Adding /browse view.

CHANGELOG.rst

@@ -7,6 +7,32 @@ smaht-portal
 Change Log
 ----------
 
+0.124.0
+=======
+
+* 2024-11-20/dmichaels - branch: dmichaels-20241119-browse-view (PR-295)
+
+* Added module browse.py for /browse; adapted from fourfront/.../search.py/browse.
+  This is for ticket: https://hms-dbmi.atlassian.net/browse/C4-1184
+
+* New endpoint /recent_files_summary which, by default, returns info for files released
+  within the past three months grouped by release-date, cell-line or donor, and 
+  ile-description. The specific fields used for these groupings are:
+  - release-date: file_status_tracking.released
+  - cell-line: file_sets.libraries.analytes.samples.sample_sources.cell_line.code
+  - donor: donors.display_title
+  - file-dsecription: release_tracker_description
+  Note that release_tracker_description is a newer (2024-12) calcprop (PR-298/sn_file_release_tracker);
+  and included in this branch are these files from the branch sn_file_release_tracker:
+  - src/encoded/item_utils/file.py
+  - src/encoded/types/file.py
+  Added these new modules to support this new endpoint:
+  - src/encoded/recent_files_summary.py
+  - src/encoded/elasticsearch_utils.py (maybe move to dcicutils eventually)
+  - src/encoded/endpoint_utils.py (maybe move to dcicutils eventually)
+  This is for ticket: https://hms-dbmi.atlassian.net/browse/C4-1192
+
+
 0.123.0
 =======
 `PR 310 SN Add liquid category <https://github.com/smaht-dac/smaht-portal/pull/310>`
@@ -23,6 +49,7 @@ Change Log
   * Assay and sequencer codes value set to XX for DSA fasta files and chain files
   * For Supplementary Files, use `haplotype`, `target_assembly`, and `source_assembly` properties to create annotated filenames for chain and fasta files
 
+
 0.121.0
 =======
 `PR 300 SN Remove basecalling <https://github.com/smaht-dac/smaht-portal/pull/300>`

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "encoded"
-version = "0.123.0"
+version = "0.123.0.1b1"  # TODO: To become  0.124.0
 description = "SMaHT Data Analysis Portal"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"
@@ -99,6 +99,7 @@ structlog = ">=19.2.0,<20"
 subprocess-middleware = "^0.3.0"
 supervisor = "^4.2.4"
 # Useful for picking apart pyproject.toml
+termcolor = "^2.4.0"
 toml = ">=0.10.1,<1"
 tqdm = "^4.59.0"
 transaction = "^3.0.0"

src/encoded/__init__.py

@@ -313,6 +313,7 @@ def main(global_config, **local_config):
     if 'elasticsearch.server' in config.registry.settings:
         config.include('snovault.elasticsearch')
         config.include('snovault.search.search')
+        config.include('encoded.browse')
         config.include('snovault.search.compound_search')
 
     # this contains fall back url, so make sure it comes just before static_resoruces

src/encoded/browse.py

@@ -0,0 +1,66 @@
+from pyramid.httpexceptions import HTTPFound
+from pyramid.security import Authenticated
+from pyramid.view import view_config
+import structlog
+from webob.multidict import MultiDict
+from urllib.parse import urlencode
+from snovault.search.search import search
+from snovault.util import debug_log
+from encoded.endpoints.recent_files_summary.recent_files_summary import recent_files_summary_endpoint
+
+log = structlog.getLogger(__name__)
+
+# 2024-11-19/dmichaels: Adapted from fourfront for C4-1184.
+
+def includeme(config):
+    config.add_route('browse', '/browse{slash:/?}')
+    config.add_route("recent_files_summary", "/recent_files_summary")
+    config.scan(__name__)
+
+
+# DEFAULT_BROWSE_TYPE = "FileSet"
+# DEFAULT_BROWSE_TYPE = "UnalignedReads"
+# DEFAULT_BROWSE_TYPE = "OutputFile"
+
+DEFAULT_BROWSE_TYPE = "File"
+DEFAULT_BROWSE_FACETS = ["file_size"]
+
+DEFAULT_BROWSE_PARAM_LISTS = {
+    "type": [DEFAULT_BROWSE_TYPE],
+    "additional_facet": DEFAULT_BROWSE_FACETS
+}
+
+@view_config(route_name='browse', request_method='GET', permission='search')
+@debug_log
+def browse(context, request, search_type=DEFAULT_BROWSE_TYPE, return_generator=False):
+    """
+    Simply use search results for browse view
+    Redirect to proper URL w. params if needed
+    """
+    orig_params = request.params
+    for k,vals in DEFAULT_BROWSE_PARAM_LISTS.items():
+        if k not in orig_params or orig_params[k] not in vals:
+            # Redirect to DEFAULT_BROWSE_PARAM_LISTS URL
+            next_qs = MultiDict()
+            for k2, v2list in DEFAULT_BROWSE_PARAM_LISTS.items():
+                for v2 in v2list:
+                    next_qs.add(k2, v2)
+            # Preserve other keys that arent in DEFAULT_BROWSE_PARAM_LISTS
+            for k2, v2 in orig_params.items():
+                if k2 not in DEFAULT_BROWSE_PARAM_LISTS:
+                    next_qs.add(k2, v2)
+            # next_qs.add("redirected_from", str(request.path_qs))
+            return HTTPFound(
+                location=str(request.path) + '?' +  urlencode(next_qs),
+                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")
+
+
+@view_config(route_name="recent_files_summary", request_method=["GET"], effective_principals=Authenticated)
+@debug_log
+def recent_files_summary(context, request):
+    return recent_files_summary_endpoint(context, request)