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kbase / execution_engine2

KBase Execution Engine
http://www.kbase.us/services/ee2
MIT License
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Errored jobs not available in narrative-dev, "when you make a copy of the narrative." #219

Open bio-boris opened 4 years ago

bio-boris commented 4 years ago

THESE ARE CORRECT https://narrative.kbase.us/narrative/ws.43273.obj.1 https://narrative-dev.kbase.us/narrative/ws.43273.obj.1

I clicked to make a COPY https://narrative.kbase.us/narrative/ws.59872.obj.272. THIS DOES NOT WORK https://narrative-dev.kbase.us/narrative/ws.59872.obj.272 THIS DOES NOT WORK

narrative.kbase.us image

narrative-dev.kbase.us image

Result of checkjob

{'authstrat': 'kbaseworkspace',
 'created': 1571762092000,
 'error_code': 0,
 'errormsg': 'Traceback (most recent call last):\n'
             '  File '
             '"/kb/module/bin/../lib/kb_phylogenomics/kb_phylogenomicsServer.py", '
             'line 95, in _call_method\n'
             '    result = method(ctx, *params)\n'
             '  File '
             '"/kb/module/lib/kb_phylogenomics/kb_phylogenomicsImpl.py", line '
             '1439, in run_DomainAnnotation_Sets\n'
             '    da_retVal = '
             'daClient.search_domains(DomainAnnotation_Params)\n'
             '  File '
             '"/kb/module/lib/installed_clients/DomainAnnotationClient.py", '
             'line 62, in search_domains\n'
             '    [input], self._service_ver, context)\n'
             '  File "/kb/module/lib/installed_clients/baseclient.py", line '
             '253, in run_job\n'
             '    job_state = self._check_job(mod, job_id)\n'
             '  File "/kb/module/lib/installed_clients/baseclient.py", line '
             '220, in _check_job\n'
             "    return self._call(self.url, service + '._check_job', "
             '[job_id])\n'
             '  File "/kb/module/lib/installed_clients/baseclient.py", line '
             '187, in _call\n'
             "    raise ServerError(**err['error'])\n"
             'ServerError: JSONRPCError: -32500. Connection has been shutdown: '
             'javax.net.ssl.SSLException: SSL peer shut down incorrectly\n'
             'javax.net.ssl.SSLException: Connection has been shutdown: '
             'javax.net.ssl.SSLException: SSL peer shut down incorrectly\n'
             '\tat '
             'sun.security.ssl.SSLSocketImpl.checkEOF(SSLSocketImpl.java:1551)\n'
             '\tat '
             'sun.security.ssl.AppInputStream.read(AppInputStream.java:95)\n'
             '\tat '
             'org.apache.http.impl.io.SessionInputBufferImpl.streamRead(SessionInputBufferImpl.java:137)\n'
             '\tat '
             'org.apache.http.impl.io.SessionInputBufferImpl.read(SessionInputBufferImpl.java:198)\n'
             '\tat '
             'org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:176)\n'
             '\tat '
             'org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:198)\n'
             '\tat '
             'org.apache.http.impl.io.ContentLengthInputStream.close(ContentLengthInputStream.java:101)\n'
             '\tat '
             'org.apache.http.entity.BasicHttpEntity.writeTo(BasicHttpEntity.java:120)\n'
             '\tat '
             'org.apache.http.impl.execchain.ResponseEntityProxy.writeTo(ResponseEntityProxy.java:101)\n'
             '\tat '
             'us.kbase.shock.client.BasicShockClient.getFile(BasicShockClient.java:355)\n'
             '\tat '
             'domainannotation.DomainAnnotationImpl.fromShock(DomainAnnotationImpl.java:118)\n'
             '\tat '
             'domainannotation.DomainAnnotationImpl.prepareLibraryFiles(DomainAnnotationImpl.java:759)\n'
             '\tat '
             'domainannotation.DomainAnnotationImpl.runDomainSearch(DomainAnnotationImpl.java:411)\n'
             '\tat '
             'domainannotation.DomainAnnotationImpl.searchDomains(DomainAnnotationImpl.java:246)\n'
             '\tat '
             'domainannotation.DomainAnnotationServer.searchDomains(DomainAnnotationServer.java:67)\n'
             '\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native '
             'Method)\n'
             '\tat '
             'sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)\n'
             '\tat '
             'sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n'
             '\tat java.lang.reflect.Method.invoke(Method.java:498)\n'
             '\tat '
             'us.kbase.common.service.JsonServerServlet.processRpcCall(JsonServerServlet.java:610)\n'
             '\tat '
             'us.kbase.common.service.JsonServerServlet.processRpcCall(JsonServerServlet.java:499)\n'
             '\tat '
             'domainannotation.DomainAnnotationServer.main(DomainAnnotationServer.java:140)\n'
             'Caused by: javax.net.ssl.SSLException: SSL peer shut down '
             'incorrectly\n'
             '\tat '
             'sun.security.ssl.InputRecord.readV3Record(InputRecord.java:596)\n'
             '\tat sun.security.ssl.InputRecord.read(InputRecord.java:532)\n'
             '\tat '
             'sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:983)\n'
             '\tat '
             'sun.security.ssl.SSLSocketImpl.readDataRecord(SSLSocketImpl.java:940)\n'
             '\tat '
             'sun.security.ssl.AppInputStream.read(AppInputStream.java:105)\n'
             '\tat '
             'org.apache.http.impl.io.SessionInputBufferImpl.streamRead(SessionInputBufferImpl.java:137)\n'
             '\tat '
             'org.apache.http.impl.io.SessionInputBufferImpl.read(SessionInputBufferImpl.java:198)\n'
             '\tat '
             'org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:176)\n'
             '\tat '
             'org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:198)\n'
             '\tat '
             'org.apache.http.entity.BasicHttpEntity.writeTo(BasicHttpEntity.java:116)\n'
             '\t... 14 more\n'
             '\n',
 'finished': 1571777659178,
 'job_id': '5daf2face4b0870657b8f4f4',
 'job_input': {'app_id': 'kb_phylogenomics/run_DomainAnnotation_Sets',
               'method': 'kb_phylogenomics.run_DomainAnnotation_Sets',
               'narrative_cell_info': {'cell_id': 'f25553f3-6f4e-431f-91d4-5dc0b852c64c',
                                       'run_id': 'cb44662e-1057-4e2c-973b-3899eb58d261',
                                       'tag': 'release',
                                       'token_id': '01b9bc76-37d6-4079-be64-c0ebbfbcf0ba'},
               'params': [{'input_genomeSet_ref': '43273/140/1',
                           'override_annot': '0',
                           'workspace_name': 'mpb:narrative_1555682254388'}],
               'service_ver': 'aed8564fcf4c6e8a3e94f6546715496e6fffbd84',
               'source_ws_objects': ['43273/140/1'],
               'wsid': 43273},
 'job_output': {'error': {'code': -32000,
                          'error': 'Traceback (most recent call last):\n'
                                   '  File '
                                   '"/kb/module/bin/../lib/kb_phylogenomics/kb_phylogenomicsServer.py", '
                                   'line 95, in _call_method\n'
                                   '    result = method(ctx, *params)\n'
                                   '  File '
                                   '"/kb/module/lib/kb_phylogenomics/kb_phylogenomicsImpl.py", '
                                   'line 1439, in run_DomainAnnotation_Sets\n'
                                   '    da_retVal = '
                                   'daClient.search_domains(DomainAnnotation_Params)\n'
                                   '  File '
                                   '"/kb/module/lib/installed_clients/DomainAnnotationClient.py", '
                                   'line 62, in search_domains\n'
                                   '    [input], self._service_ver, context)\n'
                                   '  File '
                                   '"/kb/module/lib/installed_clients/baseclient.py", '
                                   'line 253, in run_job\n'
                                   '    job_state = self._check_job(mod, '
                                   'job_id)\n'
                                   '  File '
                                   '"/kb/module/lib/installed_clients/baseclient.py", '
                                   'line 220, in _check_job\n'
                                   '    return self._call(self.url, service + '
                                   "'._check_job', [job_id])\n"
                                   '  File '
                                   '"/kb/module/lib/installed_clients/baseclient.py", '
                                   'line 187, in _call\n'
                                   "    raise ServerError(**err['error'])\n"
                                   'ServerError: JSONRPCError: -32500. '
                                   'Connection has been shutdown: '
                                   'javax.net.ssl.SSLException: SSL peer shut '
                                   'down incorrectly\n'
                                   'javax.net.ssl.SSLException: Connection has '
                                   'been shutdown: javax.net.ssl.SSLException: '
                                   'SSL peer shut down incorrectly\n'
                                   '\tat '
                                   'sun.security.ssl.SSLSocketImpl.checkEOF(SSLSocketImpl.java:1551)\n'
                                   '\tat '
                                   'sun.security.ssl.AppInputStream.read(AppInputStream.java:95)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.SessionInputBufferImpl.streamRead(SessionInputBufferImpl.java:137)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.SessionInputBufferImpl.read(SessionInputBufferImpl.java:198)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:176)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:198)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.ContentLengthInputStream.close(ContentLengthInputStream.java:101)\n'
                                   '\tat '
                                   'org.apache.http.entity.BasicHttpEntity.writeTo(BasicHttpEntity.java:120)\n'
                                   '\tat '
                                   'org.apache.http.impl.execchain.ResponseEntityProxy.writeTo(ResponseEntityProxy.java:101)\n'
                                   '\tat '
                                   'us.kbase.shock.client.BasicShockClient.getFile(BasicShockClient.java:355)\n'
                                   '\tat '
                                   'domainannotation.DomainAnnotationImpl.fromShock(DomainAnnotationImpl.java:118)\n'
                                   '\tat '
                                   'domainannotation.DomainAnnotationImpl.prepareLibraryFiles(DomainAnnotationImpl.java:759)\n'
                                   '\tat '
                                   'domainannotation.DomainAnnotationImpl.runDomainSearch(DomainAnnotationImpl.java:411)\n'
                                   '\tat '
                                   'domainannotation.DomainAnnotationImpl.searchDomains(DomainAnnotationImpl.java:246)\n'
                                   '\tat '
                                   'domainannotation.DomainAnnotationServer.searchDomains(DomainAnnotationServer.java:67)\n'
                                   '\tat '
                                   'sun.reflect.NativeMethodAccessorImpl.invoke0(Native '
                                   'Method)\n'
                                   '\tat '
                                   'sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)\n'
                                   '\tat '
                                   'sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n'
                                   '\tat '
                                   'java.lang.reflect.Method.invoke(Method.java:498)\n'
                                   '\tat '
                                   'us.kbase.common.service.JsonServerServlet.processRpcCall(JsonServerServlet.java:610)\n'
                                   '\tat '
                                   'us.kbase.common.service.JsonServerServlet.processRpcCall(JsonServerServlet.java:499)\n'
                                   '\tat '
                                   'domainannotation.DomainAnnotationServer.main(DomainAnnotationServer.java:140)\n'
                                   'Caused by: javax.net.ssl.SSLException: SSL '
                                   'peer shut down incorrectly\n'
                                   '\tat '
                                   'sun.security.ssl.InputRecord.readV3Record(InputRecord.java:596)\n'
                                   '\tat '
                                   'sun.security.ssl.InputRecord.read(InputRecord.java:532)\n'
                                   '\tat '
                                   'sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:983)\n'
                                   '\tat '
                                   'sun.security.ssl.SSLSocketImpl.readDataRecord(SSLSocketImpl.java:940)\n'
                                   '\tat '
                                   'sun.security.ssl.AppInputStream.read(AppInputStream.java:105)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.SessionInputBufferImpl.streamRead(SessionInputBufferImpl.java:137)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.SessionInputBufferImpl.read(SessionInputBufferImpl.java:198)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:176)\n'
                                   '\tat '
                                   'org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:198)\n'
                                   '\tat '
                                   'org.apache.http.entity.BasicHttpEntity.writeTo(BasicHttpEntity.java:116)\n'
                                   '\t... 14 more\n'
                                   '\n',
                          'message': 'Connection has been shutdown: '
                                     'javax.net.ssl.SSLException: SSL peer '
                                     'shut down incorrectly',
                          'name': 'Server error'},
                'id': '0603951074388',
                'version': '1.1'},
 'msg': 'Connection has been shutdown: javax.net.ssl.SSLException: SSL peer '
        'shut down incorrectly queued',
 'running': 1571762120403,
 'scheduler_id': '215873.0 - 215873.0',
 'scheduler_type': 'condor',
 'status': 'error',
 'updated': 1571777659195,
 'user': 'kbasehelp',
 'wsid': 43273}
mergeable[bot] commented 4 years ago

This is old. Is it still relevant?