ptvsd debug.log

debug14661.log

2019-12-12, 08:01:15.632 UTC
[08:01:15.633 UTC] Started @ Thu Dec 12 2019 09:01:15 GMT+0100 (Central European Standard Time)
[08:01:15.634 UTC] From Client:
[08:01:15.634 UTC] Content-Length: 313

{"command":"initialize","arguments":{"clientID":"vscode","clientName":"Visual Studio Code","adapterID":"python","pathFormat":"path","linesStartAt1":true,"columnsStartAt1":true,"supportsVariableType":true,"supportsVariablePaging":true,"supportsRunInTerminalRequest":true,"locale":"en-us"},"type":"request","seq":1}
[08:01:15.634 UTC] To Client:
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{"seq":1,"type":"response","request_seq":1,"command":"initialize","success":true,"body":{"supportsExceptionInfoRequest":true,"supportsConfigurationDoneRequest":true,"supportsDelayedStackTraceLoading":true,"supportsConditionalBreakpoints":true,"supportsSetVariable":true,"supportsExceptionOptions":true,"supportsGotoTargetsRequest":true,"supportsEvaluateForHovers":true,"supportsModulesRequest":true,"supportsValueFormattingOptions":true,"supportsHitConditionalBreakpoints":true,"supportsSetExpression":true,"supportsLogPoints":true,"supportTerminateDebuggee":true,"supportsCompletionsRequest":true,"exceptionBreakpointFilters":[{"filter":"raised","label":"Raised Exceptions","default":false},{"filter":"uncaught","label":"Uncaught Exceptions","default":true}]}}
[08:01:15.634 UTC] From Client:
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{"command":"attach","arguments":{"name":"Python: phovea_server","type":"python","request":"attach","logToFile":true,"port":5678,"host":"localhost","pathMappings":[{"localRoot":"/home/klaus/cht","remoteRoot":"/phovea"}],"debugOptions":["RedirectOutput","UnixClient","ShowReturnValue"],"justMyCode":true,"showReturnValue":true,"workspaceFolder":"/home/klaus/cht","__sessionId":"03588a7a-ccdd-412d-82af-664a60d8c020"},"type":"request","seq":2}
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[08:01:15.636 UTC] To Client:
[08:01:15.636 UTC] {"command":"attach","arguments":{"name":"Python: phovea_server","type":"python","request":"attach","logToFile":true,"port":5678,"host":"localhost","pathMappings":[{"localRoot":"/home/klaus/cht","remoteRoot":"/phovea"}],"debugOptions":["RedirectOutput","UnixClient","ShowReturnValue"],"justMyCode":true,"showReturnValue":true,"workspaceFolder":"/home/klaus/cht","__sessionId":"03588a7a-ccdd-412d-82af-664a60d8c020"},"type":"request","seq":2}
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[08:01:15.637 UTC] To Client:
[08:01:15.637 UTC] {"command":"initialize","arguments":{"clientID":"vscode","clientName":"Visual Studio Code","adapterID":"python","pathFormat":"path","linesStartAt1":true,"columnsStartAt1":true,"supportsVariableType":true,"supportsVariablePaging":true,"supportsRunInTerminalRequest":true,"locale":"en-us"},"type":"request","seq":1}
[08:01:15.638 UTC] To Client:
[08:01:15.638 UTC] Content-Length: 130

{"type": "event", "seq": 0, "event": "output", "body": {"category": "telemetry", "output": "ptvsd", "data": {"version": "4.3.2"}}}Content-Length: 113


[08:01:15.692 UTC] To Client:
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{"type": "response", "seq": 2, "request_seq": 1, "success": true, "command": "initialize", "message": "", "body": {"supportsCompletionsRequest": true, "supportsConditionalBreakpoints": true, "supportsConfigurationDoneRequest": true, "supportsDebuggerProperties": true, "supportsDelayedStackTraceLoading": true, "supportsEvaluateForHovers": true, "supportsExceptionInfoRequest": true, "supportsExceptionOptions": true, "supportsHitConditionalBreakpoints": true, "supportsLogPoints": true, "supportsModulesRequest": true, "supportsSetExpression": true, "supportsSetVariable": true, "supportsValueFormattingOptions": true, "supportTerminateDebuggee": true, "supportsGotoTargetsRequest": true, "exceptionBreakpointFilters": [{"filter": "raised", "label": "Raised Exceptions", "default": false}, {"filter": "uncaught", "label": "Uncaught Exceptions", "default": true}]}}Content-Length: 63

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[08:01:15.721 UTC] To Client:
[08:01:15.721 UTC] Content-Length: 92

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{"command":"setExceptionBreakpoints","arguments":{"filters":["uncaught"]},"type":"request","seq":3}
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{"type": "response", "seq": 6, "request_seq": 3, "success": true, "command": "setExceptionBreakpoints", "message": "", "body": {}}
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{"command":"configurationDone","type":"request","seq":4}
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[08:01:15.841 UTC] To Client:
[08:01:15.841 UTC] {"type": "response", "seq": 7, "request_seq": 4, "success": true, "command": "configurationDone", "message": "", "body": {}}
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{"command":"threads","type":"request","seq":5}
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[08:01:15.890 UTC] To Client:
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{"command":"threads","type":"request","seq":6}
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[08:01:15.950 UTC] To Client:
[08:01:15.950 UTC] {"type": "response", "seq": 9, "request_seq": 6, "success": true, "command": "threads", "message": "", "body": {"threads": [{"id": 1, "name": "MainThread"}]}}
[08:01:16.331 UTC] To Client:
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[08:01:16.331 UTC] To Client:
[08:01:16.332 UTC] {"type": "event", "seq": 10, "event": "output", "body": {"output": "08:01:16 INFO phovea_server.server: init application: <Flask 'phovea_server.mainapp'>\n", "category": "stdout", "source": {}}}
[08:01:16.333 UTC] To Client:
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{"type": "event", "seq": 11, "event": "output", "body": {"output": "08:01:16 INFO phovea_server.server: add application: caleydo-clue-screenshot at namespace: /api/clue\n", "category": "stdout", "source": {}}}Content-Length: 204

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{"type": "event", "seq": 14, "event": "output", "body": {"output": "08:01:16 INFO phovea_server.server: add application: tdp_core at namespace: /api/tdp/proxy\n", "category": "stdout", "source": {}}}Content-Length: 200

{"type": "event", "seq": 15, "event": "output", "body": {"output": "08:01:16 INFO phovea_server.server: add application: db_connector at namespace: /api/tdp/db\n", "category": "stdout", "source": {}}}Content-Length: 204

{"type": "event", "seq": 16, "event": "output", "body": {"output": "08:01:16 INFO phovea_server.server: add application: tdp_storage at namespace: /api/tdp/storage\n", "category": "stdout", "source": {}}}Content-Length: 199

{"type": "event", "seq": 17, "event": "output", "body": {"output": "08:01:16 INFO phovea_server.server: add application: tdp_swagger at namespace: /api/tdp/ui\n", "category": "stdout", "source": {}}}Content-Length: 202

{"type": "event", "seq": 18, "event": "output", "body": {"output": "08:01:16 INFO phovea_server.server: add application: tdp_config at namespace: /api/tdp/config\n", "category": "stdout", "source": {}}}Content-Length: 203

{"type": "event", "seq": 19, "event": "output", "body": {"output": "08:01:16 INFO phovea_server.server: add application: tdp_xlsx2json at namespace: /api/tdp/xlsx\n", "category": "stdout", "source": {}}}Content-Length: 93

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{"command":"threads","type":"request","seq":7}
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{"type": "response", "seq": 22, "request_seq": 7, "success": true, "command": "threads", "message": "", "body": {"threads": [{"id": 1, "name": "MainThread"}, {"id": 3, "name": "DummyThread-6"}, {"id": 2, "name": "DummyThread-7"}]}}
[08:01:26.991 UTC] To Client:
[08:01:26.991 UTC] Content-Length: 172

{"type": "event", "seq": 23, "event": "output", "body": {"output": "08:01:26 INFO tdp_student.studentdb: Setting up studentdb_view.\n", "category": "stdout", "source": {}}}
[08:01:26.992 UTC] To Client:
[08:01:26.992 UTC] Content-Length: 196

{"type": "event", "seq": 24, "event": "output", "body": {"output": "08:01:26 INFO tdp_student.studentdb: Creating a DBConnector for the studentdb database.\n", "category": "stdout", "source": {}}}
[08:01:27.103 UTC] To Client:
[08:01:27.103 UTC] Content-Length: 93

{"type": "event", "seq": 25, "event": "thread", "body": {"reason": "started", "threadId": 4}}
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{"command":"threads","type":"request","seq":8}
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{"type": "response", "seq": 26, "request_seq": 8, "success": true, "command": "threads", "message": "", "body": {"threads": [{"id": 1, "name": "MainThread"}, {"id": 3, "name": "DummyThread-6"}, {"id": 2, "name": "DummyThread-7"}, {"id": 4, "name": "DummyThread-8"}]}}
[08:01:27.754 UTC] To Client:
[08:01:27.754 UTC] Content-Length: 390

{"type": "event", "seq": 27, "event": "output", "body": {"output": "08:01:27 INFO matplotlib.font_manager: font search path ['/usr/local/lib/python3.7/site-packages/matplotlib/mpl-data/fonts/ttf', '/usr/local/lib/python3.7/site-packages/matplotlib/mpl-data/fonts/afm', '/usr/local/lib/python3.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts']\n", "category": "stdout", "source": {}}}
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[08:01:28.090 UTC] To Client:
[08:01:28.090 UTC] {"type": "response", "seq": 29, "request_seq": 9, "success": true, "command": "threads", "message": "", "body": {"threads": [{"id": 1, "name": "MainThread"}, {"id": 3, "name": "DummyThread-6"}, {"id": 2, "name": "DummyThread-7"}, {"id": 4, "name": "DummyThread-8"}, {"id": 5, "name": "Thread-9"}]}}
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[08:01:28.442 UTC] To Client:
[08:01:28.443 UTC] {"type": "event", "seq": 30, "event": "output", "body": {"output": "08:01:28 INFO matplotlib.font_manager: generated new fontManager\n", "category": "stdout", "source": {}}}
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[08:01:28.656 UTC] To Client:
[08:01:28.656 UTC] {"type": "event", "seq": 31, "event": "output", "body": {"output": "08:01:28 INFO phovea_server.server: init application: <Flask 'tdp_core.sql'>\n", "category": "stdout", "source": {}}}
[08:01:28.656 UTC] To Client:
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{"type": "event", "seq": 32, "event": "output", "body": {"output": "08:01:28 INFO tdp_core.dbmanager: run greenifier: psycopg2\n", "category": "stdout", "source": {}}}
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[08:01:28.658 UTC] To Client:
[08:01:28.658 UTC] {"type": "event", "seq": 33, "event": "output", "body": {"output": "08:01:28 INFO phovea_server.plugin: importing tdp_core.sql_use_gevent\n", "category": "stdout", "source": {}}}
[08:01:28.659 UTC] To Client:
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{"type": "event", "seq": 34, "event": "output", "body": {"output": "08:01:28 INFO tdp_core.sql_use_gevent: patching psycopg2 to be green\n", "category": "stdout", "source": {}}}
[08:01:28.981 UTC] To Client:
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[08:01:28.981 UTC] To Client:
[08:01:28.981 UTC] {"type": "event", "seq": 35, "event": "output", "body": {"output": "08:01:28 INFO tdp_core.db: fill up view\n", "category": "stdout", "source": {}}}
[08:01:29.082 UTC] To Client:
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{"type": "event", "seq": 36, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: creating session\n", "category": "stdout", "source": {}}}
[08:01:29.082 UTC] To Client:
[08:01:29.082 UTC] Content-Length: 435

{"type": "event", "seq": 37, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT min(tdpid) as tdpid_min, max(tdpid) as tdpid_max, min(strand) as strand_min, max(strand) as strand_max, min(seqregionstart) as seqregionstart_min, max(seqregionstart) as seqregionstart_max, min(seqregionend) as seqregionend_min, max(seqregionend) as seqregionend_max FROM public.tdp_gene ({})\n", "category": "stdout", "source": {}}}
[08:01:29.191 UTC] To Client:
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[08:01:29.191 UTC] To Client:
[08:01:29.191 UTC] {"type": "event", "seq": 38, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct biotype as cat FROM public.tdp_gene WHERE biotype is not NULL AND biotype <> '' ORDER BY biotype ASC ({})\n", "category": "stdout", "source": {}}}
[08:01:29.192 UTC] To Client:
[08:01:29.192 UTC] Content-Length: 269

{"type": "event", "seq": 39, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct chromosome as cat FROM public.tdp_gene WHERE chromosome is not NULL AND chromosome <> '' ORDER BY chromosome ASC ({})\n", "category": "stdout", "source": {}}}
[08:01:29.303 UTC] To Client:
[08:01:29.303 UTC] Content-Length: 158

{"type": "event", "seq": 40, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: removing session again\n", "category": "stdout", "source": {}}}
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[08:01:29.308 UTC] To Client:
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{"type": "event", "seq": 43, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT min(cosmicid) as cosmicid_min, max(cosmicid) as cosmicid_max, min(tdpid) as tdpid_min, max(tdpid) as tdpid_max FROM cellline.tdp_cellline ({})\n", "category": "stdout", "source": {}}}Content-Length: 271

{"type": "event", "seq": 44, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct tumortype as cat FROM cellline.tdp_cellline WHERE tumortype is not NULL AND tumortype <> '' ORDER BY tumortype ASC ({})\n", "category": "stdout", "source": {}}}Content-Length: 255

{"type": "event", "seq": 45, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct organ as cat FROM cellline.tdp_cellline WHERE organ is not NULL AND organ <> '' ORDER BY organ ASC ({})\n", "category": "stdout", "source": {}}}
[08:01:29.308 UTC] To Client:
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{"type": "event", "seq": 46, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct gender as cat FROM cellline.tdp_cellline WHERE gender is not NULL AND gender <> '' ORDER BY gender ASC ({})\n", "category": "stdout", "source": {}}}Content-Length: 295

{"type": "event", "seq": 47, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct metastatic_site as cat FROM cellline.tdp_cellline WHERE metastatic_site is not NULL AND metastatic_site <> '' ORDER BY metastatic_site ASC ({})\n", "category": "stdout", "source": {}}}
[08:01:29.308 UTC] To Client:
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{"type": "event", "seq": 48, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct histology_type as cat FROM cellline.tdp_cellline WHERE histology_type is not NULL AND histology_type <> '' ORDER BY histology_type ASC ({})\n", "category": "stdout", "source": {}}}
[08:01:29.308 UTC] To Client:
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{"type": "event", "seq": 49, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct morphology as cat FROM cellline.tdp_cellline WHERE morphology is not NULL AND morphology <> '' ORDER BY morphology ASC ({})\n", "category": "stdout", "source": {}}}
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{"type": "event", "seq": 52, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct age_at_surgery as cat FROM cellline.tdp_cellline WHERE age_at_surgery is not NULL AND age_at_surgery <> '' ORDER BY age_at_surgery ASC ({})\n", "category": "stdout", "source": {}}}
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[08:01:29.311 UTC] To Client:
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{"type": "event", "seq": 56, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT min(age) as age_min, max(age) as age_max, min(days_to_death) as days_to_death_min, max(days_to_death) as days_to_death_max, min(days_to_last_followup) as days_to_last_followup_min, max(days_to_last_followup) as days_to_last_followup_max, min(height) as height_min, max(height) as height_max, min(weight) as weight_min, max(weight) as weight_max, min(bmi) as bmi_min, max(bmi) as bmi_max, min(tdpid) as tdpid_min, max(tdpid) as tdpid_max, min(tumorpurity) as tumorpurity_min, max(tumorpurity) as tumorpurity_max FROM tissue.tdp_tissue ({})\n", "category": "stdout", "source": {}}}Content-Length: 259

{"type": "event", "seq": 57, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct species as cat FROM tissue.tdp_tissue WHERE species is not NULL AND species <> '' ORDER BY species ASC ({})\n", "category": "stdout", "source": {}}}Content-Length: 267

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{"type": "event", "seq": 59, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct organ as cat FROM tissue.tdp_tissue WHERE organ is not NULL AND organ <> '' ORDER BY organ ASC ({})\n", "category": "stdout", "source": {}}}Content-Length: 255

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{"type": "event", "seq": 61, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct vendorname as cat FROM tissue.tdp_tissue WHERE vendorname is not NULL AND vendorname <> '' ORDER BY vendorname ASC ({})\n", "category": "stdout", "source": {}}}Content-Length: 247

{"type": "event", "seq": 62, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct race as cat FROM tissue.tdp_tissue WHERE race is not NULL AND race <> '' ORDER BY race ASC ({})\n", "category": "stdout", "source": {}}}
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[08:01:29.521 UTC] To Client:
[08:01:29.521 UTC] {"type": "event", "seq": 63, "event": "output", "body": {"output": "08:01:29 INFO tdp_core.db: SELECT distinct ethnicity as cat FROM tissue.tdp_tissue WHERE ethnicity is not NULL AND ethnicity <> '' ORDER BY ethnicity ASC ({})\n", "category": "stdout", "source": {}}}Content-Length: 158

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{"command":"setBreakpoints","arguments":{"source":{"name":"sql.py","path":"/home/klaus/cht/tdp_core/tdp_core/sql.py"},"lines":[179],"breakpoints":[{"line":179}],"sourceModified":false},"type":"request","seq":10}
[08:01:33.601 UTC] To Client:
[08:01:33.601 UTC] Content-Length: 262

{"type": "response", "seq": 68, "request_seq": 10, "success": true, "command": "setBreakpoints", "message": "", "body": {"breakpoints": [{"verified": true, "id": 0, "source": {"name": "sql.py", "path": "/home/klaus/cht/tdp_core/tdp_core/sql.py"}, "line": 179}]}}
[08:01:35.432 UTC] To Client:
[08:01:35.432 UTC] Content-Length: 152

{"type": "event", "seq": 69, "event": "stopped", "body": {"reason": "breakpoint", "threadId": 1, "preserveFocusHint": false, "allThreadsStopped": true}}
[08:01:35.436 UTC] From Client:
[08:01:35.436 UTC] Content-Length: 47

{"command":"threads","type":"request","seq":11}
[08:01:35.642 UTC] To Client:
[08:01:35.642 UTC] Content-Length: 268


[08:01:35.692 UTC] To Client:
[08:01:35.692 UTC] {"type": "response", "seq": 70, "request_seq": 11, "success": true, "command": "threads", "message": "", "body": {"threads": [{"id": 1, "name": "MainThread"}, {"id": 3, "name": "DummyThread-6"}, {"id": 2, "name": "DummyThread-7"}, {"id": 4, "name": "DummyThread-8"}]}}
[08:01:35.694 UTC] From Client:
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[08:01:35.753 UTC] To Client:
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[08:01:35.801 UTC] To Client:
[08:01:35.802 UTC] {"type": "event", "seq": 71, "event": "thread", "body": {"reason": "started", "threadId": 6}}
[08:01:35.861 UTC] To Client:
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{"type": "response", "seq": 72, "request_seq": 12, "success": true, "command": "stackTrace", "message": "", "body": {"stackFrames": [], "totalFrames": 0}}
[08:01:35.919 UTC] From Client:
[08:01:35.919 UTC] Content-Length: 47

{"command":"threads","type":"request","seq":13}
[08:01:35.971 UTC] To Client:
[08:01:35.971 UTC] Content-Length: 305

{"type": "response", "seq": 73, "request_seq": 13, "success": true, "command": "threads", "message": "", "body": {"threads": [{"id": 1, "name": "MainThread"}, {"id": 3, "name": "DummyThread-6"}, {"id": 2, "name": "DummyThread-7"}, {"id": 4, "name": "DummyThread-8"}, {"id": 6, "name": "DummyThread-10"}]}}
[08:01:36.293 UTC] From Client:
[08:01:36.293 UTC] Content-Length: 104

{"command":"stackTrace","arguments":{"threadId":1,"startFrame":0,"levels":19},"type":"request","seq":14}
[08:01:36.402 UTC] To Client:
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{"type": "response", "seq": 74, "request_seq": 14, "success": true, "command": "stackTrace", "message": "", "body": {"stackFrames": [], "totalFrames": 0}}
[08:01:47.116 UTC] From Client:
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{"command":"evaluate","arguments":{"expression":"view","context":"repl"},"type":"request","seq":15}
[08:01:47.222 UTC] To Client:
[08:01:47.222 UTC] Content-Length: 155

{"type": "response", "seq": 75, "request_seq": 15, "success": false, "command": "evaluate", "message": "Unable to find thread for evaluation.", "body": {}}
[08:02:00.128 UTC] From Client:
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{"command":"continue","arguments":{"threadId":1},"type":"request","seq":16}
[08:02:00.129 UTC] To Client:
[08:02:00.129 UTC] Content-Length: 144


[08:02:00.130 UTC] To Client:
[08:02:00.130 UTC] {"type": "response", "seq": 76, "request_seq": 16, "success": true, "command": "continue", "message": "", "body": {"allThreadsContinued": true}}
[08:02:00.193 UTC] To Client:
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[08:02:35.594 UTC] From Client:
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{"command":"disconnect","arguments":{"restart":false},"type":"request","seq":17}
[08:02:35.595 UTC] onResponseDisconnect
[08:02:35.596 UTC] To Client:
[08:02:35.596 UTC] Content-Length: 119

{"type": "response", "seq": 78, "request_seq": 17, "success": true, "command": "disconnect", "message": "", "body": {}}
[08:02:35.599 UTC] check and shutdown