Raise if allen api human microarray services down

Author: AhmetNSimsek

docs/conf.py

@@ -16,13 +16,17 @@
 import sphinx_rtd_theme  # this import must be kept to make sphinx_rtd_theme function
 import sphinx_autopackagesummary  # this import must be kept to make autopackagesummary function
 
+print("sphinx-rtd-theme:", sphinx_rtd_theme.__version__)
+print("sphinx-autopackagesummary", sphinx_autopackagesummary.__version__)
+
 os.environ['SIIBRA_LOG_LEVEL'] = "ERROR"
 sys.path.insert(0, os.path.abspath(".."))
 print("Path:", sys.path)
 
+
 def is_allen_api_microarray_service_available():
     import requests
-    
+
     # see https://community.brain-map.org/t/human-brain-atlas-api/2876
     microarray_test_url = "http://api.brain-map.org/api/v2/data/query.json?criteria= service::human_microarray_expression[probes$eq1023146,1023147][donors$eq15496][structures$eq9148]"
     try:
@@ -31,6 +35,7 @@ def is_allen_api_microarray_service_available():
         return False
     return response["success"]
 
+
 # -- Project information -----------------------------------------------------
 
 project = "siibra-python"

examples/03_data_features/000_matchings.py

@@ -138,5 +138,12 @@
 # For example, the gene expressions retrieved from the Allen atlas are linked by the coordinate
 # For example, the gene expressions retrieved from the Allen atlas are linked by the coordinate
 # of their tissue probes in MNI space. If a coordinate is inside the selected brain regions, it is an exact match.
+#
+# .. warning::
+#     The service "web API of the Allen Brain Atlas for the human microarray expression"
+#     is not available at the moment, therefore siibra is not able to fetch
+#     gene expression features. This is a known issue which we are investigating:
+#     https://github.com/FZJ-INM1-BDA/siibra-python/issues/636.
+#
 features = siibra.features.get(v1, siibra.features.molecular.GeneExpressions, gene="TAC1")
 print(features[0].last_match_description)

examples/03_data_features/004_gene_expressions.py

@@ -17,6 +17,12 @@
 Gene expressions
 ~~~~~~~~~~~~~~~~
 
+.. warning::
+    The service "web API of the Allen Brain Atlas for the human microarray expression"
+    is not available at the moment, therefore siibra is not able to fetch
+    gene expression features. This is a known issue which we are investigating:
+    https://github.com/FZJ-INM1-BDA/siibra-python/issues/636.
+
 ``siibra`` can query gene expression data from the Allen brain atlas. The gene
 expressions are linked to atlas regions by coordinates of their probes in MNI
 space. When querying feature by a region,  ``siibra`` automatically builds a

siibra/livequeries/allen.py

@@ -35,6 +35,18 @@
 LOCATION_PRECISION_MM = 2.  # the assumed spatial precision of the probe locations in MNI space
 
 
+def is_allen_api_microarray_service_available():
+    import requests
+
+    # see https://community.brain-map.org/t/human-brain-atlas-api/2876
+    microarray_test_url = "http://api.brain-map.org/api/v2/data/query.json?criteria= service::human_microarray_expression[probes$eq1023146,1023147][donors$eq15496][structures$eq9148]"
+    try:
+        response = requests.get(microarray_test_url).json()
+    except requests.RequestException:
+        return False
+    return response["success"]
+
+
 class InvalidAllenAPIResponseException(Exception):
     pass
 
@@ -124,6 +136,13 @@ def parse_gene(spec):
         self.genes = parse_gene(gene)
 
     def query(self, concept: structure.BrainStructure) -> List[GeneExpressions]:
+        if not is_allen_api_microarray_service_available():
+            raise InvalidAllenAPIResponseException(
+                'The service "web API of the Allen Brain Atlas for the human microarray expression" '
+                'is not available at the moment, therefore siibra is not able to fetch '
+                'gene expression features. This is a known issue which we are investigating: '
+                'https://github.com/FZJ-INM1-BDA/siibra-python/issues/636.'
+            )
 
         mnispace = _space.Space.registry().get('mni152')