Merged from test, fixed conflicts

ncbi · May 13, 2019 · 899ffc5 · 899ffc5
2 parents c98fadc + da32519
commit 899ffc5
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/scripts/pgap.py b/scripts/pgap.py
@@ -148,7 +148,7 @@ def create_inputfile(self, local_input):
             f.write(u'supplemental_data: { class: Directory, location: /pgap/input }\n')
             if (self.params.report_usage != 'none'):
                 f.write(u'report_usage: {}\n'.format(self.params.report_usage))
-            if (self.params.ignore_all_errors != 'none'):
+            if (self.params.ignore_all_errors == 'true'):
                 f.write(u'ignore_all_errors: {}\n'.format(self.params.ignore_all_errors))
             f.flush()
         return yaml
@@ -239,6 +239,7 @@ def output_reader(proc, outq):
             except subprocess.TimeoutExpired:
                 print('docker did not exit cleanly.')
         t.join()
+        return proc.returncode
 
 class Setup:
 
@@ -360,7 +361,6 @@ def get_ignore_all_errors(self):
             return 'true'
         else:
             return 'false'
-        return 'none' # do we need this in Python? obviously code never reaches this
 
     def get_timeout(self):
         def str2sec(s):
@@ -460,9 +460,12 @@ def main():
 
     params = Setup(args)
 
+    retcode = 0
     if args.input:
         p = Pipeline(params, args.input)
-        p.launch()
+        retcode = p.launch()
+
+    sys.exit(retcode)
 
 if __name__== "__main__":
     main()
diff --git a/wf_common.cwl b/wf_common.cwl
@@ -352,6 +352,7 @@ steps:
             input: Prepare_Unannotated_Sequences_asnvalidate/o
             xpath_fail: {default: '//*[
                 ( @severity="ERROR" or @severity="REJECT" )
+                and not(contains(@code, "SEQ_DESCR_UnwantedCompleteFlag")) 
                 and not(contains(@code, "SEQ_PKG_NucProtProblem")) 
                 and not(contains(@code, "SEQ_INST_InternalNsInSeqRaw")) 
                 and not(contains(@code, "GENERIC_MissingPubRequirement")) 
@@ -832,6 +833,7 @@ steps:
             input: Final_Bacterial_Package_std_validation/outval
             xpath_fail: {default: '//*[
                 ( @severity="ERROR" or @severity="REJECT" )
+                and not(contains(@code, "SEQ_DESCR_UnwantedCompleteFlag")) 
                 and not(contains(@code, "SEQ_PKG_NucProtProblem")) 
                 and not(contains(@code, "SEQ_INST_InternalNsInSeqRaw")) 
                 and not(contains(@code, "GENERIC_MissingPubRequirement"))