Don't error out in rma_all for incomplete response

src/atldld/requests.py

@@ -181,14 +181,29 @@ def rma_all(rma_parameters: RMAParameters) -> list:
                 f'Expected total_rows to be {total_rows} but got {status["total_rows"]}'
             )
 
-        # Each new request should yield new data. If no data was received, then
-        # something must have gone wrong.
+        # We haven't got all the rows yet, but the query yielded zero results.
+        # This could be due to an arbitrary server-side problem, but we know
+        # of at least one query for which the number of returned results is
+        # consistently smaller than the number of reported results:
+        # RMAParameters(
+        #     "SectionDataSet",
+        #     criteria={
+        #         "specimen": {"donor": {"age": {"days": 56}}},
+        #         "probes": {"orientation": {"name": "Antisense"}}
+        #     },
+        # )
+        # this gives total_rows=50476 but len(msg)=50274.
+        # Previously we would raise an error when this happened, but since this
+        # is reproducible we now only print a warning.
         if status["num_rows"] == 0:
-            raise RuntimeError("No data received")
+            break
 
         pos += status["num_rows"]
         msg += new_msg
 
+    if not len(msg) == total_rows:
+        logger.warning("The server sent only %d of %d results", len(msg), total_rows)
+
     return msg
 
 

tests/test_requests.py

@@ -14,6 +14,7 @@
 #
 # You should have received a copy of the GNU Lesser General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
+import logging
 import re
 
 import pytest
@@ -241,7 +242,7 @@ def test_inconsistent_total_rows(self):
             rma_all(params)
 
     @responses.activate
-    def test_no_data_received(self):
+    def test_incomplete_data_received(self, caplog):
         params = RMAParameters("my-model")
         # Can at most fetch 25_000 in one request
         msg = list(range(26_000))
@@ -259,12 +260,14 @@ def test_no_data_received(self):
             "success": True,
             "id": 0,
             "start_row": len(msg_1),
-            "num_rows": 0,  # this should always be greater than 0
+            "num_rows": 0,  # this should normally always be greater than 0
             "total_rows": len(msg),
             "msg": msg_2,
         }
         responses.add(responses.GET, re.compile(""), json=return_json_1)
         responses.add(responses.GET, re.compile(""), json=return_json_2)
 
-        with pytest.raises(RuntimeError, match="No data received"):
+        with caplog.at_level(logging.WARNING, logger="atldld.requests"):
             rma_all(params)
+
+        assert "The server sent only" in caplog.text