Tkakar/cat 673 create builder for seg mask

.gitignore

@@ -129,4 +129,6 @@ dmypy.json
 .pyre/
 
 # VSCode
-.VSCode
+.VSCode
+
+.DS_Store

README.md

@@ -1,6 +1,6 @@
 # portal-visualization
 
-Given HuBMAP Dataset JSON, creates a Vitessce configuration.
+Given HuBMAP Dataset JSON (e.g. https://portal.hubmapconsortium.org/browse/dataset/004d4f157df4ba07356cd805131dfc04.json), creates a Vitessce configuration.
 
 ## Release process
 
@@ -23,22 +23,45 @@ $ pip install .
 $ src/vis-preview.py --help
 usage: vis-preview.py [-h] (--url URL | --json JSON) [--assaytypes_url URL]
                       [--assets_url URL] [--token TOKEN] [--marker MARKER]
-                      [--to_json]
+                      [--to_json] [--epic_uuid UUID] [--parent_uuid UUID]
+                      [--epic_url EPIC_URL] [--epic_json EPIC_JSON]
 
 Given HuBMAP Dataset JSON, generate a Vitessce viewconf, and load vitessce.io.
 
 optional arguments:
   -h, --help            show this help message and exit
   --url URL             URL which returns Dataset JSON
   --json JSON           File containing Dataset JSON
-  --assaytypes_url URL  AssayType service; default:
-                        https://ingest.api.hubmapconsortium.org/assaytype/
+  --assaytypes_url URL  AssayType service; default: https://ingest-
+                        api.dev.hubmapconsortium.org/assaytype/
   --assets_url URL      Assets endpoint; default:
-                        https://assets.hubmapconsortium.org
+                        https://assets.dev.hubmapconsortium.org
   --token TOKEN         Globus groups token; Only needed if data is not public
   --marker MARKER       Marker to highlight in visualization; Only used in
                         some visualizations.
   --to_json             Output viewconf, rather than open in browser.
+  --epic_uuid UUID      uuid of the EPIC dataset.
+  --parent_uuid UUID    Parent uuid - Only needed for an image-pyramid support
+                        dataset.
+  --epic_url EPIC_URL   URL which returns Dataset JSON for the EPIC dataset
+  --epic_json EPIC_JSON
+                        File containing Dataset JSON for the EPIC dataset
+  ```
+
+
+  ```
+  Notes:  
+  1. The token can be retrieved by looking for Authorization Bearer {token represented by a long string} under `search-api` network calls under the network tab in developer's tool when browsing a dataset in portal while logged in. The token is necessary to access non-public datasets, such as those in QA.
+  2. The documentation for the `vis-preview.py` script must match the contents of the readme. When a script argument is added or modified, the README must be updated to match the output of `./vis-preview.py --help`.
+
+  ```
+
+
+## Build & Testing
+  ``` 
+   To build: `python -m build`   
+  `To run the tests `./test.sh`. Install the `flake8` and `autopep8` packages.
+
   ```
 
 ## Background
@@ -47,7 +70,9 @@ optional arguments:
 
 Data for the Vitessce visualization almost always comes via raw data that is processed by [ingest-pipeline](https://github.com/hubmapconsortium/ingest-pipeline) airflow dags.
 Harvard often contributes our own custom pipelines to these dags that can be found in [portal-containers](https://github.com/hubmapconsortium/portal-containers).
-The outputs of these pipelines are then converted into view configurations for Vitessce by the [portal backend](https://github.com/hubmapconsortium/portal-ui/blob/0b43a468fff0256a466a3bf928a83893321ea1d9/context/app/api/client.py#L165),
+
+The outputs of these pipelines are then converted into view configurations for Vitessce by the [portal backend](https://github.com/hubmapconsortium/portal-visualization/blob/main/src/portal_visualization/client.py), The `vis-preview.py` mimics the invocation of `get_view_config_builder` for development and testing purposes independently, i.e., without using the [portal backend](https://github.com/hubmapconsortium/portal-ui/blob/main/context/app/routes_browse.py#L126).
+
 using code in this repo, when a `Dataset` that should be visualized is requested in the client.
 The view configurations are built using the [Vitessce-Python API](https://vitessce.github.io/vitessce-python/).
 

requirements-dev.txt

@@ -1,6 +1,9 @@
 pytest==5.2.1
 flake8==7.0.0
-autopep8==1.4.4
+autopep8==2.0.4
 pytest-mock==3.7.0
-coverage==6.3.1
-pyyaml==6.0
+coverage==7.6.4
+pyyaml==6.0.2
+anywidget==0.9.13
+starlette==0.41.0
+uvicorn==0.32.0

src/defaults.json

@@ -1,4 +1,5 @@
 {
-  "assets_url": "https://assets.hubmapconsortium.org",
-  "assaytypes_url": "https://ingest.api.hubmapconsortium.org/assaytype/"
+  "assets_url": "https://assets.dev.hubmapconsortium.org",
+  "assaytypes_url": "https://ingest-api.dev.hubmapconsortium.org/assaytype/",
+  "dataset_url":"https://portal.dev.hubmapconsortium.org/browse/dataset/"
 }

src/portal_visualization/builder_factory.py

@@ -8,6 +8,7 @@
     SeqFISHViewConfBuilder,
     IMSViewConfBuilder,
     ImagePyramidViewConfBuilder,
+    SegImagePyramidViewConfBuilder,
     NanoDESIViewConfBuilder,
 )
 from .builders.anndata_builders import (
@@ -33,6 +34,7 @@ def process_hints(hints):
     is_json = "json_based" in hints
     is_spatial = "spatial" in hints
     is_support = "is_support" in hints
+    is_segmentation_base = "segmentation_base" in hints
 
     return (
         is_image,
@@ -44,6 +46,7 @@ def process_hints(hints):
         is_json,
         is_spatial,
         is_support,
+        is_segmentation_base,
     )
 
 
@@ -53,10 +56,10 @@ def process_hints(hints):
 # The entity is a dict that contains the entity UUID and metadata.
 # `get_assaytype` is a function which takes an entity UUID and returns
 # a dict containing the assaytype and vitessce-hints for that entity.
-def get_view_config_builder(entity, get_assaytype, parent=None):
+def get_view_config_builder(entity, get_assaytype, parent=None, epic_uuid=None):
     if entity.get("uuid") is None:
         raise ValueError("Provided entity does not have a uuid")
-    assay = get_assaytype(entity)
+    assay = get_assaytype(entity.get('uuid'))
     assay_name = assay.get("assaytype")
     hints = assay.get("vitessce-hints", [])
     (
@@ -69,11 +72,16 @@ def get_view_config_builder(entity, get_assaytype, parent=None):
         is_json,
         is_spatial,
         is_support,
+        is_segmentation_base
     ) = process_hints(hints)
 
     # vis-lifted image pyramids
     if parent is not None:
-        if is_support and is_image:
+        # TODO: For now epic (base image's) support datasets doesn't have any hints
+        if epic_uuid is not None or is_segmentation_base:
+            return SegImagePyramidViewConfBuilder
+
+        elif is_support and is_image:
             ancestor_assaytype = get_assaytype(parent).get("assaytype")
             if SEQFISH == ancestor_assaytype:
                 # e.g. parent  = c6a254b2dc2ed46b002500ade163a7cc
@@ -134,5 +142,5 @@ def get_view_config_builder(entity, get_assaytype, parent=None):
 
 
 def has_visualization(entity, get_assaytype, parent=None):
-    builder = get_view_config_builder(entity, get_assaytype, parent)
+    builder = get_view_config_builder(entity, get_assaytype, parent, epic_uuid=None)
     return builder != NullViewConfBuilder

src/portal_visualization/builders/anndata_builders.py

@@ -125,7 +125,7 @@ def _set_up_marker_gene(self, marker):
                     if (marker_index >= 0):
                         marker = ensembl_ids[marker_index]
                     else:
-                        pass
+                        pass   # pragma: no cover
             # Encoding Version 0.2.0
             # https://anndata.readthedocs.io/en/latest/fileformat-prose.html#categorical-arrays
             # Our pipeline currently does not use this encoding version
@@ -243,7 +243,7 @@ def _setup_anndata_view_config(self, vc, dataset):
         # This ensures that the view config is valid for datasets with and without a spatial view
         spatial = self._add_spatial_view(dataset, vc)
 
-        views = list(filter(lambda v: v is not None, [
+        views = list(filter(lambda v: v is not None, [    # pragma: no cover
                      cell_sets, gene_list, scatterplot, cell_sets_expr, heatmap, spatial]))
 
         self._views = views

src/portal_visualization/builders/base_builders.py

@@ -1,7 +1,9 @@
 import urllib
 from collections import namedtuple
 from abc import ABC, abstractmethod
-
+# import json
+# import requests
+# from pathlib import Path
 
 ConfCells = namedtuple('ConfCells', ['conf', 'cells'])
 
@@ -74,7 +76,10 @@ def _build_assets_url(self, rel_path, use_token=True):
         'https://example.com/uuid/rel_path/to/clusters.ome.tiff?token=groups_token'
 
         """
-        base_url = urllib.parse.urljoin(self._assets_endpoint, f"{self._uuid}/{rel_path}")
+        uuid = self._uuid
+        if hasattr(self, "_epic_uuid"):  # pragma: no cover
+            uuid = self._epic_uuid
+        base_url = urllib.parse.urljoin(self._assets_endpoint, f"{uuid}/{rel_path}")
         token_param = urllib.parse.urlencode({"token": self._groups_token})
         return f"{base_url}?{token_param}" if use_token else base_url
 
@@ -118,6 +123,23 @@ def _get_file_paths(self):
         """
         return [file["rel_path"] for file in self._entity["files"]]
 
+    # def _get_epic_entity(self):
+    # TODO: might need this if we decide to read the epic_entity on run time
+    #     request_init = self._get_request_init()
+    #     file_path = Path(__file__).resolve().parent.parent.parent / 'defaults.json'
+    #     print(file_path)
+    #     defaults = json.load(file_path.open())
+    #     # headers = {"headers": {"Authorization": f"Bearer {self._groups_token}"}}
+    #     url = f'{defaults['dataset_url']}/{self._epic_uuid}.json'
+    #     print(url)
+    #     response = requests.get(url, request_init)
+    #     if response.status_code == 403:
+    #         raise Exception('Protected data: Download JSON via browser; Redo with --json')
+    #     response.raise_for_status()
+    #     json_str = response.text
+    #     entity = json.loads(json_str)
+    #     return entity
+
 
 class _DocTestBuilder(ViewConfBuilder):  # pragma: no cover
     # The doctests on the methods in this file need a concrete class to instantiate: