#14 enabled new annotations

Due to issue with opening annotation files with "-" in the name, this doesn't quite work.

cellxgene_gateway/path_util.py

@@ -13,37 +13,81 @@ from flask_api import status
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
+from cellxgene_gateway.dir_util import make_h5ad
+from cellxgene_gateway.cache_key import CacheKey
 
-
-def get_dataset(path):
+def get_key(path):
     if path == "/" or path == "":
         raise CellxgeneException(
             "No matching dataset found.", status.HTTP_404_NOT_FOUND
         )
 
     trimmed = path[:-1] if path[-1] == "/" else path
-
     try:
-        get_file_path(trimmed)
-        return trimmed
+        # valid paths come in three forms:
+        if trimmed.endswith('.h5ad') and data_file_exists(trimmed):
+            # 1) somedir/dataset.h5ad: a dataset
+            return CacheKey(trimmed, trimmed, None)
+        elif trimmed.endswith('.csv') and data_file_exists(trimmed):
+
+            # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotaitons file.
+            annotations_dir = os.path.split(trimmed)[0]
+            dataset = make_h5ad(annotations_dir)
+            if data_file_exists(dataset):
+                return CacheKey(trimmed, dataset, trimmed)
+        elif trimmed.endswith('_annotations') and data_dir_exists(trimmed):
+            # 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
+            dataset = make_h5ad(trimmed)
+            if data_file_exists(dataset):
+                return CacheKey(trimmed, dataset, '')
     except CellxgeneException:
-        split = os.path.split(trimmed)
-        return get_dataset(split[0])
+        pass
+    split = os.path.split(trimmed)
+    return get_key(split[0])
 
-
-def validate_path(file_path):
+def validate_exists(file_path):
     if not os.path.exists(file_path):
         raise CellxgeneException(
             "File does not exist: " + file_path, status.HTTP_400_BAD_REQUEST
         )
+
+def validate_is_file(file_path):
+    validate_exists(file_path)
     if not os.path.isfile(file_path):
         raise CellxgeneException(
             "Path is not file: " + file_path, status.HTTP_400_BAD_REQUEST
         )
     return
+def validate_is_dir(file_path):
+    validate_exists(file_path)
+    if not os.path.isdir(file_path):
+        raise CellxgeneException(
+            "Path is not dir: " + file_path, status.HTTP_400_BAD_REQUEST
+        )
+    return
 
-
-def get_file_path(dataset):
+def data_file_exists(dataset):
     file_path = os.path.join(env.cellxgene_data, dataset)
-    validate_path(file_path)
+    validate_is_file(file_path)
+    return True
+def data_dir_exists(dataset):
+    file_path = os.path.join(env.cellxgene_data, dataset)
+    validate_is_dir(file_path)
+    return True
+
+def get_file_path(key):
+    dataset = key.dataset
+    file_path = os.path.join(env.cellxgene_data, dataset)
+    validate_is_file(file_path)
+    return file_path
+
+def get_annotation_file_path(key):
+    print(f"getting annotaiton_file_path for {key.annotation_file}")
+    if key.annotation_file is None:
+        return None
+    if key.annotation_file == '':
+        return ''
+    file_path = os.path.join(env.cellxgene_data, key.annotation_file)
+    print(f"getting annotaiton_file_path for {key}, file_path {file_path}")
+    validate_is_file(file_path)
     return file_path