Fix #190: Add checks for gse to srp conversion

saketkc · Apr 24, 2023 · cd33b70 · cd33b70
1 parent d915803
commit cd33b70
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,10 +2,18 @@
 History
 #######
 
+******************
+Unreleased
+******************
+
+* Fix for `gse-to-srp` returning unrequested GSEs (`#186 <https://github.com/saketkc/pysradb/issues/190>`)
+
+
 ******************
 2.0.2 (2023-04-09)
 ******************
 
+<<<<<<< HEAD
 * Fix for `gse-to-srp` to handle cases where a project is missing but SRXs
   are returned (`#186 <https://github.com/saketkc/pysradb/issues/186>`)
 * Fix gse-to-gsm (`#187 <https://github.com/saketkc/pysradb/issues/187>`) 

diff --git a/pysradb/sraweb.py b/pysradb/sraweb.py
@@ -793,7 +793,7 @@ def gse_to_srp(self, gse, **kwargs):
                 {"study_alias": gse_of_interest, "study_accession": srp_unique}
             )
             gse_df_subset = pd.concat([gse_df_subset_gse, new_gse_df])
-
+        gse_df_subset = gse_df_subset.loc[gse_df_subset.study_alias.isin(gse)]
         return gse_df_subset[["study_alias", "study_accession"]].drop_duplicates()
 
     def gsm_to_srp(self, gsm, **kwargs):

diff --git a/tests/test_sraweb.py b/tests/test_sraweb.py
@@ -130,7 +130,7 @@ def test_gse_to_gsm1(sraweb_connection):
 def test_gse_to_srp(sraweb_connection):
     """Test if gse is converted to srp correctly"""
     df = sraweb_connection.gse_to_srp("GSE63858")
-    assert df["study_accession"][0] == "SRP050548"
+    assert df["study_accession"].tolist()[0] == "SRP050548"
 
 
 def test_gse_to_srp2(sraweb_connection):
@@ -254,3 +254,9 @@ def test_GCP_url(sraweb_connection):
 def test_GCP_url2(sraweb_connection):
     df = sraweb_connection.sra_metadata(["DRR138929"], detailed=True)
     assert df["gcp_url"].tolist()[-1].startswith("gs:")
+
+
+def test_gse_to_srp3(sraweb_connection):
+    # https://github.com/saketkc/pysradb/issues/190
+    df = sraweb_connection.gse_to_srp(["GSE89545"])
+    assert df["study_accession"].tolist()[0] == "SRP093251"