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MOZI-AI / annotation-service

The gene annotation service maps human gene symbols to their biological context as represented in an OpenCog Knowledge Hypergraph
https://mozi.ai
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APP input causes error #13

Closed mjsduncan closed 5 years ago

mjsduncan commented 5 years ago

APP is in the production data set, it has appeared as a biogrid annotation for another gene, but as an input gene it produces this error:

Python-Scheme Wrapper: Failed to execute '(annotate-genes (list \"APP\" ) \"fGJmJaa\" (delay (list (gene-info (list \"APP\" )) ( gene-go-annotation (list \"APP\" ) \"biological_process cellular_component molecularfunction\" 0)( gene-pathway-annotation (list \"APP\" ) \"reactome smpdb\" \"True\" \"True\" )( biogrid-interaction-annotation (list \"APP\" ) \"Proteins\" ))))'\nBacktrace:\n 14 (apply-smob/1 #<catch-closure 7f13f9da78a0>)\n 13 (apply-smob/1 #<catch-closure 7f13f9da77a0>)\nIn ice-9/boot-9.scm:\n 2312:4 12 (save-module-excursion )\nIn ice-9/eval-string.scm:\n 38:6 11 (read-and-eval #<input: string 7f13abcb37e0> #:lang )\nIn ice-9/boot-9.scm:\n 152:2 10 (with-fluid* )\n 152:2 9 (with-fluid _)\n 152:2 8 (with-fluid )\n 152:2 7 (with-fluid* )\n 152:2 6 (with-fluid _)\n 152:2 5 (with-fluid )\nIn ice-9/eval.scm:\n 155:9 4 ( )\n 619:8 3 ( #(#(#(#(#(#(#(#<directory (guile-?>) ?) ?) ?) ?) ?) ?))\nIn ice-9/ports.scm:\n 469:4 2 (with-input-from-port )\nIn ice-9/boot-9.scm:\n 751:25 1 (dispatch-exception 0 nyacc-error (\"~A:~A: parse fai?\" ?))\nIn unknown file:\n 0 (apply-smob/1 #<catch-closure 7f13f9da7760> nyacc-error ?)\n\nERROR: In procedure apply-smob/1:\nIn procedure ~A:~A: parse failed at state ~A, on input ~S: Error while printing exception.\nABORT: nyacc-error\n (/root/atomspace/opencog/cython/opencog/PyScheme.cc:63)

mjsduncan commented 5 years ago

getting an error with the new pull (this is from BRCA1 input but i'm putting it here since the newest commit was addressing this error)

annotation-service | 2019-07-09 12:03:15,542 - annotation-service - INFO - Scheme Func: (list (gene-info (list "BRCA1" )) ( gene-pathway-annotation (list "BRCA1" ) "reactome" "False" "False" )( biogrid-interaction-annotation (list "BRCA1" ) "Proteins" )) annotation-service | 2019-07-09 12:03:15,542 - annotation-service - INFO - doing annotation (annotate-genes (list "BRCA1" ) "JjXWdba" (delay (list (gene-info (list "BRCA1" )) ( gene-pathway-annotation (list "BRCA1" ) "reactome" "False" "False" )( biogrid-interaction-annotation (list "BRCA1" ) "Proteins" )))) annotation-service | 2019-07-09 12:03:17,040 - annotation-service - ERROR - Error: <traceback object at 0x7ff9519f3948> ... annotation-service | time="2019-07-09T12:03:17-04:00" level=info msg="finished streaming call" error="rpc error: code = InvalidArgument desc = Error occurred in while trying to perform request: Python-Scheme Wrapper: Failed to execute '(annotate-genes (list \"BRCA1\" ) \"JjXWdba\" (delay (list (gene-info (list \"BRCA1\" )) ( gene-pathway-annotation (list \"BRCA1\" ) \"reactome\" \"False\" \"False\" )( biogrid-interaction-annotation (list \"BRCA1\" ) \"Proteins\" ))))'\nBacktrace:\nIn ice-9/boot-9.scm:\n 152:2 19 (with-fluid* )\nIn ice-9/eval.scm:\n 293:34 18 ( #(#(#<directory (guile-user) 7ff95c717140> #<pro…> …)))\n 155:9 17 ( )\nIn unknown file:\n 16 (force #<promise #<procedure 7ff9684133c0 at ice-9/eval…>)\nIn ice-9/eval.scm:\n 163:9 15 ( #(#(#<directory (guile-user) 7ff95c717140>)))\n 619:8 14 ( #(#(#(#<directory (guile-user) 7ff95c717140>) # …) …))\nIn srfi/srfi-1.scm:\n 640:9 13 (for-each #<procedure 7ff9684059a0 at ice-9/eval.scm:3…> …)\n 640:9 12 (for-each #<procedure 7ff968405420 at ice-9/eval.scm:3…> …)\nIn ice-9/eval.scm:\n 293:34 11 ( #(#(#<directory (guile-user) 7ff95c717140> \"BR…\" …) …))\n 619:8 10 ( #(#(#(#<directory (guile-user) 7ff95c717140>) # …) …))\n 626:19 9 ( #(#(#(#<directory (guile-user) 7ff95c717140>) # …) …))\n 155:9 8 ( )\nIn srfi/srfi-1.scm:\n 592:17 7 (map1 (# # # # # # # # # # # # # # # # #))\nIn ice-9/eval.scm:\n 619:8 6 ( #(#(#(#<directory (guile-user) 7ff95c717140> …) #) …))\n 626:19 5 ( #(#(#(#<directory (guile-user) 7ff95c717140> …) #) …))\n 159:9 4 ( )\n 155:9 3 ( )\nIn unknown file:\n 2 (opencog-extension cog-execute! (#))\nIn ice-9/boot-9.scm:\n 751:25 1 (dispatch-exception 0 C++-EXCEPTION (\"cog-execute!\" \"…\"))\nIn unknown file:\n 0 (apply-smob/1 #<catch-closure 7ff9684005a0> # \"cog-exe…\" …)\n\nERROR: In procedure apply-smob/1:\nIn procedure cog-execute!: Backtrace:\nIn ice-9/eval.scm:\n 155:9 19 ( )\nIn unknown file:\n 18 (force #<promise #<procedure 7ff9684133c0 at ice-9/eval…>)\nIn ice-9/eval.scm:\n 163:9 17 ( #(#(#<directory (guile-user) 7ff95c717140>)))\n 619:8 16 (_ #(#(#(#<directory (guile-user) 7ff95c717140>) # …) …))\nIn srfi/srfi-1.scm:\n" grpc.code=InvalidArgument grpc.method=Annotate grpc.service=Annotate grpc.start_time="2019-07-09T12:02:52-04:00" grpc.time_ms=24142 span.kind=server system=grpc

mjsduncan commented 5 years ago

same error generated with IGF1 which worked in previous pull. The same error occurs when only reactome pathways are selected without proteins but works with proteins and for only GO. original error had reactome and biogrid, no proteins

mjsduncan commented 5 years ago

same error with APP $ git submodule status 2b9114fec6f3db0f2da928635a23bb8aaa2a93d9 annotation-result-ui (remotes/origin/HEAD) fac8c0d5436185e29cdbacb9d4f8e7f4c193fd3a react (remotes/origin/HEAD) f119939995069f7ebe7dc89c6ed17539fb3fb32e scheme (remotes/origin/HEAD) 2f29a5bf2c5e755c1bb3076cd321c6590460f927 utils/scm2csv (remotes/origin/HEAD)

Habush commented 5 years ago

@mjsduncan There was a malformed data for the APP GO annotation. It has been fixed now. Can you update the GO.scm and try again?

mjsduncan commented 5 years ago

error from APP after updating the datasets:

annotation-service | 2019-08-15 20:53:27,538 - annotation-service - INFO - when executing atoms:5873731
annotation-service |
annotation-service | 2019-08-15 20:53:27,539 - annotation-service - INFO - Scheme Func: (list (gene-info (list "APP" )) ( gene-go-annotation (list "APP" )  "biological_process cellular_component molecular_function" )( gene-pathway-annotation (list "APP" )  "smpdb reactome"  "True"  "True" )( biogrid-interaction-annotation (list "APP" )  "Proteins" ))
annotation-service | 2019-08-15 20:53:27,539 - annotation-service - INFO - doing annotation (annotate-genes (list "APP" ) "Oq9-Fba" (delay (list (gene-info (list "APP" )) ( gene-go-annotation (list "APP" )  "biological_process cellular_component molecular_function" )( gene-pathway-annotation (list "APP" )  "smpdb reactome"  "True"  "True" )( biogrid-interaction-annotation (list "APP" )  "Proteins" ))))
annotation-service | 2019-08-15 20:57:53,416 - annotation-service - ERROR - Error: Python-Scheme Wrapper: Failed to execute '(annotate-genes (list "APP" ) "Oq9-Fba" (delay (list (gene-info (list "APP" )) ( gene-go-annotation (list "APP" )  "biological_process cellular_component molecular_function" )( gene-pathway-annotation (list "APP" )  "smpdb reactome"  "True"  "True" )( biogrid-interaction-annotation (list "APP" )  "Proteins" ))))'
annotation-service | Backtrace:
annotation-service |            8 (apply-smob/1 #<catch-closure 7fd8f3d6d860>)
annotation-service |            7 (apply-smob/1 #<catch-closure 7fd8f3d6d760>)
annotation-service | In ice-9/boot-9.scm:
annotation-service |    2312:4  6 (save-module-excursion _)
annotation-service | In ice-9/eval-string.scm:
annotation-service |      38:6  5 (read-and-eval #<input: string 7fd8f355a0e0> #:lang _)
annotation-service | In annotation/main.scm:
annotation-service |     71:24  4 (annotate-genes _ )
annotation-service | In annotation/parser.scm:
annotation-service |     247:8  3 (atomese-parser _ _)
annotation-service | In ice-9/ports.scm:
annotation-service |     469:4  2 (with-input-from-port _ _)
annotation-service | In ice-9/boot-9.scm:
annotation-service |    751:25  1 (dispatch-exception 0 nyacc-error ("~A:~A: parse fai…" …))
annotation-service | In unknown file:
annotation-service |            0 (apply-smob/1 #<catch-closure 7fd8f3d6d720> nyacc-error …)
annotation-service |
annotation-service | ERROR: In procedure apply-smob/1:
annotation-service | In procedure ~A:~A: parse failed at state ~A, on input ~S: Error while printing exception.
annotation-service | ABORT: nyacc-error
annotation-service |  (/root/atomspace/opencog/cython/opencog/PyScheme.cc:63)
annotation-service | time="2019-08-15T20:57:53+08:00" level=error msg="finished streaming call" error="rpc error: code = Internal desc = an internal error occured. please try again" grpc.code=Internal grpc.method=Annotate grpc.service=Annotate grpc.start_time="2019-08-15T20:53:27+08:00" grpc.time_ms=265899 span.kind=server system=grpc
mjsduncan commented 5 years ago

after reloading input page and re-entering APP w/o smpdb a couple time i got these errors:

annotation-service | 2019-08-15 21:18:16,827 - annotation-service - INFO - Current PID: 88
annotation-service | 2019-08-15 21:18:16,956 - annotation-service - INFO - checking genes : (list "APP" )
annotation-service | 2019-08-15 21:18:16,960 - annotation-service - INFO - (list "APP" )
annotation-service | 2019-08-15 21:18:16,969 - annotation-service - WARNING - result : 0
annotation-service | 2019-08-15 21:18:16,974 - annotation-service - WARNING - 0
annotation-service |
annotation-service | 2019-08-15 21:19:47,187 - annotation-service - ERROR - Error: <traceback object at 0x7fd9151a5cc8>
annotation-service | time="2019-08-15T21:19:47+08:00" level=info msg="finished streaming call" error="rpc error: code = InvalidArgument desc = Error occurred in while trying to perform request: mongo:27017: [Errno -3] Temporary failure in name resolution" grpc.code=InvalidArgument grpc.method=Annotate grpc.service=Annotate grpc.start_time="2019-08-15T21:18:16+08:00" grpc.time_ms=90367 span.kind=server system=grpc
ui          | 172.18.0.1 - - [15/Aug/2019:13:44:53 +0000] "GET / HTTP/1.1" 304 0 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" "-"
ui          | 172.18.0.1 - - [15/Aug/2019:13:44:53 +0000] "GET /bundle.js HTTP/1.1" 304 0 "http://localhost:3003/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" "-"
ui          | 172.18.0.1 - - [15/Aug/2019:13:44:54 +0000] "GET /src/assets/mozi_globe.e45aa4be670209bde81189ebbdcc6aea.png HTTP/1.1" 200 189899 "http://localhost:3003/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" "-"
ui          | 172.18.0.1 - - [15/Aug/2019:13:44:54 +0000] "GET /src/assets/bg.0b9017a22b64daada94f56c0ff2765d9.svg HTTP/1.1" 304 0 "http://localhost:3003/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" "-"
annotation-service | 2019-08-15 21:45:20,862 - annotation-service - INFO - Current PID: 88
annotation-service | 2019-08-15 21:45:20,863 - annotation-service - INFO - checking genes : (list "APP" )
annotation-service | 2019-08-15 21:45:20,863 - annotation-service - INFO - (list "APP" )
annotation-service | 2019-08-15 21:45:20,864 - annotation-service - WARNING - result : 0
annotation-service | 2019-08-15 21:45:20,864 - annotation-service - WARNING - 0
annotation-service |
annotation-service | 2019-08-15 21:46:51,053 - annotation-service - ERROR - Error: <traceback object at 0x7fd9151b7248>
annotation-service | time="2019-08-15T21:46:51+08:00" level=info msg="finished streaming call" error="rpc error: code = InvalidArgument desc = Error occurred in while trying to perform request: mongo:27017: [Errno -3] Temporary failure in name resolution" grpc.code=InvalidArgument grpc.method=Annotate grpc.service=Annotate grpc.start_time="2019-08-15T21:45:20+08:00" grpc.time_ms=90193 span.kind=server system=grpc
mjsduncan commented 5 years ago

after resetting the service, it generated the scm file for APP (it exists in results folder) but i never got a results link page and the shell log generated a bunch of messages like this:

mongo_1_f9567473e027 | 2019-08-15T17:00:39.411+0000 I COMMAND  [ftdc] serverStatus was very slow: { after basic: 71, after asserts: 185, after backgroundFlushing: 362, after connections: 733, after dur: 848, after extra_info: 1095, after freeMonitoring: 1535, after globalLock: 1946, after locks: 2274, after logicalSessionRecordCache: 2404, after network: 2714, after opLatencies: 2892, after opReadConcernCounters: 3087, after opcounters: 3311, after opcountersRepl: 3447, after repl: 3554, after security: 3566, after storageEngine: 3576, after tcmalloc: 3598, after transactions: 3598, after transportSecurity: 3598, after wiredTiger: 3700, at end: 3763 }
....
us was very slow: { after basic: 61, after asserts: 417, after backgroundFlushing: 417, after connections: 461, after dur: 474, after extra_info: 474, after freeMonitoring: 637, after globalLock: 1141, after locks: 2101, after logicalSessionRecordCache: 3058, after network: 5221, after opLatencies: 6142, after opReadConcernCounters: 6644, after opcounters: 8089, after opcountersRepl: 8257, after repl: 8257, after security: 8257, after storageEngine: 8553, after tcmalloc: 11309, after transactions: 12412, after transportSecurity: 13325, after wiredTiger: 56954, at end: 56964 }
mongo_1_f9567473e027 | 2019-08-15T17:06:06.962+0000 I COMMAND  [PeriodicTaskRunner] task: DBConnectionPool-cleaner took: 1622ms
mongo_1_f9567473e027 | 2019-08-15T17:06:07.321+0000 I COMMAND  [LogicalSessionCacheRefresh] command config.system.sessions command: listIndexes { listIndexes: "system.sessions", cursor: {}, $db: "config" } numYields:0 reslen:324 locks:{ Global: { acquireCount: { r: 1 } }, Database: { acquireCount: { r: 1 } }, Collection: { acquireCount: { r: 1 } } } storage:{} protocol:op_msg 237ms
mongo_1_f9567473e027 | 2019-08-15T17:06:08.280+0000 I NETWORK  [conn2] end connection 172.18.0.5:40550 (2 connections now open)
mongo_1_f9567473e027 | 2019-08-15T17:06:08.289+0000 I NETWORK  [conn3] end connection 172.18.0.5:40552 (1 connection now open)
annotation-service | time="2019-08-16T01:06:08+08:00" level=info msg="pickfirstBalancer: HandleSubConnStateChange: 0xc420099680, TRANSIENT_FAILURE" system=system
annotation-service | time="2019-08-16T01:06:08+08:00" level=info msg="pickfirstBalancer: HandleSubConnStateChange: 0xc420099680, CONNECTING" system=system
annotation-service | time="2019-08-16T01:06:08+08:00" level=info msg="pickfirstBalancer: HandleSubConnStateChange: 0xc420099680, READY" system=system
mjsduncan commented 5 years ago

after resseting and trying again with vpn off, scheme file generated but python process filled up ram and maxed out swap drive so i had to shut it down before getting a results screen.

annotation-service | 2019-08-16 13:19:11,384 - annotation-service - INFO - doing annotation (annotate-genes (list "APP" ) "4Fk3fda" (delay (list (gene-info (list "APP" )) ( gene-go-annotation (list "APP" )  "biological_process cellular_component molecular_function" )( gene-pathway-annotation (list "APP" )  "reactome"  "True"  "True" )( biogrid-interaction-annotation (list "APP" )  "Proteins" ))))
mongo_1_f9567473e027 | 2019-08-16T05:20:44.773+0000 I COMMAND  [PeriodicTaskRunner] task: DBConnectionPool-cleaner took: 122ms
annotation-service | 2019-08-16 13:27:30,597 - annotation-service - INFO - saving result in file : /root/result/scheme/4Fk3fda.scm
annotation-service | 2019-08-16 13:27:30,604 - annotation-service - INFO - Filename: /root/result/scheme/4Fk3fda.scm
annotation-service | E0816 15:19:30.981285890     128 chttp2_transport.cc:2801]   ipv4:127.0.0.1:50762: Keepalive watchdog fired. Closing transport.
annotation-service | time="2019-08-16T15:19:31+08:00" level=info msg="pickfirstBalancer: HandleSubConnStateChange: 0xc42018a220, TRANSIENT_FAILURE" system=system
annotation-service | time="2019-08-16T15:19:31+08:00" level=info msg="pickfirstBalancer: HandleSubConnStateChange: 0xc42018a220, CONNECTING" system=system
annotation-service | time="2019-08-16T15:19:31+08:00" level=info msg="pickfirstBalancer: HandleSubConnStateChange: 0xc42018a220, READY" system=system
annotation-service | time="2019-08-16T15:19:31+08:00" level=warning msg="finished streaming call" error="rpc error: code = Unavailable desc = keepalive watchdog timeout" grpc.code=Unavailable grpc.method=Annotate grpc.service=Annotate grpc.start_time="2019-08-16T13:19:10+08:00" grpc.time_ms=7.220059e+06 span.kind=server system=grpc
annotation-service | 2019-08-16 15:19:31,593 - annotation-service - INFO - Current PID: 88
annotation-service | 2019-08-16 15:19:31,649 - annotation-service - INFO - checking genes : (list "APP" )
annotation-service | 2019-08-16 15:19:31,649 - annotation-service - INFO - (list "APP" )
annotation-service | 2019-08-16 15:19:31,753 - annotation-service - WARNING - result : 0
annotation-service | 2019-08-16 15:19:31,753 - annotation-service - WARNING - 0
annotation-service | 
mongo_1_f9567473e027 | 2019-08-16T07:19:32.142+0000 I NETWORK  [listener] connection accepted from 172.18.0.5:42964 #4 (4 connections now open)
mongo_1_f9567473e027 | 2019-08-16T07:19:32.207+0000 I NETWORK  [conn4] received client metadata from 172.18.0.5:42964 conn4: { driver: { name: "PyMongo", version: "3.9.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "4.18.0-25-generic" }, platform: "CPython 3.5.2.final.0" }
mongo_1_f9567473e027 | 2019-08-16T07:19:32.269+0000 I NETWORK  [listener] connection accepted from 172.18.0.5:42966 #5 (5 connections now open)
mongo_1_f9567473e027 | 2019-08-16T07:19:32.271+0000 I NETWORK  [conn5] received client metadata from 172.18.0.5:42966 conn5: { driver: { name: "PyMongo", version: "3.9.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "4.18.0-25-generic" }, platform: "CPython 3.5.2.final.0" }
annotation-service | 2019-08-16 15:19:32,459 - annotation-service - INFO - when executing atoms:5872616
annotation-service | 
annotation-service | 2019-08-16 15:19:32,461 - annotation-service - INFO - Scheme Func: (list (gene-info (list "APP" )) ( gene-go-annotation (list "APP" )  "biological_process cellular_component molecular_function" )( gene-pathway-annotation (list "APP" )  "reactome"  "True"  "True" )( biogrid-interaction-annotation (list "APP" )  "Proteins" ))
annotation-service | 2019-08-16 15:19:32,462 - annotation-service - INFO - doing annotation (annotate-genes (list "APP" ) "hh__1da" (delay (list (gene-info (list "APP" )) ( gene-go-annotation (list "APP" )  "biological_process cellular_component molecular_function" )( gene-pathway-annotation (list "APP" )  "reactome"  "True"  "True" )( biogrid-interaction-annotation (list "APP" )  "Proteins" ))))
annotation-service | 2019-08-16 15:32:26,847 - annotation-service - INFO - saving result in file : /root/result/scheme/hh__1da.scm
annotation-service | 2019-08-16 15:32:26,985 - annotation-service - INFO - Filename: /root/result/scheme/hh__1da.scm
mongo_1_f9567473e027 | 2019-08-16T07:53:43.275+0000 I WRITE    [conn5] update snet_annotation.sessions command: { q: { id: BinData(3, F5FFF1C7F15B4634BA15AE31A71EDF63) }, u: { $set: { annotations: [ { filters: [ { value: "biological_process cellular_component molecular_function", filter: "namespace" }, { value: "", filter: "parents" } ], function_name: "gene-go-annotation" }, { filters: [ { value: "reactome", filter: "namespace" }, { value: "True", filter: "include_prot" }, { value: "True", filter: "include_small_molecule" } ], function_name: "gene-pathway-annotation" }, { filters: [ { value: "Proteins", filter: "interaction" } ], function_name: "biogrid-interaction-annotation" } ], end_time: 0, status: -1, id: BinData(3, F5FFF1C7F15B4634BA15AE31A71EDF63), message: "", expired: false, mnemonic: "hh__1da", result: "{"nodes" : [{"data" : {"id" : "KEAP1","name" : "Kelch-like ECH-associated protein 1","definition" : "https://www.ncbi.nlm.nih.gov/gene/9817","location...", _id: ObjectId('5d5659030e353fca8a60ba4e'), csv_file: null, start_time: 1565939972.352785, genes: [ { gene_name: "APP" } ], result_file: "/root/result/scheme/hh__1da.scm" } }, multi: false, upsert: false } planSummary: COLLSCAN keysExamined:0 docsExamined:7 nMatched:1 nModified:1 numYields:2 locks:{ Global: { acquireCount: { r: 3, w: 3 } }, Database: { acquireCount: { w: 3 } }, Collection: { acquireCount: { w: 3 } } } storage:{ data: { bytesWritten: 15864233, timeWritingMicros: 2336 } } 924ms
mongo_1_f9567473e027 | 2019-08-16T07:53:43.283+0000 I COMMAND  [conn5] command snet_annotation.$cmd command: update { update: "sessions", ordered: true, lsid: { id: UUID("e1928f1e-406d-4b42-aa1b-c7e78db36090") }, $db: "snet_annotation", $readPreference: { mode: "primary" } } numYields:0 reslen:60 locks:{ Global: { acquireCount: { r: 5, w: 3 } }, Database: { acquireCount: { w: 3 } }, Collection: { acquireCount: { w: 3 } } } storage:{} protocol:op_msg 1009ms
annotation-service | 2019-08-16 15:53:43,341 - annotation-service - ERROR - Error: 
mongo_1_f9567473e027 | 2019-08-16T07:55:02.808+0000 I WRITE    [conn5] update snet_annotation.sessions command: { q: { id: BinData(3, F5FFF1C7F15B4634BA15AE31A71EDF63) }, u: { $set: { annotations: [ { filters: [ { value: "biological_process cellular_component molecular_function", filter: "namespace" }, { value: "", filter: "parents" } ], function_name: "gene-go-annotation" }, { filters: [ { value: "reactome", filter: "namespace" }, { value: "True", filter: "include_prot" }, { value: "True", filter: "include_small_molecule" } ], function_name: "gene-pathway-annotation" }, { filters: [ { value: "Proteins", filter: "interaction" } ], function_name: "biogrid-interaction-annotation" } ], end_time: 1565942097.392762, status: -1, id: BinData(3, F5FFF1C7F15B4634BA15AE31A71EDF63), message: "Error: ", expired: false, mnemonic: "hh__1da", result: "{"nodes" : [{"data" : {"id" : "KEAP1","name" : "Kelch-like ECH-associated protein 1","definition" : "https://www.ncbi.nlm.nih.gov/gene/9817","location...", _id: ObjectId('5d5659030e353fca8a60ba4e'), csv_file: null, start_time: 1565939972.352785, genes: [ { gene_name: "APP" } ], result_file: "/root/result/scheme/hh__1da.scm" } }, multi: false, upsert: false } planSummary: COLLSCAN keysExamined:0 docsExamined:7 nMatched:1 nModified:1 numYields:1 locks:{ Global: { acquireCount: { r: 2, w: 2 } }, Database: { acquireCount: { w: 2 } }, Collection: { acquireCount: { w: 2 } } } storage:{ data: { bytesWritten: 15680273, timeWritingMicros: 48519 } } 4144ms
mongo_1_f9567473e027 | 2019-08-16T07:55:02.810+0000 I COMMAND  [conn5] command snet_annotation.$cmd command: update { update: "sessions", ordered: true, lsid: { id: UUID("e1928f1e-406d-4b42-aa1b-c7e78db36090") }, $db: "snet_annotation", $readPreference: { mode: "primary" } } numYields:0 reslen:60 locks:{ Global: { acquireCount: { r: 4, w: 2 } }, Database: { acquireCount: { w: 2 } }, Collection: { acquireCount: { w: 2 } } } storage:{} protocol:op_msg 5314ms
mongo_1_f9567473e027 | 2019-08-16T07:55:02.840+0000 I NETWORK  [conn5] end connection 172.18.0.5:42966 (4 connections now open)
mongo_1_f9567473e027 | 2019-08-16T07:55:02.840+0000 I NETWORK  [conn4] end connection 172.18.0.5:42964 (3 connections now open)
annotation-service | time="2019-08-16T15:55:03+08:00" level=error msg="finished streaming call" error="rpc error: code = Internal desc = an internal error occured. please try again" grpc.code=Internal grpc.method=Annotate grpc.service=Annotate grpc.start_time="2019-08-16T15:19:31+08:00" grpc.time_ms=2.131595e+06 span.kind=server system=grpc
^CGracefully stopping... (press Ctrl+C again to force)
mjsduncan commented 5 years ago

malformed atomese fixed