
        return;
    }

@@ -236,6 +237,11 @@ function validateSingleMeasurement(measurementData) {
    // Find the specific measurement data for this Measurement at this Timepoint
    var currentMeasurement = measurement.timepoints[timepointId];

+    // Return here if the measurement was removed during validation
+    if (!currentMeasurement) {
+        return;
+    }
+
    // Include target and nodal flags on the timepoint-specific data so it is easier to validate
    // TODO: Rethink what to pass to assessSingleMeasurement?
    currentMeasurement.isTarget = measurement.isTarget;
@@ -256,10 +262,11 @@ function validateGroups() {
    var criteriaType = Session.get('TrialResponseAssessmentCriteria');

    Timepoints.find().forEach(function(timepoint) {
-        // TODO: Criteria for the specific image are retrieved from the general set of criteria.
-        // - The acquisitionSliceThickness, for example, may be pulled from the image metadata
-        // - The organ in question, e.g. Chest X-ray, may determine the exact specifications for the current trial criteria
+        // Criteria for the specific image are retrieved from the general set of criteria.
        var currentConstraints = getTrialCriteriaConstraints(criteriaType);
+        if (!currentConstraints) {
+            return;
+        }

        // Retrieve the current constraints which apply to the specific Timepoint type
        // (e.g. baseline, followup) that this Measurement is being edited on.
@@ -289,12 +296,9 @@ function validateAll() {
            currentMeasurement.lesionNumber = measurement.lesionNumber;
            currentMeasurement._id = measurement._id;

-            // TODO: Criteria for the specific image are retrieved from the general set of criteria.
-            // - The acquisitionSliceThickness, for example, may be pulled from the image metadata
-            // - The organ in question, e.g. Chest X-ray, may determine the exact specifications for the current trial criteria
+            // Criteria for the specific image are retrieved from the general set of criteria.
            var currentConstraints = getTrialCriteriaConstraints(criteriaType, currentMeasurement.imageId);
            if (!currentConstraints) {
-                log.warn('No relevant contraints could be applied');
                return;
            }

@@ -12,6 +12,10 @@ activateMeasurements = function(element, measurementId, templateData, viewportIn
    var timepointData = getTimepointObject(imageId);
    var measurementData = Measurements.findOne(measurementId);

+    if (!timepointData) {
+        return;
+    }
+
    var measurementAtTimepoint = measurementData.timepoints[timepointData.timepointId];
    if (!measurementAtTimepoint) {
        return;
@@ -5,11 +5,15 @@ clearTools = function() {
    var toolStateKeys = Object.keys(toolState).slice(0);

    var viewportElements = $('.imageViewerViewport').not('.empty');
-    var seriesInstanceUIds = []; // Holds seriesInstanceUId of imageViewerViewport elements
+    var seriesInstanceUids = []; // Holds seriesInstanceUid of imageViewerViewport elements
    viewportElements.each(function(index, element) {
        var enabledElement = cornerstone.getEnabledElement(element);
        var series = cornerstoneTools.metaData.get('series', enabledElement.image.imageId);
-        seriesInstanceUIds.push(series.seriesInstanceUid);
+        if (!series) {
+            return;
+        }
+        
+        seriesInstanceUids.push(series.seriesInstanceUid);
    });

    // Set null array for toolState data found by imageId and toolType
@@ -18,8 +22,12 @@ clearTools = function() {
            var toolTypeData = toolState[imageId][toolType];
            if (toolTypeData && toolTypeData.data.length > 0) {
                var series = cornerstoneTools.metaData.get('series', imageId);
-                // If seriesInstanceUid is found in seriesInstanceUIds, set toolState data as null
-                if (seriesInstanceUIds.indexOf(series.seriesInstanceUid) > -1) {
+                if (!series) {
+                    return;
+                }
+
+                // If seriesInstanceUid is found in seriesInstanceUids, set toolState data as null
+                if (seriesInstanceUids.indexOf(series.seriesInstanceUid) > -1) {
                    toolState[imageId][toolType] = {
                        data: []
                    };
@@ -1,10 +1,10 @@
 handleMeasurementAdded = function(e, eventData) {
-    log.info('CornerstoneToolsMeasurementAdded');
    var measurementData = eventData.measurementData;

    switch (eventData.toolType) {
        case 'nonTarget':
        case 'lesion':
+            log.info('CornerstoneToolsMeasurementAdded');
            LesionManager.updateLesionData(measurementData);
            TrialResponseCriteria.validateDelayed(measurementData);
            break;
@@ -1,10 +1,10 @@
 handleMeasurementModified = function(e, eventData) {
-    log.info('CornerstoneToolsMeasurementModified');
    var measurementData = eventData.measurementData;

    switch (eventData.toolType) {
        case 'nonTarget':
        case 'lesion':
+            log.info('CornerstoneToolsMeasurementModified');
            LesionManager.updateLesionData(measurementData);
            TrialResponseCriteria.validateDelayed(measurementData);
            break;
@@ -62,7 +62,7 @@ syncMeasurementAndToolData = function(data) {
        measurementData.isDeleted = data.isDeleted;
        measurementData.location = data.location;
        measurementData.locationUID = data.locationUID;
-        measurementData.patientId = patientId;
+        measurementData.patientId = data.patientId;
        measurementData.visible = data.visible;
        measurementData.active = data.active;
        measurementData.uid = data.uid;
@@ -33,5 +33,8 @@ function dblClickOnStudy(data) {
        return;
    }

+    // Add the Timepoint name to the Patient name to create the tab title
+    title += ' ' + getTimepointName(timepoint);
+
    openNewTabWithTimepoint(timepoint.timepointId, title);
 }
@@ -29,7 +29,6 @@ Package.onUse(function(api) {
    // Client-side collections
    api.addFiles('client/collections/LesionLocations.js', 'client');
    api.addFiles('client/collections/LocationResponses.js', 'client');
-    api.addFiles('client/collections/PatientLocations.js', 'client');

    // Additional Custom Cornerstone Tools for Lesion Tracker
    api.addFiles('client/compatibility/lesionTool.js', 'client', {
@@ -108,9 +107,6 @@ Package.onUse(function(api) {
    api.addFiles('client/components/nonTargetResponseDialog/nonTargetResponseDialog.styl', 'client');
    api.addFiles('client/components/nonTargetResponseDialog/nonTargetResponseDialog.js', 'client');

-    api.addFiles('client/components/timepointTextDialog/timepointTextDialog.html', 'client');
-    api.addFiles('client/components/timepointTextDialog/timepointTextDialog.styl', 'client');
-
    api.addFiles('client/components/lesionTrackerWorklistStudy/lesionTrackerWorklistStudy.html', 'client');
    api.addFiles('client/components/lesionTrackerWorklistStudy/lesionTrackerWorklistStudy.styl', 'client');
    api.addFiles('client/components/lesionTrackerWorklistStudy/lesionTrackerWorklistStudy.js', 'client');
@@ -186,7 +182,6 @@ Package.onUse(function(api) {
    api.export('ValidationErrors', 'client');
    api.export('LesionLocations', 'client');
    api.export('LocationResponses', 'client');
-    api.export('PatientLocations', 'client');

    // Export collections spanning both client and server
    api.export('Measurements', [ 'client', 'server' ]);
@@ -12,6 +12,12 @@ Meteor.publish('studies', function() {
    return Studies.find();
 });

+Meteor.publish('singlePatientAssociatedStudies', function(patientId) {
+    return Studies.find({
+        patientId: patientId
+    });
+});
+
 Meteor.publish('singlePatientMeasurements', function(patientId) {
    return Measurements.find({
        patientId: patientId
@@ -49,5 +49,8 @@ Meteor.methods({
    },
    removeTimepoint: function(id) {
        Timepoints.remove(id);
+    },
+    removeAssociatedStudy: function(id) {
+        Studies.remove(id);
    }
 });
				`@@ -1 +0,0 @@`
				`PatientLocations = new Meteor.Collection(null);`