1 files changed, 0 insertions, 102 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
deleted file mode 100644
index a78182e3..00000000
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ /dev/null
@@ -1,102 +0,0 @@
-import collections
-
-from utility import Bunch
-
-
-class MrnaAssayTissueData:
-
-    def __init__(self, conn, gene_symbols=None):
-        self.gene_symbols = gene_symbols
-        self.conn = conn
-        if self.gene_symbols is None:
-            self.gene_symbols = []
-
-        self.data = collections.defaultdict(Bunch)
-        results = ()
-        # Note that inner join is necessary in this query to get
-        # distinct record in one symbol group with highest mean value
-        # Due to the limit size of TissueProbeSetFreezeId table in DB,
-        # performance of inner join is
-        # acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
-        with conn.cursor() as cursor:
-            if len(self.gene_symbols) == 0:
-                cursor.execute(
-                    "SELECT t.Symbol, t.GeneId, t.DataId, "
-                    "t.Chr, t.Mb, t.description, "
-                    "t.Probe_Target_Description FROM (SELECT Symbol, "
-                    "max(Mean) AS maxmean "
-                    "FROM TissueProbeSetXRef WHERE "
-                    "TissueProbeSetFreezeId=1 AND "
-                    "Symbol != '' AND Symbol IS NOT "
-                    "Null GROUP BY Symbol) "
-                    "AS x INNER JOIN "
-                    "TissueProbeSetXRef AS t ON "
-                    "t.Symbol = x.Symbol "
-                    "AND t.Mean = x.maxmean")
-            else:
-                cursor.execute(
-                    "SELECT t.Symbol, t.GeneId, t.DataId, "
-                    "t.Chr, t.Mb, t.description, "
-                    "t.Probe_Target_Description FROM (SELECT Symbol, "
-                    "max(Mean) AS maxmean "
-                    "FROM TissueProbeSetXRef WHERE "
-                    "TissueProbeSetFreezeId=1 AND "
-                    "Symbol IN "
-                    f"({', '.join(['%s'] * len(self.gene_symbols))}) "
-                    "GROUP BY Symbol) AS x INNER JOIN "
-                    "TissueProbeSetXRef AS t ON t.Symbol = x.Symbol "
-                    "AND t.Mean = x.maxmean",
-                    tuple(self.gene_symbols))
-            results = list(cursor.fetchall())
-        lower_symbols = {}
-        for gene_symbol in self.gene_symbols:
-            if gene_symbol is not None:
-                lower_symbols[gene_symbol.lower()] = True
-
-        for result in results:
-            (symbol, gene_id, data_id, _chr, _mb,
-             descr, probeset_target_descr) = result
-            if symbol is not None and lower_symbols.get(symbol.lower()):
-                symbol = symbol.lower()
-                self.data[symbol].gene_id = gene_id
-                self.data[symbol].data_id = data_id
-                self.data[symbol].chr = _chr
-                self.data[symbol].mb = _mb
-                self.data[symbol].description = descr
-                (self.data[symbol]
-                 .probe_target_description) = probeset_target_descr
-
-
-    def get_symbol_values_pairs(self):
-        """Get one dictionary whose key is gene symbol and value is
-        tissue expression data (list type).  All keys are lower case.
-
-        The output is a symbolValuepairDict (dictionary): one
-        dictionary of Symbol and Value Pair; key is symbol, value is
-        one list of expression values of one probeSet;
-
-        """
-        id_list = [self.data[symbol].data_id for symbol in self.data]
-
-        symbol_values_dict = {}
-
-        if len(id_list) > 0:
-            results = []
-            with self.conn.cursor() as cursor:
-
-                cursor.execute(
-                    "SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value "
-                    "FROM TissueProbeSetXRef, TissueProbeSetData"
-                    f" WHERE TissueProbeSetData.Id IN ({', '.join(['%s'] * len(id_list))})"
-                    " AND TissueProbeSetXRef.DataId = TissueProbeSetData.Id"
-                    ,tuple(id_list))
-
-                results = cursor.fetchall()
-                for result in results:
-                    (symbol, value) = result
-                    if symbol.lower() not in symbol_values_dict:
-                        symbol_values_dict[symbol.lower()] = [value]
-                    else:
-                        symbol_values_dict[symbol.lower()].append(
-                            value)
-        return symbol_values_dict