igv visualiztion

src/encoded/region_search.py

@@ -797,6 +797,14 @@ def search_result_actions(request, doc_types, es_results, position=None):
                     ensembl_url = vis_format_url("ensembl", hub_url, assembly, pos)
                     if ensembl_url is not None:
                         browser_urls['Ensembl'] = ensembl_url
+                    igv_search_params = request.params.dict_of_lists()
+                    igv_search_params['assembly'] = [assembly]
+                    igv_params = {
+                        "sessionURL": request.route_url('batch_igv', _query=igv_search_params),
+                    }
+                    if pos is not None:
+                        igv_params['locus'] = pos
+                    browser_urls['IGV'] = 'https://igv.org/app/?' + urlencode(igv_params)
                     if browser_urls:
                         viz[assembly] = browser_urls
                         #actions.setdefault('visualize_batch', {})[assembly] =\

src/encoded/static/components/vis_defines.js

@@ -81,6 +81,7 @@ const ASSEMBLY_DETAILS = {
  * File types allowed for each browser.
  */
 const browserFileTypes = {
+    IGV: [],
     UCSC: [],
     Ensembl: ['bigWig', 'bigBed'],
     hic: ['hic'],
@@ -100,6 +101,12 @@ const browserFileTypes = {
 export const visOpenBrowser = (dataset, browser, assembly, files, datasetUrl) => {
     let href;
     switch (browser) {
+    case 'IGV': {
+        const ucscAssembly = (ASSEMBLY_DETAILS[assembly] || {}).ucsc_assembly || assembly;
+        const sessionURL = `${datasetUrl}@@igv.json?assembly=${encodeURIComponent(ucscAssembly)}`;
+        href=`https://igv.org/app/?sessionURL=${encodeURIComponent(sessionURL)}`;
+        break;
+    }
     case 'UCSC': {
         // UCSC does not use `files` under any circumstances.
         const ucscAssembly = ASSEMBLY_DETAILS[assembly].ucsc_assembly;
@@ -192,6 +199,7 @@ const browserOrder = [
     'UCSC',
     'hic',
     'Ensembl',
+    'IGV',
 ];
 
 

src/encoded/vis_defines.py

@@ -13,6 +13,7 @@
 from snovault.elasticsearch.interfaces import ELASTIC_SEARCH
 import time
 from pkg_resources import resource_filename
+from .vis_igv import file_igv_viewable
 
 import logging
 
@@ -1659,7 +1660,7 @@ def browsers_available(
     elif item_type not in VISIBLE_DATASET_TYPES_LC:
             return []
     browsers = set()
-    full_set = {'ucsc', 'ensembl', 'hic'}
+    full_set = {'ucsc', 'ensembl', 'hic', 'igv'}
     file_assemblies = None
     file_types = None
     if request is not None:
@@ -1681,6 +1682,8 @@ def browsers_available(
             file_assemblies = visualizable_assemblies(assemblies, files)
         if file_types is None:
             continue
+        if any(file_igv_viewable(obj) for obj in (files or []) if obj.get('assembly') == assembly):
+            browsers.add('IGV')
         if ('ucsc' not in browsers
                 and 'ucsc_assembly' in mapped_assembly.keys()
                 and not BROWSER_FILE_TYPES['ucsc'].isdisjoint(file_types)):

src/encoded/vis_igv.py

@@ -0,0 +1,123 @@
+from pyramid.httpexceptions import HTTPUnprocessableEntity
+from pyramid.view import view_config
+from snovault import TYPES
+from urllib.parse import urljoin, urlencode
+
+
+def includeme(config):
+    '''Associated views routes'''
+    config.add_route('batch_igv', '/batch-igv.json')
+    config.scan(__name__)
+
+
+@view_config(name='igv.json', context='.types.dataset.Dataset', request_method='GET', permission='view')
+def dataset_igv(context, request):
+    # Disable rendering as html.
+    request.accept = 'application/json'
+    assemblies = request.params.getall('assembly')
+    if len(assemblies) != 1:
+        return HTTPUnprocessableEntity("Must specify exactly one assembly")
+    assembly = assemblies[0]
+    obj = request.embed('/%s' % context.uuid, as_user=True)
+    index_mapping = request.registry[TYPES]["File"].schema.get('file_format_index_file_extension', {})
+    tracks = list(itertracks(assembly, request.url, index_mapping, [obj]))
+    return {
+        'reference': assembly,
+        'tracks': tracks,
+    }
+
+
+@view_config(route_name='batch_igv', request_method='GET', permission='search')
+def search_igv(context, request):
+    # Disable rendering as html.
+    request.accept = 'application/json'
+    params = request.params.dict_of_lists()
+    assemblies = params.get('assembly', [])
+    if len(assemblies) != 1:
+        return HTTPUnprocessableEntity("Must specify exactly one assembly")
+    assembly = assemblies[0]
+    view = 'region-search' if 'region' in request.params else 'search'
+    params['field'] = ALL_FIELDS
+    params['frame'] = []
+    params['limit'] = ['all']
+    results = request.embed('/%s/?%s' % (view, urlencode(params, doseq=True)), as_user=True)
+    index_mapping = request.registry[TYPES]["File"].schema.get('file_format_index_file_extension', {})
+    tracks = list(itertracks(assembly, request.url, index_mapping, results['@graph']))
+    return {
+        'reference': assembly,
+        'tracks': tracks,
+    }
+
+
+TRACK_MAP = {
+    'bigBed': { 'type': 'annotation', 'format': 'bigBed' },
+    'bigWig': { 'type': 'wig', 'format': 'bigWig' },
+
+    ## These all require tabix / bam index files to be available for efficient visualization.
+    # ('bed', 'narrowPeak'): { 'type': 'annotation', 'format': 'narrowPeak' },
+    # ('bed', 'broadPeak'): { 'type': 'annotation', 'format': 'broadPeak'  },
+    # 'gff3': { 'type': 'annotation', 'format': 'gff3'  },
+    # 'gtf': { 'type': 'annotation', 'format': 'gtf' },
+    # 'bam': { 'type': 'alignment', 'format': 'bam' },
+    # 'vcf': { 'type': 'variant', 'format': 'vcf' },
+    # ('bed', 'bedGraph'): { 'type': 'wig', 'format': 'bedGraph' },
+
+    ## I don't think wig has an index file format, just use bedGraph or bigWig.
+    # 'wig': { 'type': 'wig', 'format': 'wig' },
+}
+
+FILE_FIELDS = {
+    'file_format',
+    'file_format_type',
+    'href',
+    'accession',
+    'assembly',
+}
+DATASET_FIELDS = {
+    'accession',
+ } | {f'files.{field}' for field in FILE_FIELDS}
+ALL_FIELDS = FILE_FIELDS | DATASET_FIELDS
+
+
+def itertracks(assembly, baseurl, index_mapping, results):
+    for result in results:
+        if 'File' in result['@type']:
+            yield from filetracks(assembly, baseurl, index_mapping, result)
+        elif 'Dataset' in result['@type']:
+            for obj in result.get('files', []):
+                yield from filetracks(assembly, baseurl, index_mapping, obj)
+
+
+def filetracks(assembly, baseurl, index_mapping, obj):
+    if obj.get('assembly') != assembly:
+        return
+    file_format = obj.get('file_format')
+    file_format_type = obj.get('file_format_type')
+    base = TRACK_MAP.get((file_format, file_format_type))
+    if base is None:
+        base = TRACK_MAP.get(file_format)
+    if base is None:
+        return
+    if 'href' not in obj or 'accession' not in obj:
+        return
+    url = urljoin(baseurl, obj['href'])
+    data = {
+        "name": obj['accession'],
+        "url": url,
+    }
+    ext = index_mapping.get(file_format)
+    if ext:
+        data["indexURL"] = url + ext
+    data.update(base)
+    yield data
+
+
+def file_igv_viewable(obj):
+    if 'href' not in obj or 'accession' not in obj or 'assembly' not in obj:
+        return False
+    file_format = obj.get('file_format')
+    file_format_type = obj.get('file_format_type')
+    base = TRACK_MAP.get((file_format, file_format_type))
+    if base is None:
+        base = TRACK_MAP.get(file_format)
+    return base is not None

src/encoded/visualization.py

@@ -32,6 +32,7 @@
 log.setLevel(logging.INFO)
 
 def includeme(config):
+    config.include('.vis_igv')
     config.add_route('batch_hub', '/batch_hub/{search_params}/{txt}')
     config.add_route('batch_hub:trackdb', '/batch_hub/{search_params}/{assembly}/{txt}')
     config.scan(__name__)