Restore manually the commits; JIRA: PGAPX-453

Using the output of git show -w for each of the SHA1 numbers below, restore manually the following commits:

    bbefcfe
    ef26674
    d715669

pgap.cwl

@@ -28,7 +28,8 @@ inputs:
   submol: File
   ignore_all_errors:
         type: boolean?
-
+  no_internet:
+    type: boolean?
 outputs:
   gbk:
     outputSource: standard_pgap/gbk
@@ -106,6 +107,7 @@ steps:
       submol: submol
       taxon_db: passdata/taxon_db
       ignore_all_errors: ignore_all_errors
+      no_internet: no_internet
     out: [output_seq_submit, output_entries, locus_tag_prefix, submol_block_json, taxid]
   fastaval:
     run: progs/fastaval.cwl

prepare_user_input2.cwl

@@ -17,7 +17,10 @@ inputs:
   taxon_db:
     type: File
   ignore_all_errors:
-        type: boolean?
+    type: boolean?
+  no_internet:
+    type: boolean?
+
 outputs:
     input_asn_type: 
         type: string
@@ -53,6 +56,7 @@ steps:
             input_fasta: fasta
             taxon_db: taxon_db
             ignore_all_errors: ignore_all_errors
+            no_internet: no_internet
         out: [output_annotation, output_ltp, input_asn_type, taxid]
     file2string_ltp:
         run: progs/file2string.cwl

progs/pgapx_yaml_ctl.cwl

@@ -27,6 +27,10 @@ inputs:
         type: boolean?
         inputBinding:
             prefix: -ignore-all-errors    
+    no_internet:
+      type: boolean?            
+        inputBinding:
+          prefix: -no-internet
     ofmt:
         type: string
         default: 'JSON'

scripts/pgap.py

@@ -195,6 +195,8 @@ def create_inputfile(self, local_input):
                 fOut.write(u'report_usage: {}\n'.format(self.params.report_usage))
             if (self.params.ignore_all_errors == 'true'):
                 fOut.write(u'ignore_all_errors: {}\n'.format(self.params.ignore_all_errors))
+            if (self.params.no_internet == 'true'):
+                fOut.write(u'no_internet: {}\n'.format(self.params.no_internet))
             fOut.flush()
         return yaml
 
@@ -311,6 +313,7 @@ def __init__(self, args):
         self.remote_versions = self.get_remote_versions()
         self.report_usage    = self.get_report_usage()
         self.ignore_all_errors    = self.get_ignore_all_errors()
+        self.no_internet     = self.get_no_internet()
         self.timeout         = self.get_timeout()
         self.check_status()
         if args.version:
@@ -431,6 +434,12 @@ def get_ignore_all_errors(self):
         else:
             return 'false'
 
+    def get_no_internet(self):
+        if (self.args.no_internet):
+            return 'true'
+        else:
+            return 'false'
+
     def get_timeout(self):
         def str2sec(s):
             return sum(x * int(t) for x, t in