Fix/sqmass access

massdash/loaders/access/OSWDataAccess.py

@@ -340,15 +340,15 @@ def _getTransitionsFromPrecursorId(self, precursor_id:int) -> pd.DataFrame:
                     ANNOTATION 
                     FROM TRANSITION_PRECURSOR_MAPPING 
                     INNER JOIN TRANSITION ON TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID= TRANSITION.ID
-                    WHERE TRANSITION.DETECTING = 1 and PRECURSOR_ID = {precursor_id}
+                    WHERE TRANSITION.DETECTING = 1 and PRECURSOR_ID = {precursor_id} order by TRANSITION_ID
                 '''
         else:
             stmt = f'''
             SELECT TRANSITION_ID,
                     TRANSITION.TYPE || TRANSITION.ORDINAL || '^' || TRANSITION.CHARGE AS ANNOTATION
                     FROM TRANSITION_PRECURSOR_MAPPING 
                     INNER JOIN TRANSITION ON TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID = TRANSITION.ID
-                    WHERE TRANSITION.DETECTING = 1 and PRECURSOR_ID = {precursor_id}
+                    WHERE TRANSITION.DETECTING = 1 and PRECURSOR_ID = {precursor_id} order by TRANSITION_ID
             '''
         return pd.read_sql(stmt, self.conn)
 

massdash/loaders/access/SqMassDataAccess.py

@@ -85,11 +85,12 @@ def _getChromatogramsHelper(self, ids: List[str], labels: List[str]):
         return self._returnDataForChromatogram(data)
 
     def _getChromatogramsHelperFromNativeIds(self, native_ids: List[str]):
-        stmt ="SELECT CHROMATOGRAM_ID, COMPRESSION, DATA_TYPE, DATA FROM DATA INNER JOIN CHROMATOGRAM ON CHROMATOGRAM.ID = CHROMATOGRAM_ID WHERE NATIVE_ID IN ("
+        stmt ="SELECT NATIVE_ID, COMPRESSION, DATA_TYPE, DATA FROM DATA INNER JOIN CHROMATOGRAM ON CHROMATOGRAM.ID = CHROMATOGRAM_ID WHERE NATIVE_ID IN ("
         for myid in native_ids:
             stmt += str(myid) + ","
         stmt = stmt[:-1]
         stmt += ")"
+        stmt += " ORDER BY NATIVE_ID"
 
         data = [row for row in self.c.execute(stmt)]
         return self._returnDataForChromatogram(data)
@@ -135,31 +136,6 @@ def getDataForChromatograms(self, ids: List[str], labels: List[str]) -> List[Chr
 
         return c
 
-    def getDataForChromatogram(self, myid: str, label: str) -> Chromatogram:
-        """
-        Get data from a single chromatogram
-
-        - compression is one of 0 = no, 1 = zlib, 2 = np-linear, 3 = np-slof, 4 = np-pic, 5 = np-linear + zlib, 6 = np-slof + zlib, 7 = np-pic + zlib
-        - data_type is one of 0 = mz, 1 = int, 2 = rt
-        - data contains the raw (blob) data for a single data array
-        """
-
-        data = [row for row in self.c.execute("SELECT CHROMATOGRAM_ID, COMPRESSION, DATA_TYPE, DATA FROM DATA WHERE CHROMATOGRAM_ID = %s" % myid )]
-        res = list(self._returnDataForChromatogram(data).values())[0]
-        return Chromatogram(res[0], res[1], label)
-
-    def getDataForChromatogramFromNativeId(self, native_id):
-        """
-        Get data from a single chromatogram
-
-        - compression is one of 0 = no, 1 = zlib, 2 = np-linear, 3 = np-slof, 4 = np-pic, 5 = np-linear + zlib, 6 = np-slof + zlib, 7 = np-pic + zlib
-        - data_type is one of 0 = mz, 1 = int, 2 = rt
-        - data contains the raw (blob) data for a single data array
-        """
-
-        data = [row for row in self.c.execute("SELECT CHROMATOGRAM_ID, COMPRESSION, DATA_TYPE, DATA FROM DATA INNER JOIN CHROMATOGRAM ON CHROMATOGRAM.ID = CHROMATOGRAM_ID WHERE NATIVE_ID = %s" % native_id )]
-        return list(self._returnDataForChromatogram(data).values())[0]
-
     def getDataForChromatogramsFromNativeIdsDf(self, native_ids: List[str], labels: List[str]) -> pd.DataFrame:
         '''
         Get chromatogram data as a dataframe
@@ -202,7 +178,7 @@ def getDataForChromatogramsFromNativeIds(self, native_ids: List, labels: List[st
 
     def _returnDataForChromatogram(self, data):
         # prepare result
-        chr_ids = set([chr_id for chr_id, compr, data_type, d in data] )
+        chr_ids = [chr_id for chr_id, compr, data_type, d in data]
         res = OrderedDict()
         numpress_config = po.NumpressConfig()
         for i in chr_ids:

test/loaders/access/test_SqMassDataAccess.py

@@ -40,18 +40,6 @@ def test_getDataForChromatograms(mass_data_access, snapshot_pandas):
     data_out = pd.concat([d.toPandasDf() for d in data]) 
     assert snapshot_pandas == data_out
 
-def test_getDataForChromatogram(mass_data_access, snapshot_pandas):
-    myid = 424
-    data = mass_data_access.getDataForChromatogram(myid, "y4^1")
-    data_out = data.toPandasDf()
-    assert snapshot_pandas == data_out
-
-def test_getDataForChromatogramFromNativeId(mass_data_access, snapshot_pandas):
-    native_id = 992928
-    data = mass_data_access.getDataForChromatogramFromNativeId(native_id)
-    data_out = pd.DataFrame(data)
-    assert snapshot_pandas == data_out
-
 def test_getDataForChromatogramsFromNativeIds(mass_data_access, snapshot_pandas):
     native_ids = [180, 181, 182, 183, 183, 185]
     labels = ["y4^1", "y3^1", "y6^1", "y7^1", "y7^1", "y8^1"]