Change query-datasets command-line to use the butler it creates

Without this change the chained datastore created and populated
is not used in the actual chaining test and so the tests are
not testing what it is stated to test.

tests/config/basic/posixDatastore2.yaml

@@ -23,3 +23,4 @@ datastore:
     StructuredDataPickle: lsst.daf.butler.formatters.pickle.PickleFormatter
     ThingOne: lsst.daf.butler.formatters.pickle.PickleFormatter
     MetricsConversion: lsst.daf.butler.formatters.json.JsonFormatter
+    StructuredDataDataTest: lsst.daf.butler.tests.testFormatters.MetricsExampleDataFormatter

tests/test_cliCmdQueryDatasets.py

@@ -157,8 +157,8 @@ def _queryDatasets(
             find_first=find_first,
             show_uri=show_uri,
             limit=limit,
-            repo=repo,
             order_by=order_by,
+            butler=repo,
         )
         return list(query.getTables())
 
@@ -174,9 +174,11 @@ def testChained(self):
             self.repoDir, configFile=os.path.join(TESTDIR, "config/basic/butler-chained.yaml")
         )
 
-        tables = self._queryDatasets(repo=self.repoDir, show_uri=True)
+        tables = self._queryDatasets(repo=testRepo.butler, show_uri=True)
 
-        # Want second datastore root.
+        # Want second datastore root since in-memory is ephemeral and
+        # all the relevant datasets are stored in the second as well as third
+        # datastore.
         roots = testRepo.butler.get_datastore_roots()
         datastore_root = roots[testRepo.butler.get_datastore_names()[1]]
 
@@ -190,7 +192,7 @@ def testShowURI(self):
         """Test for expected output with show_uri=True."""
         testRepo = MetricTestRepo(self.repoDir, configFile=self.configFile)
 
-        tables = self._queryDatasets(repo=self.repoDir, show_uri=True)
+        tables = self._queryDatasets(repo=testRepo.butler, show_uri=True)
 
         roots = testRepo.butler.get_datastore_roots()
         datastore_root = list(roots.values())[0]
@@ -201,9 +203,9 @@ def testShowURI(self):
 
     def testNoShowURI(self):
         """Test for expected output without show_uri (default is False)."""
-        _ = MetricTestRepo(self.repoDir, configFile=self.configFile)
+        testRepo = MetricTestRepo(self.repoDir, configFile=self.configFile)
 
-        tables = self._queryDatasets(repo=self.repoDir)
+        tables = self._queryDatasets(repo=testRepo.butler)
 
         expectedTables = (
             AstropyTable(
@@ -223,9 +225,9 @@ def testWhere(self):
         """Test using the where clause to reduce the number of rows returned by
         queryDatasets.
         """
-        _ = MetricTestRepo(self.repoDir, configFile=self.configFile)
+        testRepo = MetricTestRepo(self.repoDir, configFile=self.configFile)
 
-        tables = self._queryDatasets(repo=self.repoDir, where="instrument='DummyCamComp' AND visit=423")
+        tables = self._queryDatasets(repo=testRepo.butler, where="instrument='DummyCamComp' AND visit=423")
 
         expectedTables = (
             AstropyTable(
@@ -237,7 +239,7 @@ def testWhere(self):
         self.assertAstropyTablesEqual(tables, expectedTables, filterColumns=True)
 
         with self.assertRaises(RuntimeError):
-            self._queryDatasets(repo=self.repoDir, collections="*", find_first=True)
+            self._queryDatasets(repo=testRepo.butler, collections="*", find_first=True)
 
     def testGlobDatasetType(self):
         """Test specifying dataset type."""
@@ -262,7 +264,7 @@ def testGlobDatasetType(self):
         testRepo.addDataset(dataId={"instrument": "DummyCamComp", "visit": 425}, datasetType=datasetType)
 
         # verify the new dataset type increases the number of tables found:
-        tables = self._queryDatasets(repo=self.repoDir)
+        tables = self._queryDatasets(repo=testRepo.butler)
 
         expectedTables = (
             AstropyTable(
@@ -285,10 +287,10 @@ def testGlobDatasetType(self):
     def test_limit_order(self):
         """Test limit and ordering."""
         # Create and register an additional DatasetType
-        MetricTestRepo(self.repoDir, configFile=self.configFile)
+        testRepo = MetricTestRepo(self.repoDir, configFile=self.configFile)
 
         with self.assertLogs("lsst.daf.butler.script.queryDatasets", level="WARNING") as cm:
-            tables = self._queryDatasets(repo=self.repoDir, limit=-1, order_by=("visit"))
+            tables = self._queryDatasets(repo=testRepo.butler, limit=-1, order_by=("visit"))
 
         self.assertIn("increase this limit", cm.output[0])
 
@@ -301,7 +303,7 @@ def test_limit_order(self):
         self.assertAstropyTablesEqual(tables, expectedTables, filterColumns=True)
 
         with self.assertLogs("lsst.daf.butler.script.queryDatasets", level="WARNING") as cm:
-            tables = self._queryDatasets(repo=self.repoDir, limit=-1, order_by=("-visit"))
+            tables = self._queryDatasets(repo=testRepo.butler, limit=-1, order_by=("-visit"))
         self.assertIn("increase this limit", cm.output[0])
 
         expectedTables = [
@@ -322,7 +324,7 @@ def testFindFirstAndCollections(self):
         testRepo.addDataset(run="foo", dataId={"instrument": "DummyCamComp", "visit": 424})
 
         # Verify that without find-first, duplicate datasets are returned
-        tables = self._queryDatasets(repo=self.repoDir, collections=["foo", "ingest/run"], show_uri=True)
+        tables = self._queryDatasets(repo=testRepo.butler, collections=["foo", "ingest/run"], show_uri=True)
 
         # The test should be running with a single FileDatastore.
         roots = testRepo.butler.get_datastore_roots()
@@ -465,7 +467,7 @@ def testFindFirstAndCollections(self):
         # Verify that with find first the duplicate dataset is eliminated and
         # the more recent dataset is returned.
         tables = self._queryDatasets(
-            repo=self.repoDir, collections=["foo", "ingest/run"], show_uri=True, find_first=True
+            repo=testRepo.butler, collections=["foo", "ingest/run"], show_uri=True, find_first=True
         )
 
         expectedTables = (