BUG: fix various errors

* fix inconsistent use of class/instance variables
* fix instance download tests accordingly

Author: fedorov

idc_index/index.py

@@ -133,6 +133,11 @@ def __init__(self):
             },
         }
 
+        # these will point to the dataframes containing the respective indices, once installed
+        self.sm_index = None
+        self.sm_instance_index = None
+        self.clinical_index = None
+
         # Lookup s5cmd
         self.s5cmdPath = shutil.which("s5cmd")
         if self.s5cmdPath is None:
@@ -355,7 +360,9 @@ def fetch_index(self, index_name) -> None:
                 #    self.index[["series_aws_url", "SeriesInstanceUID"]],
                 #    on="SeriesInstanceUID", how="left"
                 # )
-                setattr(self.__class__, index_name, index_table)
+                # TODO: consider switching to class variable!
+                # setattr(self.__class__, index_name, index_table)
+                setattr(self, index_name, index_table)
                 self.indices_overview[index_name]["installed"] = True
                 self.indices_overview[index_name]["file_path"] = filepath
 
@@ -695,12 +702,18 @@ def get_instance_file_URL(self, sopInstanceUID, source_bucket_location="aws"):
         # sm_instance_index is required to complete this operation - install it!
         self.fetch_index("sm_instance_index")
 
-        if sopInstanceUID not in self.sm_instance_index["SOPInstanceUID"].values:
+        if self.sm_instance_index is None:
+            logger.error(
+                "sm_instance_index could not be installed. Please install it first using fetch_index."
+            )
+            return None
+
+        if sopInstanceUID not in self.sm_instance_index["SOPInstanceUID"].values:  # pylint: disable=unsubscriptable-object
             raise ValueError("SOPInstanceUID not found in IDC sm_instance_index.")
 
         # merge with the main index to get series_aws_url
-        selected_instance_df = self.sm_instance_index[
-            self.sm_instance_index["SOPInstanceUID"] == sopInstanceUID
+        selected_instance_df = self.sm_instance_index[  # pylint: disable=unsubscriptable-object
+            self.sm_instance_index["SOPInstanceUID"] == sopInstanceUID  # pylint: disable=unsubscriptable-object
         ].copy()[["SeriesInstanceUID", "SOPInstanceUID", "crdc_instance_uuid"]]
         selected_instance_df = pd.merge(
             selected_instance_df,
@@ -1765,8 +1778,8 @@ def download_from_selection(
         # If SOPInstanceUID(s) are given, we need to join the main index with the instance-level index
         sm_instance_index = None
         if sopInstanceUID:
-            if hasattr(
-                self, "sm_instance_index"
+            if (
+                self.sm_instance_index is not None
             ):  # check if instance-level index is installed
                 download_df = self.sm_instance_index
                 sm_instance_index = self.sm_instance_index
@@ -2182,12 +2195,12 @@ def sql_query(self, sql_query):
         logger.debug("Executing SQL query: " + sql_query)
         # TODO: find a more elegant way to automate the following:  https://www.perplexity.ai/search/write-python-code-that-iterate-XY9ppywbQFSRnOpgbwx_uQ
         index = self.index
-        if hasattr(self, "sm_index"):
+        if self.sm_index is not None:
             sm_index = self.sm_index
-        if hasattr(self, "sm_instance_index"):
+        if self.sm_instance_index is not None:
             sm_instance_index = self.sm_instance_index
-        if hasattr(self, "clinical_index"):
+        if self.clinical_index is not None:
             clinical_index = self.clinical_index
-        if hasattr(self, "prior_versions_index"):
+        if self.prior_versions_index is not None:
             prior_versions_index = self.prior_versions_index
         return duckdb.query(sql_query).to_df()

tests/idcindex.py

@@ -190,8 +190,7 @@ def test_download_dicom_series(self):
             self.assertEqual(sum([len(files) for r, d, files in os.walk(temp_dir)]), 3)
 
     def test_download_dicom_instance(self):
-        i = IDCClient()
-        i.fetch_index("sm_instance_index")
+        self.client.fetch_index("sm_instance_index")
         with tempfile.TemporaryDirectory() as temp_dir:
             self.client.download_dicom_instance(
                 sopInstanceUID="1.3.6.1.4.1.5962.99.1.528744472.1087975700.1641206284312.14.0",
@@ -210,8 +209,7 @@ def test_download_dicom_series_gcs(self):
             self.assertEqual(sum([len(files) for r, d, files in os.walk(temp_dir)]), 3)
 
     def test_download_dicom_instance_gcs(self):
-        i = IDCClient()
-        i.fetch_index("sm_instance_index")
+        self.client.fetch_index("sm_instance_index")
         with tempfile.TemporaryDirectory() as temp_dir:
             self.client.download_dicom_instance(
                 sopInstanceUID="1.3.6.1.4.1.5962.99.1.528744472.1087975700.1641206284312.14.0",