Handle missing filepath in SRAdb

- Fixes #26 
- Closes #27

pysradb/basedb.py

@@ -2,6 +2,7 @@
 import sys
 
 import pandas as pd
+import os
 
 from .utils import _extract_first_field
 
@@ -24,7 +25,8 @@ def __init__(self, sqlite_file):
 
     def open(self):
         """Open sqlite connection."""
-        self.db = sqlite3.connect(self.sqlite_file)
+        # Originally sqlite3.connect(self.sqlite_file)
+        self.db = sqlite3.connect("file:{}?mode=ro".format(self.sqlite_file), uri=True)
         self.db.text_factory = str
 
     def close(self):

pysradb/cli.py

@@ -43,7 +43,8 @@ def _print_save_df(df, saveto=None):
             to_print = []
             for line in to_print_split:
                 to_print.append(line.lstrip())
-            print(("{}".format(os.linesep)).join(to_print))
+            sys.stdout.write(("{}".format(os.linesep)).join(to_print))
+            # print(("{}".format(os.linesep)).join(to_print))
 
 
 def _check_sradb_file(db):

pysradb/sradb.py

@@ -151,7 +151,7 @@ def _verify_srametadb(filepath):
         db = BASEdb(filepath)
     except:
         print(
-            "{} not a valid SRAmetadb.sqlite file.\n".format(filepath)
+            "{} not a valid SRAmetadb.sqlite file or path.\n".format(filepath)
             + "Please download one using `pysradb metadb`."
         )
         sys.exit(1)
@@ -177,8 +177,8 @@ def __init__(self, sqlite_file):
 
 
         """
-        super(SRAdb, self).__init__(sqlite_file)
         _verify_srametadb(sqlite_file)
+        super(SRAdb, self).__init__(sqlite_file)
         self._db_type = "SRA"
         self.valid_in_acc_type = [
             "SRA",

pysradb/sraweb.py

@@ -198,7 +198,6 @@ def get_esummary_response(self, db, term, usehistory="y"):
         if isinstance(term, list):
             term = " OR ".join(term)
         payload += [("term", term)]
-
         request = requests.get(self.base_url["esearch"], params=OrderedDict(payload))
         esearch_response = request.json()
         if "esummaryresult" in esearch_response:

tests/_test_sradb.py

@@ -5,6 +5,7 @@
 import pytest
 from pysradb import SRAdb
 from pysradb.filter_attrs import guess_cell_type, guess_tissue_type, guess_strain_type
+from sqlite3 import OperationalError
 
 
 @pytest.fixture(scope="module")
@@ -77,6 +78,10 @@ def test_all_row_counts(sradb_connection):
     assert sradb_connection.all_row_counts().loc["metaInfo", "count"] == 2
 
 
+def test_all_row_counts2(sradb_connection):
+    assert len(sradb_connection.all_row_counts()) == 13
+
+
 def test_sra_metadata(sradb_connection):
     df = sradb_connection.sra_metadata("SRP017942")
     assert df["experiment_accession"][0] == "SRX217027"
@@ -94,11 +99,29 @@ def test_search(sradb_connection):
     assert len(df.index)
 
 
+def test_search2(sradb_connection):
+    df = sradb_connection.search_sra(
+        '"salivary microbiome" AND "diabetes mellitus"', detailed=True
+    )
+    assert "SRP241848" in df["study_accession"].to_list()
+
+
 def test_search_by_expt_id(sradb_connection):
     df = sradb_connection.search_by_expt_id("SRX1254413")
     assert df.study_name.tolist()[0] == "GSE73136"
 
 
+def test_search_by_expt_id2(sradb_connection):
+    srx_id = "SRX116363"
+    df_expt = sradb_connection.search_by_expt_id(srx_id)
+    sra_id = df_expt["submission_accession"].loc[0]
+    df = sradb_connection.sra_metadata(sra_id)
+    connected_srp = sradb_connection.srx_to_srp("SRX116363").iloc[0, 1]
+    assert (srx_id in df["experiment_accession"].to_list()) and (
+        connected_srp == "SRP010374"
+    )
+
+
 # def test_download_fasp(sradb_connection):
 #    df = sradb_connection.sra_metadata("SRP098789")
 #    df = df[df.experiment_accession == "SRX2536403"]
@@ -148,3 +171,37 @@ def test_strain_type(sradb_connection):
         "s288c",
         "s288c",
     ]
+
+
+def test_srp_to_srx(sradb_connection):
+    assert len(sradb_connection.srp_to_srx("SRP082570")) == 14
+
+
+def test_srp_to_srr(sradb_connection):
+    df = sradb_connection.srp_to_srr("SRP091987")
+    assert sorted(list(df["run_accession"])[:3]) == [
+        "SRR4447104",
+        "SRR4447105",
+        "SRR4447106",
+    ]
+
+
+def test_srp_to_gse(sradb_connection):
+    gse_id = sradb_connection.srp_to_gse("SRP050443").iloc[0, 1]
+    df = sradb_connection.gse_to_gsm(gse_id)
+    assert "GSM1557451" in df["experiment_alias"].to_list()
+
+
+def test_gsm_to_gse(sradb_connection):
+    df = sradb_connection.gsm_to_gse(["GSM1020651", "GSM1020664", "GSM1020771"])
+    assert set(list(df["study_alias"])) == {"GSE41637"}
+
+
+def test_srs_to_gsm(sradb_connection):
+    df = sradb_connection.srs_to_gsm("SRS1757470")
+    assert "GSM2358940" == df.iloc[0, 1]
+
+
+@pytest.mark.xfail(raises=ValueError)
+def test_wrong_input_metadata(sradb_connection):
+    df = sradb_connection.sra_metadata("should_throw_error")

tests/test_sradb.py

@@ -0,0 +1,20 @@
+"""Tests for sradb.py
+"""
+
+import os
+import pytest
+from pysradb import SRAdb
+from pysradb.filter_attrs import guess_cell_type, guess_tissue_type, guess_strain_type
+from sqlite3 import OperationalError
+
+
+def test_not_valid_file():
+    """Test to check for error if file is either not
+        present or not a valid sqlite file"""
+    path = "SRAmetadb.sqlite"
+    try:
+        db = SRAdb(path)
+    except SystemExit:
+        assert os.path.isfile(path) == False
+    except OperationalError:
+        assert True