Merged main and fixed readme

hubmapconsortium · Dec 18, 2024 · 3a26b2d · 3a26b2d
2 parents 76eb0c3 + e84b829
commit 3a26b2d
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diff --git a/README.md b/README.md
@@ -21,27 +21,25 @@ $ cd portal-visualization
 $ 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] [--parent_uuid UUID]
+usage: vis-preview.py [-h] (--url URL | --json JSON) [--assets_url URL]
+                      [--token TOKEN] [--marker MARKER] [--to_json]
+                      [--epic_uuid UUID] [--parent_uuid UUID]
 
 Given HuBMAP Dataset JSON, generate a Vitessce viewconf, and load vitessce.io.
 
 options:
-  -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.dev.hubmapconsortium.org/assaytype/
-  --assets_url URL      Assets endpoint; default:
-                        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.
+  -h, --help          show this help message and exit
+  --url URL           URL which returns Dataset JSON
+  --json JSON         File containing Dataset JSON
+  --assets_url URL    Assets endpoint; default:
+                      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.
   ```
 
 

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-0.2.9
+0.3.6
diff --git a/src/defaults.json b/src/defaults.json
@@ -1,5 +1,4 @@
 {
   "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/"
 }
diff --git a/src/portal_visualization/builder_factory.py b/src/portal_visualization/builder_factory.py
@@ -52,14 +52,11 @@ def process_hints(hints):
 # It returns the correct builder for the given entity.
 #
 # 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, epic_uuid=None):
+def get_view_config_builder(entity, get_entity, parent=None, epic_uuid=None):
     if entity.get("uuid") is None:
         raise ValueError("Provided entity does not have a uuid")
-    assay = get_assaytype(entity.get('uuid'))
-    assay_name = assay.get("assaytype")
-    hints = assay.get("vitessce-hints", [])
+    assay_name = entity.get("soft_assaytype")
+    hints = entity.get("vitessce-hints", [])
     (
         is_image,
         is_rna,
@@ -79,7 +76,7 @@ def get_view_config_builder(entity, get_assaytype, parent=None, epic_uuid=None):
             return SegImagePyramidViewConfBuilder
 
         elif is_support and is_image:
-            ancestor_assaytype = get_assaytype(parent).get("assaytype")
+            ancestor_assaytype = get_entity(parent).get("soft_assaytype")
             if SEQFISH == ancestor_assaytype:
                 # e.g. parent  = c6a254b2dc2ed46b002500ade163a7cc
                 # e.g. support = 9db61adfc017670a196ea9b3ca1852a0
@@ -138,6 +135,6 @@ def get_view_config_builder(entity, get_assaytype, parent=None, epic_uuid=None):
     return NullViewConfBuilder
 
 
-def has_visualization(entity, get_assaytype, parent=None, epic_uuid=None):
-    builder = get_view_config_builder(entity, get_assaytype, parent, epic_uuid)
+def has_visualization(entity, get_entity, parent=None, epic_uuid=None):
+    builder = get_view_config_builder(entity, get_entity, parent, epic_uuid)
     return builder != NullViewConfBuilder
diff --git a/src/portal_visualization/client.py b/src/portal_visualization/client.py
@@ -246,7 +246,11 @@ def get_vitessce_conf_cells_and_lifted_uuid(
         # Otherwise, just try to visualize the data for the entity itself:
         else:  # pragma: no cover  # We have separate tests for the builder logic
             try:
-                Builder = get_view_config_builder(entity, self._get_assaytype(), parent, epic_uuid)
+                def get_entity(entity):
+                    if (type(entity) is str):
+                        return self.get_entity(uuid=entity)
+                    return self.get_entity(uuid=entity.get('uuid'))
+                Builder = get_view_config_builder(entity, get_entity, parent, epic_uuid)
                 builder = Builder(entity, self.groups_token, self.assets_endpoint)
                 vitessce_conf = builder.get_conf_cells(marker=marker)
             except Exception as e:
@@ -272,42 +276,6 @@ def get_vitessce_conf_cells_and_lifted_uuid(
             vitessce_conf=vitessce_conf, vis_lifted_uuid=vis_lifted_uuid
         )
 
-    # Helper to create a function that fetches assaytype from the API with current headers
-    def _get_assaytype(self):  # pragma: no cover
-        def get_assaytype(param):
-            if isinstance(param, str):
-                uuid = param
-            else:
-                uuid = param.get("uuid")
-
-            url = f"{self.soft_assay_url}/{uuid}"
-            headers = self._get_headers()
-            try:
-                response = requests.get(url, headers=headers)
-                return response.json()
-            except Exception as e:
-                # Redact Authorization header from logs
-                cleaned_headers = self._clean_headers(headers)
-                if response:
-                    status = response.status_code
-                else:
-                    status = None
-                current_app.logger.error(
-                    {
-                        "source": "get_assaytype",
-                        "url": url,
-                        "headers": cleaned_headers,
-                        "status": status,
-                        "error": str(e),
-                    }
-                )
-                current_app.logger.error(
-                    f"Fetching assaytype threw error: {traceback.format_exc()}"
-                )
-                raise e
-
-        return get_assaytype
-
     def _file_request(self, url):
         headers = (
             {"Authorization": "Bearer " + self.groups_token}

diff --git a/src/vis-preview.py b/src/vis-preview.py
@@ -16,7 +16,6 @@
 def main():  # pragma: no cover
     defaults = json.load((Path(__file__).parent / 'defaults.json').open())
     assets_default_url = defaults['assets_url']
-    assaytypes_default_url = defaults['assaytypes_url']
 
     parser = argparse.ArgumentParser(description='''
         Given HuBMAP Dataset JSON, generate a Vitessce viewconf, and load vitessce.io.''')
@@ -26,10 +25,6 @@ def main():  # pragma: no cover
     input.add_argument(
         '--json', type=Path, help='File containing Dataset JSON')
 
-    parser.add_argument(
-        '--assaytypes_url', metavar='URL',
-        help=f'AssayType service; default: {assaytypes_default_url}',
-        default=assaytypes_default_url)
     parser.add_argument(
         '--assets_url', metavar='URL',
         help=f'Assets endpoint; default: {assets_default_url}',
@@ -60,21 +55,7 @@ def main():  # pragma: no cover
     headers = get_headers(args.token)
     entity = get_entity(args.url, args.json, headers)
 
-    def get_assaytype(uuid):
-        try:
-            response = requests.get(f'{defaults["assaytypes_url"]}{uuid}', headers=headers)
-            if response.status_code != 200:
-                print(f"Error: Received status code {response.status_code}")
-            else:
-                try:
-                    data = response.json()
-                    return data
-                except Exception as e:
-                    print(f"Error in parsing the response {str(e)}")
-        except Exception as e:
-            print(f"Error accessing {defaults['assaytypes_url']}{uuid}: {str(e)}")
-
-    Builder = get_view_config_builder(entity, get_assaytype, parent_uuid, epic_uuid)
+    Builder = get_view_config_builder(entity, get_entity, parent_uuid, epic_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)

diff --git a/test/assaytype-fixtures/04e7385339167e541ad42a2636e18398.json b/test/assaytype-fixtures/04e7385339167e541ad42a2636e18398.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "codex_cytokit_v1",
-    "contains-pii": false,
-    "description": "CODEX [Cytokit + SPRM]",
-    "primary": false,
+    "soft_assaytype": "codex_cytokit_v1",
     "vitessce-hints": [
       "codex",
       "is_image",

diff --git a/test/assaytype-fixtures/210d118a14c8624b6bb9610a9062656e.json b/test/assaytype-fixtures/210d118a14c8624b6bb9610a9062656e.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "sn_atac_seq",
-    "contains-pii": false,
-    "description": "snATAC-seq [SnapATAC]",
-    "primary": false,
+    "soft_assaytype": "sn_atac_seq",
     "vitessce-hints": [
       "is_sc",
       "atac"

diff --git a/test/assaytype-fixtures/272789a950b2b5d4b9387a1cf66ad487.json b/test/assaytype-fixtures/272789a950b2b5d4b9387a1cf66ad487.json
@@ -1,9 +1,5 @@
 {
-    "assaytype": "multiome-10x",
-    "contains-pii": false,
-    "description": "10X Multiome [Salmon + ArchR + Muon]",
-    "is-multi-assay": true,
-    "primary": false,
+    "soft_assaytype": "multiome-10x",
     "vitessce-hints": [
       "is_sc",
       "rna",

diff --git a/test/assaytype-fixtures/2a590db3d7ab1e1512816b165d95cdcf.json b/test/assaytype-fixtures/2a590db3d7ab1e1512816b165d95cdcf.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "salmon_rnaseq_slideseq",
-    "contains-pii": false,
-    "description": "Slide-seq [Salmon]",
-    "primary": false,
+    "soft_assaytype": "salmon_rnaseq_slideseq",
     "vitessce-hints": [
       "is_sc",
       "rna"

diff --git a/test/assaytype-fixtures/2c2179ea741d3bbb47772172a316a2bf.json b/test/assaytype-fixtures/2c2179ea741d3bbb47772172a316a2bf.json
@@ -1,9 +1,4 @@
 {
-    "assaytype": "bulk-RNA",
-    "contains-pii": true,
-    "description": "Bulk RNA-seq",
-    "dir-schema": "bulkrnaseq-v0",
-    "primary": true,
-    "tbl-schema": "bulkrnaseq-v0",
+    "soft_assaytype": "bulk-RNA",
     "vitessce-hints": []
   }
diff --git a/test/assaytype-fixtures/3bc3ad124014a632d558255626bf38c9.json b/test/assaytype-fixtures/3bc3ad124014a632d558255626bf38c9.json
@@ -1,10 +1,5 @@
 {
-    "assaytype": "MALDI-IMS",
-    "contains-pii": false,
-    "description": "MALDI IMS",
-    "dir-schema": "ims-v0",
-    "primary": true,
-    "tbl-schema": "ims-v2",
+    "soft_assaytype": "MALDI-IMS",
     "vitessce-hints": [
       "maldi"
     ]

diff --git a/test/assaytype-fixtures/43213991a54ce196d406707ffe2e86bd.json b/test/assaytype-fixtures/43213991a54ce196d406707ffe2e86bd.json
@@ -1,8 +1,5 @@
 {
-  "assaytype": "codex_cytokit_v1",
-  "contains-pii": false,
-  "description": "CODEX [Cytokit + SPRM]",
-  "primary": false,
+  "soft_assaytype": "codex_cytokit_v1",
   "vitessce-hints": [
     "codex",
     "is_image",

diff --git a/test/assaytype-fixtures/6b93107731199733f266bbd0f3bc9747.json b/test/assaytype-fixtures/6b93107731199733f266bbd0f3bc9747.json
@@ -1,9 +1,4 @@
 {
-  "assaytype": "NanoDESI",
-  "contains-pii": false,
-  "description": "NanoDESI",
-  "dir-schema": "ims-v0",
-  "primary": true,
-  "tbl-schema": "ims-v2",
+  "soft_assaytype": "NanoDESI",
   "vitessce-hints": []
 }
diff --git a/test/assaytype-fixtures/72ec02cf1390428c1e9dc2c88928f5f5.json b/test/assaytype-fixtures/72ec02cf1390428c1e9dc2c88928f5f5.json
@@ -1,9 +1,5 @@
 {
-    "assaytype": "visium-no-probes",
-    "contains-pii": false,
-    "description": "Visium (no probes) [Salmon + Scanpy]",
-    "is-multi-assay": true,
-    "primary": false,
+    "soft_assaytype": "visium-no-probes",
     "vitessce-hints": [
       "rna",
       "is_image",

diff --git a/test/assaytype-fixtures/8adc3c31ca84ec4b958ed20a7c4f4919.json b/test/assaytype-fixtures/8adc3c31ca84ec4b958ed20a7c4f4919.json
@@ -1,10 +1,4 @@
 {
-    "assaytype": "PAS",
-    "contains-pii": false,
-    "dataset-type": "Histology",
-    "description": "PAS Stained Microscopy",
-    "dir-schema": "stained-v0",
-    "primary": true,
-    "tbl-schema": "stained-v0",
+    "soft_assaytype": "PAS",
     "vitessce-hints": []
   }
diff --git a/test/assaytype-fixtures/9db61adfc017670a196ea9b3ca1852a0.json b/test/assaytype-fixtures/9db61adfc017670a196ea9b3ca1852a0.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "image_pyramid",
-    "contains-pii": false,
-    "description": "Image Pyramid",
-    "primary": false,
+    "soft_assaytype": "image_pyramid",
     "vitessce-hints": [
       "is_image",
       "pyramid",

diff --git a/test/assaytype-fixtures/a6116772446f6d1c1f6b3d2e9735cfe0.json b/test/assaytype-fixtures/a6116772446f6d1c1f6b3d2e9735cfe0.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "image_pyramid",
-    "contains-pii": false,
-    "description": "Image Pyramid",
-    "primary": false,
+    "soft_assaytype": "image_pyramid",
     "vitessce-hints": [
       "is_image",
       "pyramid",

diff --git a/test/assaytype-fixtures/b69d1e2ad1bf1455eee991fce301b191.json b/test/assaytype-fixtures/b69d1e2ad1bf1455eee991fce301b191.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "codex_cytokit_v1",
-    "contains-pii": false,
-    "description": "CODEX [Cytokit + SPRM]",
-    "primary": false,
+    "soft_assaytype": "codex_cytokit_v1",
     "vitessce-hints": [
       "codex",
       "is_image",

diff --git a/test/assaytype-fixtures/c019a1cd35aab4d2b4a6ff221e92aaab.json b/test/assaytype-fixtures/c019a1cd35aab4d2b4a6ff221e92aaab.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "salmon_sn_rnaseq_10x",
-    "contains-pii": false,
-    "description": "snRNA-seq [Salmon]",
-    "primary": false,
+    "soft_assaytype": "salmon_sn_rnaseq_10x",
     "vitessce-hints": [
       "is_sc",
       "rna",

diff --git a/test/assaytype-fixtures/c3be5650e93907b68ddbdb22b948db32.json b/test/assaytype-fixtures/c3be5650e93907b68ddbdb22b948db32.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "celldive_deepcell",
-    "contains-pii": false,
-    "description": "CellDIVE [DeepCell + SPRM]",
-    "primary": false,
+    "soft_assaytype": "celldive_deepcell",
     "vitessce-hints": [
       "sprm",
       "anndata",

diff --git a/test/assaytype-fixtures/c6a254b2dc2ed46b002500ade163a7cc.json b/test/assaytype-fixtures/c6a254b2dc2ed46b002500ade163a7cc.json
@@ -1,9 +1,4 @@
 {
-    "assaytype": "seqFish",
-    "contains-pii": false,
-    "description": "seqFISH",
-    "dir-schema": "seqfish-v0",
-    "primary": true,
-    "tbl-schema": "seqfish-v0",
+    "soft_assaytype": "seqFish",
     "vitessce-hints": []
   }
diff --git a/test/assaytype-fixtures/d4493657cde29702c5ed73932da5317c.json b/test/assaytype-fixtures/d4493657cde29702c5ed73932da5317c.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "sc_atac_seq_sci",
-    "contains-pii": false,
-    "description": "sciATAC-seq [SnapATAC]",
-    "primary": false,
+    "soft_assaytype": "sc_atac_seq_sci",
     "vitessce-hints": [
       "is_sc",
       "atac"

diff --git a/test/assaytype-fixtures/df7cac7cb67a822f7007b57c4d8f5e7d.json b/test/assaytype-fixtures/df7cac7cb67a822f7007b57c4d8f5e7d.json
@@ -1,9 +1,3 @@
 {
-    "contains-pii": false,
-    "dataset-type": "Histology",
-    "description": "Segmentation Mask",
-    "dir-schema": "stained-v0",
-    "primary": true,
-    "tbl-schema": "stained-v0",
-    "vitessce-hints":  ["segmentation_mask","is_image","pyramid"]
-  }
+  "vitessce-hints": ["segmentation_mask", "is_image", "pyramid"]
+}
diff --git a/test/assaytype-fixtures/e1c4370da5523ab5c9be581d1d76ca20.json b/test/assaytype-fixtures/e1c4370da5523ab5c9be581d1d76ca20.json
@@ -1,8 +1,5 @@
 {
-    "assaytype": "image_pyramid",
-    "contains-pii": false,
-    "description": "Image Pyramid",
-    "primary": false,
+    "soft_assaytype": "image_pyramid",
     "vitessce-hints": [
       "is_image",
       "pyramid",