Extend DICOMweb assetstore support

import_tracker/__init__.py

@@ -1,6 +1,6 @@
 import time
 
-from girder import logger, plugin
+from girder import plugin
 from girder.api.describe import autoDescribeRoute
 from girder.api.rest import boundHandler
 from girder.constants import AccessType
@@ -28,30 +28,34 @@ def wrapImportData(assetstoreResource):
     def importDataWrapper(
             self, assetstore, importPath, destinationId, destinationType,
             progress, leafFoldersAsItems, fileIncludeRegex, fileExcludeRegex,
-            excludeExisting):
+            excludeExisting, **kwargs):
         # We don't actually wrap importData, as it would be excessive
         # monkey-patching to make the import trackable and cancelable.
         user = self.getCurrentUser()
         parent = ModelImporter.model(destinationType).load(
             destinationId, user=user, level=AccessType.ADMIN, exc=True)
 
-        # create a job, set it to running
-        # alter ProgressContext so update updates the job or raises if
-        # canceling
+        # Capture any additional parameters passed to route
+        extraParams = kwargs.get('params', {})
+
         params = {
             'destinationId': destinationId,
             'destinationType': destinationType,
             'importPath': importPath,
             'leafFoldersAsItems': str(leafFoldersAsItems).lower(),
             'progress': str(progress).lower(),
+            **extraParams
         }
+
         if fileIncludeRegex:
             params['fileIncludeRegex'] = fileIncludeRegex
         if fileExcludeRegex:
             params['fileExcludeRegex'] = fileExcludeRegex
         if excludeExisting:
             params['excludeExisting'] = str(excludeExisting).lower()
+
         importRecord = AssetstoreImport().createAssetstoreImport(assetstore, params)
+
         job = Job().createJob(
             title='Import from %s : %s' % (assetstore['name'], importPath),
             type='assetstore_import',
@@ -63,6 +67,7 @@ def importDataWrapper(
             time.strftime('%Y-%m-%d %H:%M:%S'),
             assetstore['name'], importPath,
         ), status=JobStatus.RUNNING)
+
         try:
             with ProgressContext(progress, user=user, title='Importing data') as ctx:
                 try:
@@ -76,10 +81,7 @@ def importDataWrapper(
                     self._model.importData(
                         assetstore, parent=parent, parentType=destinationType,
                         params={
-                            'fileIncludeRegex': fileIncludeRegex,
-                            'fileExcludeRegex': fileExcludeRegex,
-                            'importPath': importPath,
-                            'excludeExisting': excludeExisting,
+                            **params,
                             '_job': jobRec,
                         },
                         progress=ctx, user=user,
@@ -103,6 +105,7 @@ def importDataWrapper(
                 exc,
             ), status=JobStatus.ERROR)
             success = False
+
         importRecord = AssetstoreImport().markEnded(importRecord, success)
         return importRecord
 
@@ -158,100 +161,12 @@ def shouldImportFileWrapper(self, path, params):
     AbstractAssetstoreAdapter.shouldImportFile = shouldImportFileWrapper
 
 
-def wrapDICOMImport(assetstoreResource):
-    baseImportData = assetstoreResource.importData
-    baseImportData.description.param(
-        'excludeExisting',
-        'If true, then a file with an import path that is already in the '
-        'system is not imported, even if it is not in the destination '
-        'hierarchy.', dataType='boolean', required=False, default=False)
-
-    @boundHandler(ctx=assetstoreResource)
-    @autoDescribeRoute(baseImportData.description)
-    def dwaImportDataWrapper(self, assetstore, destinationId, destinationType, filters,
-                             progress, excludeExisting):
-
-        user = self.getCurrentUser()
-        params = {
-            'destinationId': destinationId,
-            'destinationType': destinationType,
-            'filters': filters,
-            'progress': str(progress).lower(),
-        }
-        if excludeExisting:
-            params['excludeExisting'] = str(excludeExisting).lower()
-
-        importRecord = AssetstoreImport().createAssetstoreImport(assetstore, params)
-        job = Job().createJob(
-            title=f'Import from {assetstore["name"]}',
-            type='assetstore_import',
-            public=False,
-            user=user,
-            kwargs=params,
-        )
-        job = Job().updateJob(job, '%s - Starting import from %s\n' % (
-            time.strftime('%Y-%m-%d %H:%M:%S'),
-            assetstore['name']
-        ), status=JobStatus.RUNNING)
-
-        try:
-            with ProgressContext(progress, user=user, title='Importing data') as ctx:
-                try:
-                    jobRec = {
-                        'id': str(job['_id']),
-                        'count': 0,
-                        'skip': 0,
-                        'lastlog': time.time(),
-                        'logcount': 0,
-                    }
-                    self._importData(
-                        assetstore,
-                        params={
-                            **params,
-                            '_job': jobRec},
-                        progress=ctx)
-
-                    success = True
-                    Job().updateJob(job, '%s - Finished.  Checked %d, skipped %d\n' % (
-                        time.strftime('%Y-%m-%d %H:%M:%S'),
-                        jobRec['count'], jobRec['skip'],
-                    ), status=JobStatus.SUCCESS)
-
-                except ImportTrackerCancelError:
-                    Job().updateJob(job, '%s - Canceled' % (
-                        time.strftime('%Y-%m-%d %H:%M:%S'),
-                    ))
-                    success = 'canceled'
-
-        except Exception as exc:
-            Job().updateJob(job, '%s - Failed with %s\n' % (
-                time.strftime('%Y-%m-%d %H:%M:%S'),
-                exc,
-            ), status=JobStatus.ERROR)
-            success = False
-
-        importRecord = AssetstoreImport().markEnded(importRecord, success)
-        return importRecord
-
-    for key in {'accessLevel', 'description', 'requiredScopes'}:
-        setattr(dwaImportDataWrapper, key, getattr(baseImportData, key))
-
-    assetstoreResource.importData = dwaImportDataWrapper
-    assetstoreResource.removeRoute('POST', (':id', 'import'))
-    assetstoreResource.route('POST', (':id', 'import'), assetstoreResource.importData)
-
-
 class GirderPlugin(plugin.GirderPlugin):
     DISPLAY_NAME = 'import_tracker'
     CLIENT_SOURCE_PATH = 'web_client'
 
     def load(self, info):
         plugin.getPlugin('jobs').load(info)
-        try:
-            import large_image_source_dicom  # noqa
-            plugin.getPlugin('dicomweb').load(info)
-        except (ImportError, AttributeError):
-            pass
         ModelImporter.registerModel(
             'assetstoreImport', AssetstoreImport, 'import_tracker'
         )
@@ -263,8 +178,3 @@ def load(self, info):
         wrapImportData(info['apiRoot'].assetstore)
 
         info['apiRoot'].folder.route('PUT', (':id', 'move'), moveFolder)
-
-        if hasattr(info['apiRoot'], 'dicomweb_assetstore'):
-            wrapDICOMImport(info['apiRoot'].dicomweb_assetstore)
-        else:
-            logger.info('dicomweb_assetstore not found')

import_tracker/web_client/main.js

@@ -3,6 +3,7 @@ import $ from 'jquery';
 import AssetstoreView from '@girder/core/views/body/AssetstoresView';
 import FilesystemImportView from '@girder/core/views/body/FilesystemImportView';
 import S3ImportView from '@girder/core/views/body/S3ImportView';
+import DICOMwebImportView from '@girder/dicomweb/views/DICOMwebImportView';
 
 import CollectionModel from '@girder/core/models/CollectionModel';
 import FolderModel from '@girder/core/models/FolderModel';
@@ -54,21 +55,26 @@ wrap(S3ImportView, 'render', function (render) {
 
     this.$('.form-group').last().after(excludeExistingInput({ type: 's3' }));
 });
+wrap(DICOMwebImportView, 'render', function (render) {
+    render.call(this);
+
+    this.$('.form-group').last().after(excludeExistingInput({ type: 'dwas' }));
+});
 
 const setBrowserRoot = (view, type) => {
     const browserWidget = view._browserWidgetView;
-    const destType = view.$(`#g-${type}-import-dest-type`).val();
-    const destId = view.$(`#g-${type}-import-dest-id`).val();
-    const resourceId = destId.trim().split(/\s/)[0];
+    const destinationType = view.$(`#g-${type}-import-dest-type`).val();
+    const destinationId = view.$(`#g-${type}-import-dest-id`).val();
+    const resourceId = destinationId.trim().split(/\s/)[0];
 
     const models = {
         collection: CollectionModel,
         folder: FolderModel,
         user: UserModel
     };
 
-    if (resourceId && destType in models) {
-        const model = new models[destType]({ _id: resourceId });
+    if (resourceId && destinationType in models) {
+        const model = new models[destinationType]({ _id: resourceId });
 
         model.once('g:fetched', () => {
             if (!browserWidget.root || browserWidget.root.id !== model.id) {
@@ -79,7 +85,7 @@ const setBrowserRoot = (view, type) => {
             if (err.status === 400) {
                 events.trigger('g:alert', {
                     icon: 'cancel',
-                    text: `No ${destType.toUpperCase()} with ID ${resourceId} found.`,
+                    text: `No ${destinationType.toUpperCase()} with ID ${resourceId} found.`,
                     type: 'danger',
                     timeout: 4000
                 });
@@ -97,52 +103,55 @@ wrap(S3ImportView, '_openBrowser', function (_openBrowser) {
     setBrowserRoot(this, 's3');
     _openBrowser.call(this);
 });
+wrap(DICOMwebImportView, '_openBrowser', function (_openBrowser) {
+    setBrowserRoot(this, 'dwas');
+    _openBrowser.call(this);
+});
 
 // We can't just wrap the submit events, as we need to modify what is passed to
 // the assetstore import method
+const importSubmit = (view, type) => {
+    const destinationId = view.$(`#g-${type}-import-dest-id`).val().trim().split(/\s/)[0];
+    const destinationType = view.$(`#g-${type}-import-dest-type`).val();
+    const excludeExisting = view.$(`#g-${type}-import-exclude-existing`).val();
+
+    const importParams = { destinationId, destinationType, excludeExisting, progress: true };
+
+    if (type === 'filesystem') {
+        importParams.leafFoldersAsItems = view.$(`#g-${type}-import-leaf-items`).val();
+    }
+    if (type === 'dwas') {
+        importParams.filters = view.$(`#g-${type}-import-filters`).val().trim();
+        importParams.limit = view.$(`#g-${type}-import-limit`).val().trim();
+    } else {
+        importParams.importPath = view.$(`#g-${type}-import-path`).val().trim();
+    }
+
+    view.$('.g-validation-failed-message').empty();
+    view.$(`.g-submit-${type}-import`).addClass('disabled');
+
+    let model = view.assetstore;
+    model = model.off().on('g:imported', function () {
+        router.navigate(destinationType + '/' + destinationId, { trigger: true });
+    }, view).on('g:error', function (err) {
+        view.$(`.g-submit-${type}-import`).removeClass('disabled');
+        view.$('.g-validation-failed-message').html(err.responseJSON.message);
+    }, view);
+
+    model.import(importParams);
+};
+
 FilesystemImportView.prototype.events['submit .g-filesystem-import-form'] = function (e) {
     e.preventDefault();
-
-    var destId = this.$('#g-filesystem-import-dest-id').val().trim().split(/\s/)[0],
-        destType = this.$('#g-filesystem-import-dest-type').val(),
-        foldersAsItems = this.$('#g-filesystem-import-leaf-items').val(),
-        excludeExisting = this.$('#g-filesystem-import-exclude-existing').val();
-
-    this.$('.g-validation-failed-message').empty();
-
-    this.assetstore.off('g:imported').on('g:imported', function () {
-        router.navigate(destType + '/' + destId, { trigger: true });
-    }, this).on('g:error', function (resp) {
-        this.$('.g-validation-failed-message').text(resp.responseJSON.message);
-    }, this).import({
-        importPath: this.$('#g-filesystem-import-path').val().trim(),
-        leafFoldersAsItems: foldersAsItems,
-        destinationId: destId,
-        destinationType: destType,
-        excludeExisting: excludeExisting,
-        progress: true
-    });
+    importSubmit(this, 'filesystem');
 };
 S3ImportView.prototype.events['submit .g-s3-import-form'] = function (e) {
     e.preventDefault();
-
-    var destId = this.$('#g-s3-import-dest-id').val().trim().split(/\s/)[0],
-        destType = this.$('#g-s3-import-dest-type').val(),
-        excludeExisting = this.$('#g-s3-import-exclude-existing').val();
-
-    this.$('.g-validation-failed-message').empty();
-
-    this.assetstore.off('g:imported').on('g:imported', function () {
-        router.navigate(destType + '/' + destId, { trigger: true });
-    }, this).on('g:error', function (resp) {
-        this.$('.g-validation-failed-message').text(resp.responseJSON.message);
-    }, this).import({
-        importPath: this.$('#g-s3-import-path').val().trim(),
-        destinationId: destId,
-        destinationType: destType,
-        excludeExisting: excludeExisting,
-        progress: true
-    });
+    importSubmit(this, 's3');
+};
+DICOMwebImportView.prototype.events['submit .g-dwas-import-form'] = function (e) {
+    e.preventDefault();
+    importSubmit(this, 'dwas');
 };
 
 // Setup router to assetstore imports view

import_tracker/web_client/views/importList.js

@@ -5,7 +5,7 @@ import PaginateWidget from '@girder/core/views/widgets/PaginateWidget';
 import Collection from '@girder/core/collections/Collection';
 
 import AssetstoreModel from '@girder/core/models/AssetstoreModel';
-import { AssetstoreType, SORT_DESC } from '@girder/core/constants';
+import { SORT_DESC } from '@girder/core/constants';
 import View from '@girder/core/views/View';
 import router from '@girder/core/router';
 import { restRequest } from '@girder/core/rest';
@@ -34,11 +34,7 @@ var importList = View.extend({
             }, this);
 
             assetstore.once('g:fetched', () => {
-                if (assetstore.get('type') === AssetstoreType.DICOMWEB) {
-                    assetstore.dicomwebImport(importEvent.get('params'));
-                } else {
-                    assetstore.import(importEvent.get('params'));
-                }
+                assetstore.import(importEvent.get('params'));
             }).fetch();
         },
         'click .re-import-edit-btn': function (e) {
@@ -52,13 +48,7 @@ var importList = View.extend({
             const navigate = (assetstoreId, importId) => {
                 const assetstore = new AssetstoreModel({ _id: assetstoreId });
                 assetstore.once('g:fetched', () => {
-                    if (assetstore.get('type') === AssetstoreType.DICOMWEB) {
-                        // Avoid adding previous import data for DICOMweb imports by navigating to blank import
-                        // TODO: Add DICOMweb-specific re-import view
-                        router.navigate(`dicomweb_assetstore/${assetstoreId}/import`, { trigger: true });
-                    } else {
-                        router.navigate(`assetstore/${assetstoreId}/re-import/${importId}`, { trigger: true });
-                    }
+                    router.navigate(`assetstore/${assetstoreId}/re-import/${importId}`, { trigger: true });
                 }).fetch();
             };