From 13ccfc2147c1f7c52f8e9fc624fd2cc4aa061105 Mon Sep 17 00:00:00 2001
From: Jake <jmiller@neb.com>
Date: Mon, 5 Feb 2024 13:25:21 -0500
Subject: [PATCH] Adds logging based on historic troubleshooting incidents.
 Could be expanded in the future based on future issues

---
 fatools/lib/fautil/cmds.py   | 15 ++++++++++++++-
 fatools/lib/fautil/mixin2.py | 13 ++++++++++++-
 2 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/fatools/lib/fautil/cmds.py b/fatools/lib/fautil/cmds.py
index 7038456..5190161 100644
--- a/fatools/lib/fautil/cmds.py
+++ b/fatools/lib/fautil/cmds.py
@@ -140,6 +140,7 @@ def init_argparser(parser=None):
 
 
 def main(args):
+    cerr('***** Entering main in FATools *****')
 
     if args.verbose != 0:
         set_verbosity(args.verbose)
@@ -203,6 +204,7 @@ def main(args):
 
         
 def do_facmds(args, fsa_list, _params, dbh=None):
+    cerr('***** Entering do_facmds in FATools *****')
 
     if args.ladder_rfu_threshold >= 0:
         _params.ladder.min_rfu = args.ladder_rfu_threshold
@@ -286,12 +288,16 @@ def do_align( args, fsa_list, _params, f_bad_files, dbh ):
             fsa.align(_params)
             good_fsa.append( (fsa, fsa_index) )
         except LadderMismatchException:
+            cerr('***** LadderMismatchException: {} *****'.format(fsa))
+
             f_bad_files.write(("LadderMismatch: %s\n") % fsa.filename)
-            
+
+    cerr('***** good_fsas: {} *****'.format(good_fsa))
     return good_fsa
 
 
 def do_call( args, fsa_list, params, dbh ):
+    cerr('***** Entering do_call *****')
 
     cerr('I: Calling non-ladder peaks...')
 
@@ -319,6 +325,7 @@ def do_normalize( args, fsa_list, params ):
     panel = Panel.get_panel(args.panel)
     
     ladder_means = panel.get_ladder_area_means(fsa_list)
+    cerr('***** ladder_means: {} *****'.format(ladder_means))
 
     # normalize areas for each FSA
     for (fsa, fsa_index) in fsa_list:
@@ -641,6 +648,8 @@ def open_fsa( args, _params ):
             os.makedirs('.fatools_caches/channels')
 
     if args.file:
+        cerr('***** Reading args.file *****')
+
         for fsa_filename in args.file.split(','):
             fsa_filename = fsa_filename.strip()
 
@@ -655,6 +664,7 @@ def open_fsa( args, _params ):
             index += 1
 
     elif args.infile:
+        cerr('***** Reading args.infile *****')
 
         with open(args.infile) as f:
             buf, delim = detect_buffer( f.read() )
@@ -691,6 +701,8 @@ def open_fsa( args, _params ):
                 index += 1
 
     elif args.indir:
+        cerr('***** Reading args.indir *****')
+
         import glob
         for fsa_filename in sorted(glob.glob(args.indir+"/*.fsa")):
 
@@ -700,6 +712,7 @@ def open_fsa( args, _params ):
             fsa_list.append( (fsa, str(index)) )
             index += 1
 
+    cerr('***** fsa_list: {} *****'.format(fsa_list))
     return fsa_list
 
 
diff --git a/fatools/lib/fautil/mixin2.py b/fatools/lib/fautil/mixin2.py
index ca54717..8442fd3 100644
--- a/fatools/lib/fautil/mixin2.py
+++ b/fatools/lib/fautil/mixin2.py
@@ -62,7 +62,9 @@ def assign(self):
             self.marker = marker
 
 
-    def get_alleles(self, broad_peaks_only=True):       
+    def get_alleles(self, broad_peaks_only=True):
+        cerr('***** Entering ChannelMixin.get_alleles *****')
+
         if self.status == const.channelstatus.reseted:
             # create alleles first
             raise RuntimeError('E: channel needs to be scanned first')
@@ -73,6 +75,7 @@ def get_alleles(self, broad_peaks_only=True):
 
     # ChannelMixIn scan method
     def scan(self, parameters):
+        cerr('***** Entering ChannelMixin.scan *****')
 
         if self.status != const.channelstatus.reseted:
             return
@@ -81,6 +84,7 @@ def scan(self, parameters):
 
 
     def preannotate(self, parameters):
+        cerr('***** Entering ChannelMixin.preannotate *****')
 
         params = parameters.ladder if self.is_ladder() else parameters.nonladder
 
@@ -90,6 +94,8 @@ def preannotate(self, parameters):
     # ChannelMixIn align method
     def align(self, parameters, ladder=None, anchor_pairs=None, saturated_peak_rtimes=[]):
         # sanity checks
+        cerr('***** Entering ChannelMixin.align *****')
+
         if self.marker.code != 'ladder':
             raise RuntimeError('E: align() must be performed on ladder channel!')
 
@@ -277,6 +283,7 @@ def create_channels(self, params):
 
     # FSAMixIn scan method
     def scan(self, parameters):
+        cerr('***** Entering FSAMixIn.scan *****')
 
         if self.scan_done: return
 
@@ -291,6 +298,7 @@ def scan(self, parameters):
 
     # FSAMixIn align method
     def align(self, parameters=None):
+        cerr('***** Entering FSAMixIn.align *****')
 
         self.scan(parameters)
 
@@ -299,6 +307,7 @@ def align(self, parameters=None):
 
     # FSAMixIn call method
     def call(self, parameters):
+        cerr('***** Entering FSAMixIn.call *****')
 
         if self.call_done: return
         
@@ -335,6 +344,7 @@ def get_ladder_channel(self):
 
         for c in self.channels:
             if c.marker.code == 'ladder':
+                cerr('***** get_ladder_channel: {} *****'.format(c))
                 return c
         raise RuntimeError('E: ladder channel not found')
     
@@ -442,6 +452,7 @@ def get_marker(self, dye):
 
 
     def get_ladder(self):
+        cerr('***** ladder: {} *****'.format(const.ladders[ self.data['ladder']]))
         return const.ladders[ self.data['ladder']]