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PATRIC3 / patric3_website

Legacy PATRIC Website (JBoss Portal Version)
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workspace ftp server crash #2316

Open olsonanl opened 5 years ago

olsonanl commented 5 years ago

The workspace node.js ftp server crashed with this error. Any ideas?

Error: Error Reading Stream from Workspace: /halilkurt@patricbrc.org/home/cmx/.R4-P2/.bin.4.1798454/load_files/genome_sequence.json
    at Error (native)
    at /homes/olson/P3/ftp/p3-ws-ftpd/wsReadStream.js:22:10
    at /homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:380:6
    at notify (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:201:22)
    at notifyAll (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:180:5)
    at Promise.Deferred.reject.reject.errback.emitError (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:236:3)
    at notify (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:209:24)
    at notifyAll (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:180:5)
    at Promise.Deferred.resolve.callback.emitSuccess (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:223:3)
    at Request._callback (/homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:50:8)
dmachi commented 5 years ago

Was there anything before this in the log? Like “STAT ERROR: ….”?

On Oct 17, 2019, at 1:03 PM, olsonanl notifications@github.com wrote:

The workspace node.js ftp server crashed with this error. Any ideas?

Error: Error Reading Stream from Workspace: /halilkurt@patricbrc.org/home/cmx/.R4-P2/.bin.4.1798454/load_files/genome_sequence.json at Error (native) at /homes/olson/P3/ftp/p3-ws-ftpd/wsReadStream.js:22:10 at /homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:380:6 at notify (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:201:22) at notifyAll (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:180:5) at Promise.Deferred.reject.reject.errback.emitError (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:236:3) at notify (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:209:24) at notifyAll (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:180:5) at Promise.Deferred.resolve.callback.emitSuccess (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:223:3) at Request._callback (/homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:50:8) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/2316?email_source=notifications&email_token=AABOQ3RWRE6XGX24FLWICUTQPCLHPA5CNFSM4JB4QLSKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HSQW26Q, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABOQ3WTGRQJGDWGUOAXIELQPCLHPANCNFSM4JB4QLSA.

olsonanl commented 5 years ago

Yes:

Start Read for  /halilkurt@patricbrc.org/home/cmx/.R4-P2/.bin.5.2026780/bin.5.2026780.contigs.fasta
STAT:  /halilkurt@patricbrc.org/home/cmx/.R4-P2/.bin.5.2026780/bin.5.2026780.contigs.fasta
STAT ERROR:  Error: Object not found: 
    at /homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:97:27
    at notify (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:201:22)
    at notifyAll (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:180:5)
    at Promise.Deferred.resolve.callback.emitSuccess (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:223:3)
    at Request._callback (/homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:50:8)
    at Request.self.callback (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/request/request.js:186:22)
    at emitTwo (events.js:106:13)
    at Request.emit (events.js:191:7)
    at Request.<anonymous> (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/request/request.js:1163:10)
    at emitOne (events.js:96:13)
    at Request.emit (events.js:188:7)
STAT ERROR:  Error: Object not found: 
    at /homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:97:27
    at notify (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:201:22)
    at notifyAll (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:180:5)
    at Promise.Deferred.resolve.callback.emitSuccess (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:223:3)
    at Request._callback (/homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:50:8)
    at Request.self.callback (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/request/request.js:186:22)
    at emitTwo (events.js:106:13)
    at Request.emit (events.js:191:7)
    at Request.<anonymous> (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/request/request.js:1163:10)
    at emitOne (events.js:96:13)
    at Request.emit (events.js:188:7)
dmachi commented 5 years ago

Strange.

The error happens when it cannot retrieve that file’s data meta object from the workspace api. I su’d to that account and the file does exist, so its not clear to me why that part was happening in the first place.

Outside of that, it doesn’t seem like the ftpd server is capturing an error from that stat() operation it is calling. I am throwing an error in this case, but perhaps I’m not supposed to be. I will investigate and see if I can figure out what it wants here. It may be expecting the stream to emit an error rather than throwing an error as I currently do.

On Oct 17, 2019, at 1:30 PM, olsonanl notifications@github.com wrote:

Yes:

Start Read for /halilkurt@patricbrc.org/home/cmx/.R4-P2/.bin.5.2026780/bin.5.2026780.contigs.fasta STAT: /halilkurt@patricbrc.org/home/cmx/.R4-P2/.bin.5.2026780/bin.5.2026780.contigs.fasta STAT ERROR: Error: Object not found: at /homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:97:27 at notify (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:201:22) at notifyAll (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:180:5) at Promise.Deferred.resolve.callback.emitSuccess (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:223:3) at Request._callback (/homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:50:8) at Request.self.callback (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/request/request.js:186:22) at emitTwo (events.js:106:13) at Request.emit (events.js:191:7) at Request. (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/request/request.js:1163:10) at emitOne (events.js:96:13) at Request.emit (events.js:188:7) STAT ERROR: Error: Object not found: at /homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:97:27 at notify (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:201:22) at notifyAll (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:180:5) at Promise.Deferred.resolve.callback.emitSuccess (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/promised-io/promise.js:223:3) at Request._callback (/homes/olson/P3/ftp/p3-ws-ftpd/workspaceFileSystem.js:50:8) at Request.self.callback (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/request/request.js:186:22) at emitTwo (events.js:106:13) at Request.emit (events.js:191:7) at Request. (/homes/olson/P3/ftp/p3-ws-ftpd/node_modules/request/request.js:1163:10) at emitOne (events.js:96:13) at Request.emit (events.js:188:7) — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/2316?email_source=notifications&email_token=AABOQ3XRS2GLONT26HJ2KZTQPCOL3A5CNFSM4JB4QLSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBQ42TA#issuecomment-543280460, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABOQ3UGRNI7KY62P5NT5BDQPCOL3ANCNFSM4JB4QLSA.