John conroy/switch auth globus groups

CHANGELOG-switch-auth-globus-groups.md

@@ -0,0 +1 @@
+- Switch Globus authentication from Globus Nexus to Globus Groups.

context/.storybook/preview.js

@@ -13,11 +13,11 @@ export const parameters = {
 }
 
 const mockEndpoints = {};
-const mockNexusToken=""
+const mockGroupsToken=""
 
 export const decorators = [
   (Story) => (
-    <Providers endpoints={mockEndpoints} nexusToken={mockNexusToken}>
+    <Providers endpoints={mockEndpoints} groupsToken={mockGroupsToken}>
       <Story />
     </Providers>
   ),

context/app/api/client.py

@@ -19,12 +19,12 @@ class VitessceConfLiftedUUID:
 
 
 class ApiClient():
-    def __init__(self, url_base=None, nexus_token=None):
+    def __init__(self, url_base=None, groups_token=None):
         self.url_base = url_base
-        self.nexus_token = nexus_token
+        self.groups_token = groups_token
 
     def _request(self, url, body_json=None):
-        headers = {'Authorization': 'Bearer ' + self.nexus_token} if self.nexus_token else {}
+        headers = {'Authorization': 'Bearer ' + self.groups_token} if self.groups_token else {}
         try:
             response = (
                 requests.post(url, headers=headers, json=body_json)
@@ -109,7 +109,7 @@ def get_entity(self, uuid=None, hbm_id=None):
             body_json=query)
 
         hits = response_json['hits']['hits']
-        return _get_entity_from_hits(hits, has_token=self.nexus_token, uuid=uuid, hbm_id=hbm_id)
+        return _get_entity_from_hits(hits, has_token=self.groups_token, uuid=uuid, hbm_id=hbm_id)
 
     def get_latest_entity_uuid(self, uuid, type):
         lowercase_type = type.lower()
@@ -147,7 +147,7 @@ def get_vitessce_conf_cells_and_lifted_uuid(self, entity):
             if isinstance(Builder, NullViewConfBuilder):
                 vc = Builder()
             else:
-                vc = Builder(entity, self.nexus_token)
+                vc = Builder(entity, self.groups_token)
             return VitessceConfLiftedUUID(vc.get_conf_cells(), None)
         except Exception:
             message = f'Building vitessce conf threw error: {traceback.format_exc()}'

context/app/api/vitessce_confs/assay_confs.py

@@ -130,7 +130,7 @@ def get_conf_cells(self):
         for tile in sorted(found_tiles):
             vc = SPRMJSONViewConfBuilder(
                 entity=self._entity,
-                nexus_token=self._nexus_token,
+                groups_token=self._groups_token,
                 is_mock=self._is_mock,
                 base_name=tile,
                 imaging_path=CODEX_TILE_DIR
@@ -149,8 +149,8 @@ class RNASeqViewConfBuilder(AbstractScatterplotViewConfBuilder):
     from h5ad-to-arrow.cwl (August 2020 release).
     """
 
-    def __init__(self, entity, nexus_token, is_mock=False):
-        super().__init__(entity, nexus_token, is_mock)
+    def __init__(self, entity, groups_token, is_mock=False):
+        super().__init__(entity, groups_token, is_mock)
         # All "file" Vitessce objects that do not have wrappers.
         self._files = [
             {
@@ -172,8 +172,8 @@ class ATACSeqViewConfBuilder(AbstractScatterplotViewConfBuilder):
     from h5ad-to-arrow.cwl.
     """
 
-    def __init__(self, entity, nexus_token, is_mock=False):
-        super().__init__(entity, nexus_token, is_mock)
+    def __init__(self, entity, groups_token, is_mock=False):
+        super().__init__(entity, groups_token, is_mock)
         # All "file" Vitessce objects that do not have wrappers.
         self._files = [
             {
@@ -210,7 +210,7 @@ def get_conf_cells(self):
         for region in sorted(found_regions):
             vc = SPRMAnnDataViewConfBuilder(
                 entity=self._entity,
-                nexus_token=self._nexus_token,
+                groups_token=self._groups_token,
                 is_mock=self._is_mock,
                 base_name=region,
                 imaging_path=STITCHED_IMAGE_DIR,
@@ -234,8 +234,8 @@ class RNASeqAnnDataZarrViewConfBuilder(ViewConfBuilder):
     https://portal.hubmapconsortium.org/browse/dataset/e65175561b4b17da5352e3837aa0e497
     """
 
-    def __init__(self, entity, nexus_token, is_mock=False):
-        super().__init__(entity, nexus_token, is_mock)
+    def __init__(self, entity, groups_token, is_mock=False):
+        super().__init__(entity, groups_token, is_mock)
         # Spatially resolved RNA-seq assays require some special handling,
         # and others do not.
         self._is_spatial = False
@@ -290,8 +290,8 @@ class SpatialRNASeqAnnDataZarrViewConfBuilder(RNASeqAnnDataZarrViewConfBuilder):
     https://portal.hubmapconsortium.org/browse/dataset/e65175561b4b17da5352e3837aa0e497
     """
 
-    def __init__(self, entity, nexus_token, is_mock=False):
-        super().__init__(entity, nexus_token, is_mock)
+    def __init__(self, entity, groups_token, is_mock=False):
+        super().__init__(entity, groups_token, is_mock)
         # Spatially resolved RNA-seq assays require some special handling,
         # and others do not.
         self._is_spatial = True
@@ -322,8 +322,8 @@ class IMSViewConfBuilder(ImagePyramidViewConfBuilder):
     of all the channels separated out.
     """
 
-    def __init__(self, entity, nexus_token, is_mock=False):
-        super().__init__(entity, nexus_token, is_mock)
+    def __init__(self, entity, groups_token, is_mock=False):
+        super().__init__(entity, groups_token, is_mock)
         # Do not show the separated mass-spec images.
         self.image_pyramid_regex = (
             re.escape(IMAGE_PYRAMID_DIR) + r"(?!/ometiffs/separate/)"

context/app/api/vitessce_confs/base_confs.py

@@ -30,18 +30,19 @@ def get_conf_cells(self):
 
 
 class ViewConfBuilder:
-    def __init__(self, entity=None, nexus_token=None, is_mock=False):
+    def __init__(self, entity=None, groups_token=None, is_mock=False):
         """Object for building the vitessce configuration.
         :param dict entity: Entity response from search index (from the entity API)
-        :param str nexus_token: Nexus token for use in authenticating API
+        :param str groups_token: Groups token for use in authenticating API
         :param bool is_mock: Wether or not this class is being mocked.
 
-        >>> vc = ViewConfBuilder(entity={"uuid": "uuid"}, nexus_token='nexus_token', is_mock=True)
+        >>> vc = ViewConfBuilder(
+        ...     entity={"uuid": "uuid"}, groups_token='groups_token', is_mock=True)
 
         """
 
         self._uuid = entity["uuid"]
-        self._nexus_token = nexus_token
+        self._groups_token = groups_token
         self._entity = entity
         self._is_mock = is_mock
         self._files = []
@@ -54,12 +55,13 @@ def _replace_url_in_file(self, file):
         :param dict file: File dict which will have its rel_path replaced by url
         :rtype: dict The file with rel_path replaced by url
         >>> from pprint import pprint
-        >>> vc = ViewConfBuilder(entity={"uuid": "uuid"}, nexus_token='nexus_token', is_mock=True)
+        >>> vc = ViewConfBuilder(
+        ...     entity={"uuid": "uuid"}, groups_token='groups_token', is_mock=True)
         >>> file = { 'data_type': 'CELLS', 'file_type': 'cells.json', 'rel_path': 'cells.json' }
         >>> pprint(vc._replace_url_in_file(file))
         {'data_type': 'CELLS',\n\
          'file_type': 'cells.json',\n\
-         'url': 'https://example.com/uuid/cells.json?token=nexus_token'}
+         'url': 'https://example.com/uuid/cells.json?token=groups_token'}
         """
 
         return {
@@ -71,20 +73,21 @@ def _replace_url_in_file(self, file):
     def _build_assets_url(self, rel_path, use_token=True):
         """Create a url for an asset.
         :param str rel_path: The path off of which the url should be built
-        :param bool use_token: Whether or not to append a nexus token to the URL, default True
+        :param bool use_token: Whether or not to append a groups token to the URL, default True
         :rtype: dict The file with rel_path replaced by url
 
-        >>> vc = ViewConfBuilder(entity={"uuid": "uuid"}, nexus_token='nexus_token', is_mock=True)
+        >>> vc = ViewConfBuilder(
+        ...     entity={"uuid": "uuid"}, groups_token='groups_token', is_mock=True)
         >>> vc._build_assets_url("rel_path/to/clusters.ome.tiff")
-        'https://example.com/uuid/rel_path/to/clusters.ome.tiff?token=nexus_token'
+        'https://example.com/uuid/rel_path/to/clusters.ome.tiff?token=groups_token'
 
         """
         if not self._is_mock:
             assets_endpoint = current_app.config["ASSETS_ENDPOINT"]
         else:
             assets_endpoint = MOCK_URL
         base_url = urllib.parse.urljoin(assets_endpoint, f"{self._uuid}/{rel_path}")
-        token_param = urllib.parse.urlencode({"token": self._nexus_token})
+        token_param = urllib.parse.urlencode({"token": self._groups_token})
         return f"{base_url}?{token_param}" if use_token else base_url
 
     def _get_request_init(self):
@@ -93,14 +96,14 @@ def _get_request_init(self):
         not the above _build_assets_url function.
 
         >>> entity = {"uuid": "uuid", "status": "QA"}
-        >>> vc = ViewConfBuilder(entity=entity, nexus_token='nexus_token', is_mock=True)
+        >>> vc = ViewConfBuilder(entity=entity, groups_token='groups_token', is_mock=True)
         >>> vc._get_request_init()
-        {'headers': {'Authorization': 'Bearer nexus_token'}}
+        {'headers': {'Authorization': 'Bearer groups_token'}}
         >>> entity = {"uuid": "uuid", "status": "Published"}
-        >>> vc = ViewConfBuilder(entity=entity, nexus_token='nexus_token', is_mock=True)
+        >>> vc = ViewConfBuilder(entity=entity, groups_token='groups_token', is_mock=True)
         >>> assert vc._get_request_init() is None # None because dataset is Published (public)
         """
-        request_init = {"headers": {"Authorization": f"Bearer {self._nexus_token}"}}
+        request_init = {"headers": {"Authorization": f"Bearer {self._groups_token}"}}
         # Extra headers outside of a select few cause extra CORS-preflight requests which
         # can slow down the webpage.  If the dataset is published, we don't need to use
         # heaeder to authenticate access to the assets API.
@@ -113,7 +116,7 @@ def _get_file_paths(self):
 
         >>> files = [{ "rel_path": "path/to/file" }, { "rel_path": "path/to/other_file" }]
         >>> entity = {"uuid": "uuid", "files": files}
-        >>> vc = ViewConfBuilder(entity=entity, nexus_token='nexus_token', is_mock=True)
+        >>> vc = ViewConfBuilder(entity=entity, groups_token='groups_token', is_mock=True)
         >>> vc._get_file_paths()
         ['path/to/file', 'path/to/other_file']
         """
@@ -130,11 +133,11 @@ def _get_img_and_offset_url(self, img_path, img_dir):
 
         >>> from pprint import pprint
         >>> vc = AbstractImagingViewConfBuilder(entity={ "uuid": "uuid" },\
-            nexus_token='nexus_token', is_mock=True)
+            groups_token='groups_token', is_mock=True)
         >>> pprint(vc._get_img_and_offset_url("rel_path/to/clusters.ome.tiff",\
             "rel_path/to"))
-        ('https://example.com/uuid/rel_path/to/clusters.ome.tiff?token=nexus_token',\n\
-         'https://example.com/uuid/output_offsets/clusters.offsets.json?token=nexus_token')
+        ('https://example.com/uuid/rel_path/to/clusters.ome.tiff?token=groups_token',\n\
+         'https://example.com/uuid/output_offsets/clusters.offsets.json?token=groups_token')
 
         """
         img_url = self._build_assets_url(img_path)
@@ -159,13 +162,13 @@ def _setup_view_config_raster(self, vc, dataset, disable_3d=[]):
 
 
 class ImagePyramidViewConfBuilder(AbstractImagingViewConfBuilder):
-    def __init__(self, entity, nexus_token, is_mock=False):
+    def __init__(self, entity, groups_token, is_mock=False):
         """Wrapper class for creating a standard view configuration for image pyramids,
         i.e for high resolution viz-lifted imaging datasets like
         https://portal.hubmapconsortium.org/browse/dataset/dc289471333309925e46ceb9bafafaf4
         """
         self.image_pyramid_regex = IMAGE_PYRAMID_DIR
-        super().__init__(entity, nexus_token, is_mock)
+        super().__init__(entity, groups_token, is_mock)
 
     def get_conf_cells(self):
         file_paths_found = self._get_file_paths()
@@ -269,9 +272,9 @@ class SPRMJSONViewConfBuilder(SPRMViewConfBuilder):
     https://portal.hubmapconsortium.org/browse/dataset/dc31a6d06daa964299224e9c8d6cafb3
     """
 
-    def __init__(self, entity, nexus_token, is_mock=False, **kwargs):
+    def __init__(self, entity, groups_token, is_mock=False, **kwargs):
         # All "file" Vitessce objects that do not have wrappers.
-        super().__init__(entity, nexus_token, is_mock)
+        super().__init__(entity, groups_token, is_mock)
         # These are both something like R001_X009_Y009 because
         # there is no mask used here or shared name with the mask data.
         self._base_name = kwargs["base_name"]
@@ -348,8 +351,8 @@ class SPRMAnnDataViewConfBuilder(SPRMViewConfBuilder):
     of the image and mask relative to image_pyramid_regex
     """
 
-    def __init__(self, entity, nexus_token, is_mock=False, **kwargs):
-        super().__init__(entity, nexus_token, is_mock)
+    def __init__(self, entity, groups_token, is_mock=False, **kwargs):
+        super().__init__(entity, groups_token, is_mock)
         self._base_name = kwargs["base_name"]
         self._mask_name = kwargs["mask_name"]
         self._image_name = kwargs["image_name"]

context/app/api/vitessce_confs/fixtures/output_expected/atac_conf.json

@@ -8,12 +8,12 @@
       "name": "Visualization Files",
       "files": [
         {
-          "url": "https://example.com/210d118a14c8624b6bb9610a9062656e/output/umap_coords_clusters.cells.json?token=nexus_token",
+          "url": "https://example.com/210d118a14c8624b6bb9610a9062656e/output/umap_coords_clusters.cells.json?token=groups_token",
           "type": "cells",
           "fileType": "cells.json"
         },
         {
-          "url": "https://example.com/210d118a14c8624b6bb9610a9062656e/output/umap_coords_clusters.cell-sets.json?token=nexus_token",
+          "url": "https://example.com/210d118a14c8624b6bb9610a9062656e/output/umap_coords_clusters.cell-sets.json?token=groups_token",
           "type": "cell-sets",
           "fileType": "cell-sets.json"
         }

context/app/api/vitessce_confs/fixtures/output_expected/cytokit_anndata_conf.json

@@ -27,7 +27,7 @@
             },
             "requestInit": {
               "headers": {
-                "Authorization": "Bearer nexus_token"
+                "Authorization": "Bearer groups_token"
               }
             }
           },
@@ -67,7 +67,7 @@
             ],
             "requestInit": {
               "headers": {
-                "Authorization": "Bearer nexus_token"
+                "Authorization": "Bearer groups_token"
               }
             }
           },
@@ -80,7 +80,7 @@
             },
             "requestInit": {
               "headers": {
-                "Authorization": "Bearer nexus_token"
+                "Authorization": "Bearer groups_token"
               }
             }
           },
@@ -95,19 +95,19 @@
                 {
                   "name": "reg1_stitched_expressions",
                   "type": "ome-tiff",
-                  "url": "https://example.com/2f8d43199ca3167e991b320038024b77/ometiff-pyramids/stitched/expressions/reg1_stitched_expressions.ome.tiff?token=nexus_token",
+                  "url": "https://example.com/2f8d43199ca3167e991b320038024b77/ometiff-pyramids/stitched/expressions/reg1_stitched_expressions.ome.tiff?token=groups_token",
                   "metadata": {
                     "isBitmask": false,
-                    "omeTiffOffsetsUrl": "https://example.com/2f8d43199ca3167e991b320038024b77/output_offsets/stitched/expressions/reg1_stitched_expressions.offsets.json?token=nexus_token"
+                    "omeTiffOffsetsUrl": "https://example.com/2f8d43199ca3167e991b320038024b77/output_offsets/stitched/expressions/reg1_stitched_expressions.offsets.json?token=groups_token"
                   }
                 },
                 {
                   "name": "reg1_stitched_mask",
                   "type": "ome-tiff",
-                  "url": "https://example.com/2f8d43199ca3167e991b320038024b77/ometiff-pyramids/stitched/mask/reg1_stitched_mask.ome.tiff?token=nexus_token",
+                  "url": "https://example.com/2f8d43199ca3167e991b320038024b77/ometiff-pyramids/stitched/mask/reg1_stitched_mask.ome.tiff?token=groups_token",
                   "metadata": {
                     "isBitmask": true,
-                    "omeTiffOffsetsUrl": "https://example.com/2f8d43199ca3167e991b320038024b77/output_offsets/stitched/mask/reg1_stitched_mask.offsets.json?token=nexus_token"
+                    "omeTiffOffsetsUrl": "https://example.com/2f8d43199ca3167e991b320038024b77/output_offsets/stitched/mask/reg1_stitched_mask.offsets.json?token=groups_token"
                   }
                 }
               ]
@@ -229,7 +229,7 @@
             },
             "requestInit": {
               "headers": {
-                "Authorization": "Bearer nexus_token"
+                "Authorization": "Bearer groups_token"
               }
             }
           },
@@ -269,7 +269,7 @@
             ],
             "requestInit": {
               "headers": {
-                "Authorization": "Bearer nexus_token"
+                "Authorization": "Bearer groups_token"
               }
             }
           },
@@ -282,7 +282,7 @@
             },
             "requestInit": {
               "headers": {
-                "Authorization": "Bearer nexus_token"
+                "Authorization": "Bearer groups_token"
               }
             }
           },
@@ -297,19 +297,19 @@
                 {
                   "name": "reg2_stitched_expressions",
                   "type": "ome-tiff",
-                  "url": "https://example.com/2f8d43199ca3167e991b320038024b77/ometiff-pyramids/stitched/expressions/reg2_stitched_expressions.ome.tiff?token=nexus_token",
+                  "url": "https://example.com/2f8d43199ca3167e991b320038024b77/ometiff-pyramids/stitched/expressions/reg2_stitched_expressions.ome.tiff?token=groups_token",
                   "metadata": {
                     "isBitmask": false,
-                    "omeTiffOffsetsUrl": "https://example.com/2f8d43199ca3167e991b320038024b77/output_offsets/stitched/expressions/reg2_stitched_expressions.offsets.json?token=nexus_token"
+                    "omeTiffOffsetsUrl": "https://example.com/2f8d43199ca3167e991b320038024b77/output_offsets/stitched/expressions/reg2_stitched_expressions.offsets.json?token=groups_token"
                   }
                 },
                 {
                   "name": "reg2_stitched_mask",
                   "type": "ome-tiff",
-                  "url": "https://example.com/2f8d43199ca3167e991b320038024b77/ometiff-pyramids/stitched/mask/reg2_stitched_mask.ome.tiff?token=nexus_token",
+                  "url": "https://example.com/2f8d43199ca3167e991b320038024b77/ometiff-pyramids/stitched/mask/reg2_stitched_mask.ome.tiff?token=groups_token",
                   "metadata": {
                     "isBitmask": true,
-                    "omeTiffOffsetsUrl": "https://example.com/2f8d43199ca3167e991b320038024b77/output_offsets/stitched/mask/reg2_stitched_mask.offsets.json?token=nexus_token"
+                    "omeTiffOffsetsUrl": "https://example.com/2f8d43199ca3167e991b320038024b77/output_offsets/stitched/mask/reg2_stitched_mask.offsets.json?token=groups_token"
                   }
                 }
               ]