Fix #1: deal with splitted BLAST databases

primerserver2/cmd/primertool.py

@@ -122,13 +122,9 @@ def check_templates(args):
         if os.path.isfile(template) is False:
             raise Exception(f'File not found: {template}')
         if os.path.isfile(template+'.fai') is False:
-            code = os.system(f'samtools faidx {template} 2>/dev/null')
-            if code != 0:
-                raise Exception(f'File {template} cannot be indexed by samtools faidx. Perhaps it is not in FASTA format')
+            raise Exception(f'File {template} has not been indexed by samtools faidx.')
         if os.path.isfile(re.sub('[.]gz$', '', template)+'.nhr') is False and os.path.isfile(re.sub('\.gz$', '', template)+'.nal') is False:
-            code = os.system(f'makeblastdb -dbtype nucl -in {template} 2>/dev/null')
-            if code != 0:
-                raise Exception(f'File {template} cannot be indexed by makeblastdb.')
+            raise Exception(f'File {template} has not been indexed by makeblastdb.')
 
         # qPCR specific
         if i==0:

primerserver2/core/version.py

@@ -1,2 +1,2 @@
 def get():
-    return '2.0.0b18'
+    return '2.0.0b19'

primerserver2/web/config.py

@@ -9,6 +9,7 @@
 import os
 import sys
 import json
+import re
 
 def load():
     home_dir = os.environ['HOME']
@@ -52,8 +53,8 @@ def check():
             else:
                 msg = f'File {db_dir}/{dbname} does not exist'
                 return {'status': status, 'msg': msg}
-        if os.path.isfile(f'{db_dir}/{dbname}.nhr') is False and os.path.isfile(f'{db_dir}/{dbname.replace(".gz", "")}.nhr') is False:
-            msg = f'File {db_dir}/{dbname}.nhr does not exist. Use "makeblastdb" to index {db_dir}/{dbname}'
+        if os.path.isfile(re.sub('[.]gz$', '', f'{db_dir}/{dbname}')+'.nhr') is False and os.path.isfile(re.sub('[.]gz$', '', f'{db_dir}/{dbname}')+'.nal') is False:
+            msg = f'File {db_dir}/{dbname} has no index. Use "makeblastdb" to index {db_dir}/{dbname}'
             return {'status': status, 'msg': msg}
         if os.path.isfile(f'{db_dir}/{dbname}.fai') is False:
             msg = f'File {db_dir}/{dbname}.fai does not exist. Use "samtools faidx" to index {db_dir}/{dbname}'