Merge pull request #1514 from ImagingDataCommons/idc-prod-sp

Release 49

Author: s-paquette

Dockerfile

@@ -29,12 +29,12 @@ RUN apt-get update
 RUN apt-get install -y wget
 # TODO: we need to start using the keyring instead
 RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv A8D3785C
-RUN wget "http://repo.mysql.com/mysql-apt-config_0.8.30-1_all.deb" -P /tmp
+RUN wget "http://repo.mysql.com/mysql-apt-config_0.8.35-1_all.deb" -P /tmp
 
 # install lsb-release (a dependency of mysql-apt-config), since dpkg doesn't
 # do dependency resolution
 RUN apt-get install -y lsb-release
-RUN dpkg --install /tmp/mysql-apt-config_0.8.30-1_all.deb
+RUN dpkg --install /tmp/mysql-apt-config_0.8.35-1_all.deb
 
 # fetch the updated package metadata (in particular, mysql-server)
 RUN apt-get update

etl/etl.py

@@ -59,10 +59,10 @@
 COLLECTION_HEADER_CHK = "collection_uuid"
 
 FIELD_MAP = {x: i for i, x in enumerate([
-            "collection_id", "collection_uuid", "name", "collections", "image_types", "supporting_data", "subject_count", "doi",
-            "source_url", "cancer_type", "species", "location", "analysis_artifacts", "description", "collection_type",
-            "program", "access", "date_updated", "tcia_wiki_collection_id", "license_short_name", "active"
-    ])}
+    "collection_id", "collection_uuid", "name", "collections", "image_types", "supporting_data", "subject_count", "doi",
+    "source_url", "cancer_type", "species", "location", "analysis_artifacts", "description", "collection_type",
+    "program", "access", "date_updated", "tcia_wiki_collection_id", "license_short_name", "active", "total_size", "total_size_with_ar"
+])}
 
 TOKENIZED_FIELDS = ["PatientID", "SeriesInstanceUID", "StudyInstanceUID"]
 
@@ -146,8 +146,8 @@
 }
 
 SOLR_SINGLE_VAL = {
-    "StudyInstanceUID": ["PatientID", "StudyInstanceUID", "crdc_study_uuid"],
-    "SeriesInstanceUID": ["PatientID", "StudyInstanceUID", "SeriesInstanceUID", "crdc_study_uuid", "crdc_series_uuid"]
+    "StudyInstanceUID": ["PatientID", "StudyInstanceUID", "crdc_study_uuid","instance_size"],
+    "SeriesInstanceUID": ["PatientID", "StudyInstanceUID", "SeriesInstanceUID", "crdc_study_uuid", "crdc_series_uuid", "instance_size"]
 }
 
 ETL_CONFIG = {}
@@ -356,7 +356,7 @@ def load_collections(filename, data_version="8.0"):
         exact_collection_fields = [
             "collection_id", "collection_uuid", "name", "collections", "image_types", "supporting_data", "subject_count", "doi",
             "source_url", "cancer_type", "species", "location", "analysis_artifacts", "description", "collection_type",
-            "access", "date_updated", "active"]
+            "access", "date_updated", "active", "total_size", "total_size_with_ar"]
         field_map = FIELD_MAP
         for line in csv_reader(collection_file):
             if COLLECTION_HEADER_CHK in line:
@@ -366,7 +366,6 @@ def load_collections(filename, data_version="8.0"):
                 for field in line:
                     field_map[field] = i
                     i += 1
-                print(field_map)
                 continue
             collex = {
                 'data': { x: line[field_map[x]] for x in exact_collection_fields },

idc/demo_views.py

@@ -144,7 +144,7 @@ def explore_demo_page(request):
     is_json = False
 
     try:
-        req = request.GET if request.GET else request.POST
+        req = request.GET if request.method == 'GET' else request.POST
         is_dicofdic = (req.get('is_dicofdic', "False").lower() == "true")
         source = req.get('data_source_type', DataSource.SOLR)
         versions = json.loads(req.get('versions', '[]'))

idc/urls.py

@@ -49,8 +49,8 @@
     re_path(r'^explore/filters/', views.parse_explore_filters, name='parse_explore_filters'),
     re_path(r'^explore/bq_string/$', get_query_str_response, name='explore_bq_string'),
     re_path(r'^explore/manifest/$', views.explorer_manifest, name='get_explore_manifest'),
+    re_path(r'^explore/manifest/series/$', views.explorer_manifest, name='get_series_ids_manifest'),
     re_path(r'^tables/', views.populate_tables, name='populate_tables'),
-    re_path(r'^studymp/', views.studymp, name='studymp'),
     re_path(r'^warning/', views.warn_page, name='warn'),
     re_path(r'^about/$', views.about_page, name='about_page'),
     re_path(r'^dashboard/', views.dashboard_page, name='dashboard'),
@@ -60,8 +60,11 @@
     re_path(r'^cart/$', views.cart_page, name='cart'),
     re_path(r'^explore/cart/$', views.cart_page, name='get_explore_cart'),
     re_path(r'^cart_data/$', views.cart_data, name='get_cart_data'),
-    re_path(r'^series_ids/(?P<patient_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_case'),
-    re_path(r'^series_ids/(?P<patient_id>[A-Za-z0-9\.\-_]+)/(?P<study_uid>[0-9\.]+)/$', views.get_series, name='get_series'),
+    re_path(r'^series_ids/$', views.get_series, name='get_series_ids_base'),
+    re_path(r'^series_ids_filter/$', views.get_series, name='get_series_ids_filter'),
+    re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_collex'),
+    re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/(?P<patient_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_case'),
+    re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/(?P<patient_id>[A-Za-z0-9\.\-_]+)/(?P<study_uid>[0-9\.]+)/$', views.get_series, name='get_series'),
     re_path(r'^collaborators/$', views.collaborators, name='collaborators'),
     re_path(r'^collections/', include('idc_collections.urls')),
     re_path(r'^citations/', views.get_citations, name='get_citations'),