Minor fixes of readme and args

README.md

@@ -23,7 +23,7 @@ $ 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] [--epic_uuid UUID]
+ [--to_json] [--epic_uuid UUID] [--parent_uuid UUID]
 
 Given HuBMAP Dataset JSON, generate a Vitessce viewconf, and load vitessce.io.
 
@@ -39,20 +39,20 @@ optional arguments:
  --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
+ --epic_uuid UUID uuid of the EPIC dataset.
+ --parent_uuid UUID Parent uuid - Only needed for an image-pyramid support
+ dataset.
  ```
 
 
  ```
  Notes: 
- 1. To get the token, look for Authorization Bearer {token represented by a long string} under `search-api` network calls under th network tab in developer's tool when browsing a dataset in portal
- 2. If you added an argument to the vis-preview.py script, do update the help docs in README, otherwise build will throw error
- 3. 
-
+ 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` 
@@ -66,7 +66,8 @@ 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 `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/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/).

src/portal_visualization/builders/epic_builders.py

@@ -79,9 +79,9 @@ def _apply(self, conf):
  seg_path = f'{self.segmentations_url("seg")}/'
  # print(seg_path)
  seg_path = (
- 'https://assets.hubmapconsortium.org/c9d9ab5c9ee9642b60dd351024968627/'
- 'ometiff-pyramids/VAN0042-RK-3-18-registered-PAS-to-postAF-registered.ome_mask.ome.tif?'
- 'token=AgzQXm7nvOW32vWw0EPpKonwbOqjNBzNvvW1p15855NoYglJxyfkC8rlJJWy8V6E8MeyXOwlpKdNBnHb5qnv7f8oeeG'
+ f"""https://assets.hubmapconsortium.org/c9d9ab5c9ee9642b60dd351024968627/
+ ometiff-pyramids/VAN0042-RK-3-18-registered-PAS-to-postAF-registered.ome_mask.ome.tif?
+ token={self._groups_token}"""
  )
  mask_names = self.read_metadata_from_url()
  mask_names = ['mask1', 'mask2'] # for testing purposes

src/vis-preview.py

@@ -43,13 +43,13 @@ def main(): # pragma: no cover
  parser.add_argument(
  '--to_json', action='store_true',
  help='Output viewconf, rather than open in browser.')
- # parser.add_argument(
- # '--parent_uuid', action='store_true',
- # help='Parent uuid for the dataset',
- # default=None)
  parser.add_argument(
  '--epic_uuid', metavar='UUID',
- help='uuid of the EPIC dataset',
+ help='uuid of the EPIC dataset.',
+ default=None)
+ parser.add_argument(
+ '--parent_uuid', metavar='UUID',
+ help='Parent uuid - Only needed for an image-pyramid support dataset.',
  default=None)
 
  #
@@ -62,10 +62,11 @@ def main(): # pragma: no cover
  marker = args.marker
  # epic_builder = args.epic_builder
  epic_uuid = args.epic_uuid
- # parent_uuid = args.parent_uuid # this may not be needed, as the --url provides the parent dataset json?
+ parent_uuid = args.parent_uuid
 
+ headers = get_headers(args.token)
  if args.url:
- response = requests.get(args.url)
+ response = requests.get(args.url, headers=headers)
  if response.status_code == 403:
  raise Exception('Protected data: Download JSON via browser; Redo with --json')
  response.raise_for_status()
@@ -76,9 +77,6 @@ def main(): # pragma: no cover
 
  def get_assaytype(entity):
  uuid = entity.get("uuid")
- headers = {}
- if args.token:
- headers['Authorization'] = f'Bearer {args.token}'
  try:
  response = requests.get(f'{defaults["assaytypes_url"]}{uuid}', headers=headers)
  if response.status_code != 200:
@@ -92,7 +90,7 @@ def get_assaytype(entity):
  except Exception as e:
  print(f"Error accessing {defaults['assaytypes_url']}{uuid}: {str(e)}")
 
- Builder = get_view_config_builder(entity, get_assaytype)
+ Builder = get_view_config_builder(entity, get_assaytype, parent_uuid)
  builder = Builder(entity, args.token, args.assets_url)
  print(f'Using: {builder.__class__.__name__}', file=stderr)
  conf_cells = builder.get_conf_cells(marker=marker)
@@ -123,5 +121,12 @@ def get_assaytype(entity):
  open_new_tab(vitessce_url)
 
 
+def get_headers(token): # pragma: no cover
+ headers = {}
+ if token:
+ headers['Authorization'] = f'Bearer {token}'
+ return headers
+
+
 if __name__ == "__main__": # pragma: no cover
  main()