Bm browse view

CHANGELOG.rst

@@ -7,13 +7,25 @@ smaht-portal
 Change Log
 ----------
 
+0.127.0
+=======
+`PR 305: BM Browse View <https://github.com/smaht-dac/smaht-portal/pull/305>`_
+
+* Implements UI of browse view + generalization of benchmarking layout
+* Rework navbar to include new structure
+* Adjustments to home page to include only two tiers
+* Slight schema edits for facets and columns
+* Update to SPC version 0.1.92
+
+
 0.126.1
 =======
-`PR 313 SN Reference file columns <https://github.com/smaht-dac/smaht-portal/pull/313>`
+`PR 313 SN Reference file columns <https://github.com/smaht-dac/smaht-portal/pull/313>`_
 
 * Add `title` and `version` to columns for ReferenceFile
 * Minor fix: remove Basecalling from the automated spreadsheet script
 
+
 0.126.0
 =======
 `PR246: feat: homepage updates <https://github.com/smaht-dac/smaht-portal/pull/246>`_
@@ -60,7 +72,7 @@ Change Log
 
 0.124.1
 =======
-`PR BM Register Text Fix <https://github.com/smaht-dac/smaht-portal/pull/297>`_
+`PR 297: BM Register Text Fix <https://github.com/smaht-dac/smaht-portal/pull/297>`_
 
 * Update text in UserRegistrationModal to not refer to 2023 data release
 

package.json

@@ -72,7 +72,7 @@
     "@gmod/tabix": "^1.5.3",
     "@gmod/vcf": "^5.0.6",
     "@hms-dbmi-bgm/react-workflow-viz": "0.1.11",
-    "@hms-dbmi-bgm/shared-portal-components": "github:4dn-dcic/shared-portal-components#0.1.91",
+    "@hms-dbmi-bgm/shared-portal-components": "github:4dn-dcic/shared-portal-components#0.1.92",
     "@reduxjs/toolkit": "^2.2.6",
     "auth0-lock": "^12.5.1",
     "d3": "^7.8.5",

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "encoded"
-version = "0.126.1"
+version = "0.127.0"
 description = "SMaHT Data Analysis Portal"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

src/encoded/browse.py

@@ -27,7 +27,9 @@ def includeme(config):
 
 DEFAULT_BROWSE_PARAM_LISTS = {
     "type": [DEFAULT_BROWSE_TYPE],
-    "additional_facet": DEFAULT_BROWSE_FACETS
+    "sample_summary.studies": ["Production"],
+    "status": ["released"],
+    # "additional_facet": DEFAULT_BROWSE_FACETS
 }
 
 @view_config(route_name='browse', request_method='GET', permission='search')
@@ -55,8 +57,6 @@ def browse(context, request, search_type=DEFAULT_BROWSE_TYPE, return_generator=F
                 detail="Redirected from " + str(request.path_info)
             )
 
-    # TODO
-    # No real /browse specific UI yet; initially just basically copied static/components/SearchView.js to BrowseView.js.
     return search(context, request, search_type, return_generator, forced_type="Browse")
 
 

src/encoded/homepage.py

@@ -189,7 +189,7 @@ def home(context, request):
         'date': f'{time.strftime("%Y-%m-%d %H:%M")} EST',
         '@graph': [
             {
-                "title": "Tier 0: Benchmarking",
+                "title": "Benchmarking",
                 "subtitle": "with all technologies",
                 "categories": [
                     {
@@ -237,7 +237,7 @@ def home(context, request):
                 ]
             },
             {
-                "title": "Tier 1",
+                "title": "Production",
                 "subtitle": "with core + additional technologies",
                 "categories": [
                     {
@@ -251,21 +251,6 @@ def home(context, request):
                     }
                 ]
             },
-            {
-                "title": "Tier 2",
-                "subtitle": "with core technologies",
-                "categories": [
-                    {
-                        "title": "Primary Tissues",
-                        "figures": [
-                            { "value": 0, "unit": "Donors" },
-                            { "value": 0, "unit": "Tissue Types" },
-                            { "value": 0, "unit": "Assays" },
-                            { "value": 0, "unit": "Files Generated" }
-                        ]
-                    }
-                ]
-            }
         ]
     }
     return response

src/encoded/metadata.py

@@ -39,6 +39,7 @@ class MetadataArgs(NamedTuple):
     accessions: List[str]
     sort_param: str
     type_param: str
+    status: str
     include_extra_files: bool
     download_file_name: str
     header: Tuple[List[str], List[str], List[str]]
@@ -250,6 +251,7 @@ def handle_metadata_arguments(context, request):
             accessions = post_params.get('accessions', [])
             type_param = post_params.get('type')
             sort_param = post_params.get('sort')
+            status = post_params.get('status')
             cli = post_params.get('cli', False)
             download_file_name = post_params.get('download_file_name')
             include_extra_files = post_params.get('include_extra_files', False)
@@ -260,6 +262,7 @@ def handle_metadata_arguments(context, request):
         accessions = json.loads(post_params.get('accessions', ''))
         type_param = post_params.get('type')
         sort_param = post_params.get('sort')
+        status = post_params.get('status')
         cli = post_params.get('cli', False)
         download_file_name = post_params.get('download_file_name')
         include_extra_files = post_params.get('include_extra_files', False)
@@ -277,7 +280,7 @@ def handle_metadata_arguments(context, request):
     # Note that this will become more complex as we add additional header types
     header = generate_file_download_header(download_file_name, cli=cli)
     tsv_mapping = TSV_MAPPING[FILE]
-    return MetadataArgs(accessions, sort_param, type_param, include_extra_files, download_file_name, header,
+    return MetadataArgs(accessions, sort_param, type_param, status, include_extra_files, download_file_name, header,
                         tsv_mapping, cli)
 
 
@@ -303,6 +306,8 @@ def peek_metadata(context, request):
         search_param['accession'] = args.accessions
     if args.sort_param:
         search_param['sort'] = args.sort_param
+    if args.status:
+        search_param['status'] = args.status
     search_param['limit'] = [1]  # we don't care about results, just the facets
     search_param['additional_facet'] = ['file_size']
     if args.include_extra_files:
@@ -337,6 +342,8 @@ def metadata_tsv(context, request):
         search_param['accession'] = args.accessions
     if args.sort_param:
         search_param['sort'] = args.sort_param
+    if args.status:
+        search_param['status'] = args.status
     cli = args.cli
     search_iter = get_iterable_search_results(request, param_lists=search_param)
 

src/encoded/schemas/file.json

@@ -225,22 +225,66 @@
         }
     },
     "facets": {
+        "access_status": {
+            "title": "Access"
+        },
+        "donors.display_title": {
+            "title": "Donor",
+            "search_type": "sayt",
+            "sayt_item_type": "Donor"
+        },
+        "donors.age": {
+            "title": "Donor Age",
+            "aggregation_type": "range",
+            "number_step": 1,
+            "ranges": [
+                {
+                    "from": 18,
+                    "to": 30
+                },
+                {
+                    "from": 30,
+                    "to": 55
+                },
+                {
+                    "from": 55,
+                    "to": 65
+                },
+                {
+                    "from": 65
+                }
+            ]
+        },
+        "file_sets.libraries.analytes.samples.sample_sources.donor.sex": {
+            "title": "Donor Sex"
+        },
+        "sample_summary.tissues": {
+            "title": "Tissue"
+        },
         "file_sets.libraries.assay.display_title": {
-            "title": "Experimental Assay"
+            "title": "Experimental Assay",
+            "search_type": "sayt",
+            "sayt_item_type": "Donor"
         },
         "file_sets.sequencing.sequencer.display_title": {
             "title": "Sequencing Platform"
         },
-        "donors.display_title": {
-            "title": "Donor",
-            "default_hidden": true
-        },
         "file_format.display_title": {
             "title": "Data Format"
         },
-        "data_type": {
+        "data_category": {
             "title": "Data Category"
         },
+        "data_type": {
+            "title": "Data Type"
+        },
+        "reference_genome.display_title": {
+            "title": "Reference Genome"
+        },
+        "date_created": {
+            "title" : "Release Date",
+            "aggregation_type" : "stats"
+        },
         "sequencing_center.display_title": {
             "title": "Sequencing Center"
         },