used logging instead of print

VoSeq · Jan 6, 2018 · e6fa946 · e6fa946
1 parent b4fbfc8
commit e6fa946
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Showing 5 changed files with 39 additions and 22 deletions.
diff --git a/voseq/blast_local/views.py b/voseq/blast_local/views.py
@@ -1,3 +1,4 @@
+import logging
 from subprocess import CalledProcessError
 
 from django.shortcuts import render
@@ -7,6 +8,9 @@
 from core.utils import BLAST
 
 
+log = logging.getLogger(__name__)
+
+
 def index(request, voucher_code, gene_code):
     version, stats = get_version_stats()
     username = get_username(request)
@@ -18,7 +22,7 @@ def index(request, voucher_code, gene_code):
         try:
             blast.create_blast_db()
         except CalledProcessError:
-            print("there are no sequences for gene {}".format(gene_code))
+            log.warning("there are no sequences for gene {}".format(gene_code))
 
     good_sequence = blast.save_query_to_file()
     if good_sequence:

diff --git a/voseq/core/utils.py b/voseq/core/utils.py
@@ -1,5 +1,6 @@
 import datetime
 import glob
+import logging
 import os
 import re
 import subprocess
@@ -18,6 +19,8 @@
 from public_interface.models import Sequences
 
 
+log = logging.getLogger(__name__)
+
 
 def get_voucher_codes(cleaned_data):
     """Processes list of voucher codes entered by users.
@@ -120,7 +123,8 @@ def clean_positions(a_list):
         return ['1st-2nd']
     elif len(a_list) == 2:  # 1st and 3rd, or 2nd and 3rd
         raise exceptions.InadequateCodonPositions(
-            "Cannot create dataset for only codon positions {0} and {1}.".format(a_list[0], a_list[1])
+            "Cannot create dataset for only codon positions {0} and {1}."
+            "".format(a_list[0], a_list[1])
         )
     else:
         return a_list
@@ -235,15 +239,15 @@ def create_blast_db(self):
         Optionally eliminates low-complexity regions from the sequences.
 
         """
-        print("Creating blast db")
+        log.debug("Creating blast db")
         if self.mask:
             command = 'dustmasker -in ' + self.seq_file + ' -infmt fasta '
             command += '-outfmt maskinfo_asn1_bin -out ' + self.seq_file + '_dust.asnb'
             subprocess.check_output(command, shell=True)  # identifying low-complexity regions.
 
             command = 'makeblastdb -in ' + self.seq_file + ' -input_type fasta -dbtype nucl '
             command += '-mask_data ' + self.seq_file + '_dust.asnb '
-            command += '-out ' + self.seq_file + ' -title "Whole Genome without low-complexity regions"'
+            command += '-out ' + self.seq_file + ' -title "Whole Genome without low-complexity regions"'  # noqa
             subprocess.check_output(command, shell=True)  # Overwriting the genome file.
         else:
             command = 'makeblastdb -in ' + self.seq_file + ' -input_type fasta -dbtype nucl '

diff --git a/voseq/genbank_fasta/views.py b/voseq/genbank_fasta/views.py
@@ -1,3 +1,4 @@
+import logging
 import os
 
 from django.contrib.auth.decorators import login_required
@@ -12,6 +13,9 @@
 from create_dataset.utils import CreateDataset
 
 
+log = logging.getLogger(__name__)
+
+
 @login_required
 def index(request):
     version, stats = get_version_stats()
@@ -51,7 +55,7 @@ def results(request):
 
             dataset_creator = CreateDataset(cleaned_data)
             dataset = dataset_creator.dataset_str
-            dataset_short = dataset[0:1500] + '\n...\n\n\n' + '#######\nComplete dataset file available for download.\n#######'
+            dataset_short = dataset[0:1500] + '\n...\n\n\n' + '#######\nComplete dataset file available for download.\n#######'  # noqa
             errors = dataset_creator.errors
             warnings = dataset_creator.warnings
             dataset_file_abs = dataset_creator.dataset_file
@@ -98,7 +102,7 @@ def results(request):
 
 @login_required
 def serve_file(request, file_name):
-    print("Requested file by user: {0}".format(request.user))
+    log.debug("Requested file by user: {0}".format(request.user))
     cwd = os.path.dirname(__file__)
     fasta_file = os.path.join(cwd,
                               '..',

diff --git a/voseq/public_interface/views.py b/voseq/public_interface/views.py
@@ -1,5 +1,6 @@
 from itertools import chain
 import json
+import logging
 
 from django.contrib.auth.decorators import login_required
 from django.db.models import Q
@@ -13,12 +14,16 @@
 from haystack.query import ValuesSearchQuerySet
 
 from core.utils import get_version_stats, get_username
-from .utils import VoSeqSearchView, get_simple_query, get_correct_url_query, get_voucher_code_list
+from .utils import get_simple_query, get_correct_url_query, get_voucher_code_list
 from .models import Vouchers, FlickrImages, LocalImages, Sequences, Primers
 from .forms import AdvancedSearchForm, BatchChangesForm
 
 
+log = logging.getLogger(__name__)
+
+
 def index(request):
+    log.debug("Index")
     version, stats = get_version_stats()
     username = get_username(request)
 
@@ -188,7 +193,7 @@ def search_advanced(request):
                         'result_count': len(sqs),
                         'version': version,
                         'stats': stats,
-                })
+                    })
             else:
                 return render(request, 'public_interface/search_results.html',
                               {

diff --git a/voseq/voseq/settings/base.py b/voseq/voseq/settings/base.py
@@ -164,59 +164,59 @@
             'propagate': False,
         },
         'blast_local': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'blast_local_full': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'blast_ncbi': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'blast_new': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'core': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'create_dataset': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'gbif': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'genbank_fasta': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'gene_table': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'overview_table': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'public_interface': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'stats': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'view_genes': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
         'voucher_table': {
-            'handlers': ['terminal', 'file', 'mail_admins'],
+            'handlers': ['terminal', 'file', 'file_debug', 'mail_admins'],
             'level': 'DEBUG',
         },
     },