GR-933 open cache files only once

application/dash_application/utility/df_manipulation.py

@@ -3,6 +3,7 @@
 from pandas import DataFrame
 from typing import List
 
+from gsiqcetl import QCETLCache
 import gsiqcetl.column
 import pinery
 
@@ -22,6 +23,15 @@
 rnaseqqc_ius_columns = [RNASEQQC_COL.Run, RNASEQQC_COL.Lane,
                         RNASEQQC_COL.Barcodes]
 
+"""
+Open a single instance of each cache, and use copies for the reports. 
+"""
+cache = QCETLCache()
+_rnaseqqc = cache.rnaseqqc.rnaseqqc
+_bamqc = cache.bamqc.bamqc
+_bamqc3 = cache.bamqc3.bamqc3
+_ichorcna = cache.ichorcna.ichorcna
+
 _pinery_client = pinery.PineryClient()
 _provenance_client = pinery.PineryProvenanceClient(provider="pinery-miso-v5")
 _pinery_samples = _provenance_client.get_all_samples()
@@ -61,6 +71,22 @@
     )
 
 
+def get_rnaseqqc():
+    return _rnaseqqc.copy(deep=True)
+
+
+def get_bamqc():
+    return _bamqc.copy(deep=True)
+
+
+def get_bamqc3():
+    return _bamqc3.copy(deep=True)
+
+
+def get_ichorcna():
+    return _ichorcna.copy(deep=True)
+
+
 def get_pinery_samples():
     """Get Pinery Sample Provenance DataFrame"""
     return _pinery_samples.copy(deep=True)

application/dash_application/views/pre_exome.py

@@ -10,7 +10,6 @@
 from ..table_builder import build_table
 from ..utility import df_manipulation as util
 from ..utility import slider_utils
-from gsiqcetl import QCETLCache
 from gsiqcetl.column import BamQcColumn
 import pinery
 
@@ -54,7 +53,7 @@
 
 
 def get_bamqc_data():
-    bamqc_df = QCETLCache().bamqc.bamqc
+    bamqc_df = util.get_bamqc()
     bamqc_df = util.df_with_normalized_ius_columns(bamqc_df, BAMQC_COL.Run, BAMQC_COL.Lane, BAMQC_COL.Barcodes)
 
     pinery_samples = util.get_pinery_samples_from_active_projects()

application/dash_application/views/preqc_rna.py

@@ -10,7 +10,6 @@
 from ..utility import df_manipulation as util
 from ..plot_builder import fill_in_colour_col, fill_in_shape_col, generate
 from ..table_builder import build_table
-from gsiqcetl import QCETLCache
 from gsiqcetl.column import RnaSeqQcColumn as RnaColumn
 import pinery
 
@@ -107,7 +106,7 @@ def get_rna_data():
     #  * QCETLCache().rnaseqqc.rnaseqqc: returns the DataFrame/cache named
     #  "rnaseqqc" within the rnaseqqc cache (as some caches like bcl2fastq
     #  contain multiple DataFrame/caches)
-    rna_df = QCETLCache().rnaseqqc.rnaseqqc
+    rna_df = util.get_rnaseqqc()
     # Cast the primary key/join columns to explicit types
     rna_df = util.df_with_normalized_ius_columns(rna_df, RNA_COL.Run,
                                                  RNA_COL.Lane, RNA_COL.Barcodes)

application/dash_application/views/preqc_wgs.py

@@ -7,7 +7,6 @@
 
 import gsiqcetl.column
 import pinery
-from gsiqcetl import QCETLCache
 from . import navbar
 from ..dash_id import init_ids
 from ..plot_builder import terminal_output, fill_in_shape_col, fill_in_colour_col, generate
@@ -104,14 +103,14 @@ def get_wgs_data():
       * Runs (needed to join Pinery to Instruments)
     """
     # Get the BamQC data
-    cache = QCETLCache()
 
-    ichorcna_df = cache.ichorcna.ichorcna[[ICHOR_COL.Run,
+    ichorcna_df = util.get_ichorcna()
+    ichorcna_df = ichorcna_df[[ICHOR_COL.Run,
                                            ICHOR_COL.Lane,
                                            ICHOR_COL.Barcodes,
                                            ICHOR_COL.Ploidy,
                                            ICHOR_COL.TumorFraction]]
-    bamqc_df = cache.bamqc3.bamqc3
+    bamqc_df = util.get_bamqc3()
     wgs_df = bamqc_df.merge(
         ichorcna_df, how="left", left_on=[
             BAMQC_COL.Run, BAMQC_COL.Lane, BAMQC_COL.Barcodes], right_on=[