PDF conversion - Unexpected error in the server log
I was testing the PDF conversion for the below manuscript and PDF is generated and displayed in the UI. But spotted many errors in the server log. It seems to me that the error is related to this manuscript only.
https://beta.plus.europepmc.org/submission/EMS90402/review
root@3c25b642f55c:~# node server/pdf-conversion/api
info: Polling our database for manuscripts to be converted to PDF...
info: Start depositing EMS90402
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/
info: deposit_id=a6508dd9-d876-4a10-b9eb-869666a634e2, items=[created=2019-04-18T10:12:49.976559-04:00, updated=2019-04-18T10:12:49.983031-04:00, depositor=ebi, item_id=e5d11832-32ec-489f-9d77-4bbb22dfb00b, item=https://beta.plus.europepmc.org/download/0661067c-d6ff-4823-ab66-82566017bdc1.tif, item_type=URL, state=READY_FOR_PROCESSING, result=false, item_size=1433680, created=2019-04-18T10:12:50.008346-04:00, updated=2019-04-18T10:12:50.010228-04:00, depositor=ebi, item_id=e12284c3-d573-4174-8c60-b0b977d5d619, item=https://beta.plus.europepmc.org/download/9fa23018-c6c4-406c-8f97-ca1a79518fea.tif, item_type=URL, state=READY_FOR_PROCESSING, result=false, item_size=1993452, created=2019-04-18T10:12:50.018766-04:00, updated=2019-04-18T10:12:50.020596-04:00, depositor=ebi, item_id=5e8314db-0ed7-4a9d-ae42-16a3de97c1a1, item=https://beta.plus.europepmc.org/download/e8c6aa1b-b4a3-4dd0-8dec-961c5e335705.tif, item_type=URL, state=READY_FOR_PROCESSING, result=false, item_size=1512832, created=2019-04-18T10:12:50.034609-04:00, updated=2019-04-18T10:12:50.036442-04:00, depositor=ebi, item_id=42d8a320-da90-4363-8509-5579f67230c3, item=https://beta.plus.europepmc.org/download/8833a6bd-00f2-461a-bb52-508a325f63b7.tif, item_type=URL, state=READY_FOR_PROCESSING, result=false, item_size=1003076, created=2019-04-18T10:12:50.043880-04:00, updated=2019-04-18T10:12:50.092440-04:00, depositor=ebi, item_id=5264c741-affc-4981-9790-698fd3b56b0c, item=https://beta.plus.europepmc.org/download/195791f1-a511-4a11-9ebc-c278726f604a.nxml, item_type=URL, state=READY_FOR_PROCESSING, result=false, item_size=271138], created=2019-04-18T10:12:49.967538-04:00, updated=2019-04-18T10:12:50.115194-04:00, state=COMMITTED, depositor=ebi, domain=ukpmcpa
info: Deposit done. Stored depositId: a6508dd9-d876-4a10-b9eb-869666a634e2
info: Start depositing EMS90640
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/
info: items=[item_size=[This field may not be null.], ]
info: Deposit done. Stored depositId: undefined
info: Polling NCBI for replies from the PDF conversion service...
info: Check status of conversion: EMS90402
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/a6508dd9-d876-4a10-b9eb-869666a634e2
info: NCBI conversion status for : EMS90402: COMMITTED
info: Nothing found to be processed.
info: PDF conversion: closing connection to the database...
info: PDF conversion process finished in 3327 ms
root@3c25b642f55c:~# node server/pdf-conversion/api
info: Polling our database for manuscripts to be converted to PDF...
info: Start depositing EMS90640
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/
info: items=[item_size=[This field may not be null.], ]
info: Deposit done. Stored depositId: undefined
info: Polling NCBI for replies from the PDF conversion service...
info: Check status of conversion: EMS90402
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/a6508dd9-d876-4a10-b9eb-869666a634e2
info: NCBI conversion status for : EMS90402: WAITING_FOR_RESULT
info: Nothing found to be processed.
info: PDF conversion: closing connection to the database...
info: PDF conversion process finished in 2313 ms
root@3c25b642f55c:~# node server/pdf-conversion/api
info: Polling our database for manuscripts to be converted to PDF...
info: Start depositing EMS90640
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/
info: items=[item_size=[This field may not be null.], ]
info: Deposit done. Stored depositId: undefined
info: Polling NCBI for replies from the PDF conversion service...
info: Check status of conversion: EMS90402
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/a6508dd9-d876-4a10-b9eb-869666a634e2
info: NCBI conversion status for : EMS90402: WAITING_FOR_RESULT
info: Nothing found to be processed.
info: PDF conversion: closing connection to the database...
info: PDF conversion process finished in 1659 ms
root@3c25b642f55c:~# clear
root@3c25b642f55c:~# node server/pdf-conversion/api
info: Polling our database for manuscripts to be converted to PDF...
info: Start depositing EMS90640
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/
info: items=[item_size=[This field may not be null.], ]
info: Deposit done. Stored depositId: undefined
info: Polling NCBI for replies from the PDF conversion service...
info: Check status of conversion: EMS90402
info: Calling https://api.ncbi.nlm.nih.gov/lit/jats2pdf/api/deposits/a6508dd9-d876-4a10-b9eb-869666a634e2
info: NCBI conversion status for : EMS90402: RESULT_IS_READY
info: PDF conversion is ready: EMS90402. Fetching...
info: PDF file uploaded to minio
error: Nothing was inserted
error: message=manuscriptId: should be string, stack=ValidationError: manuscriptId: should be string
at Function.createValidationError (/home/xpub/node_modules/objection/lib/model/Model.js:356:12)
at parseValidationError (/home/xpub/node_modules/objection/lib/model/AjvValidator.js:189:21)
at AjvValidator.validate (/home/xpub/node_modules/objection/lib/model/AjvValidator.js:78:19)
at validate (/home/xpub/node_modules/objection/lib/model/modelValidate.js:35:20)
at File.$validate (/home/xpub/node_modules/objection/lib/model/Model.js:133:12)
at setJson (/home/xpub/node_modules/objection/lib/model/modelSet.js:28:16)
at File.$setJson (/home/xpub/node_modules/objection/lib/model/Model.js:171:12)
at Function.fromJson (/home/xpub/node_modules/objection/lib/model/Model.js:315:11)
at Function.ensureModel (/home/xpub/node_modules/objection/lib/model/Model.js:583:25)
at UpdateOperation.onAdd (/home/xpub/node_modules/objection/lib/queryBuilder/operations/UpdateOperation.js:21:29)
at QueryBuilder.callOperationMethod (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:353:33)
at QueryBuilder.addOperationUsingMethod (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:389:28)
at QueryBuilder.addOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:380:22)
at writeOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:894:12)
at writeOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:1458:5)
at QueryBuilder.patch (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:891:12), name=ValidationError, type=ModelValidation, manuscriptId=[message=should be string, keyword=type, type=string], statusCode=400
error: Nothing was inserted
error: message=manuscriptId: should be string, stack=ValidationError: manuscriptId: should be string
at Function.createValidationError (/home/xpub/node_modules/objection/lib/model/Model.js:356:12)
at parseValidationError (/home/xpub/node_modules/objection/lib/model/AjvValidator.js:189:21)
at AjvValidator.validate (/home/xpub/node_modules/objection/lib/model/AjvValidator.js:78:19)
at validate (/home/xpub/node_modules/objection/lib/model/modelValidate.js:35:20)
at File.$validate (/home/xpub/node_modules/objection/lib/model/Model.js:133:12)
at setJson (/home/xpub/node_modules/objection/lib/model/modelSet.js:28:16)
at File.$setJson (/home/xpub/node_modules/objection/lib/model/Model.js:171:12)
at Function.fromJson (/home/xpub/node_modules/objection/lib/model/Model.js:315:11)
at Function.ensureModel (/home/xpub/node_modules/objection/lib/model/Model.js:583:25)
at UpdateOperation.onAdd (/home/xpub/node_modules/objection/lib/queryBuilder/operations/UpdateOperation.js:21:29)
at QueryBuilder.callOperationMethod (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:353:33)
at QueryBuilder.addOperationUsingMethod (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:389:28)
at QueryBuilder.addOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:380:22)
at writeOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:894:12)
at writeOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:1458:5)
at QueryBuilder.patch (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:891:12), name=ValidationError, type=ModelValidation, manuscriptId=[message=should be string, keyword=type, type=string], statusCode=400
error: Unhandled Rejection at Promise: Promise {
<rejected> { ValidationError: manuscriptId: should be string
at Function.createValidationError (/home/xpub/node_modules/objection/lib/model/Model.js:356:12)
at parseValidationError (/home/xpub/node_modules/objection/lib/model/AjvValidator.js:189:21)
at AjvValidator.validate (/home/xpub/node_modules/objection/lib/model/AjvValidator.js:78:19)
at validate (/home/xpub/node_modules/objection/lib/model/modelValidate.js:35:20)
at File.$validate (/home/xpub/node_modules/objection/lib/model/Model.js:133:12)
at setJson (/home/xpub/node_modules/objection/lib/model/modelSet.js:28:16)
at File.$setJson (/home/xpub/node_modules/objection/lib/model/Model.js:171:12)
at Function.fromJson (/home/xpub/node_modules/objection/lib/model/Model.js:315:11)
at Function.ensureModel (/home/xpub/node_modules/objection/lib/model/Model.js:583:25)
at UpdateOperation.onAdd (/home/xpub/node_modules/objection/lib/queryBuilder/operations/UpdateOperation.js:21:29)
at QueryBuilder.callOperationMethod (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:353:33)
at QueryBuilder.addOperationUsingMethod (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:389:28)
at QueryBuilder.addOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:380:22)
at writeOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:894:12)
at writeOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:1458:5)
at QueryBuilder.patch (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:891:12)
name: 'ValidationError',
type: 'ModelValidation',
data: { manuscriptId: [Array] },
statusCode: 400 } }
error: Reason: message=manuscriptId: should be string, stack=ValidationError: manuscriptId: should be string
at Function.createValidationError (/home/xpub/node_modules/objection/lib/model/Model.js:356:12)
at parseValidationError (/home/xpub/node_modules/objection/lib/model/AjvValidator.js:189:21)
at AjvValidator.validate (/home/xpub/node_modules/objection/lib/model/AjvValidator.js:78:19)
at validate (/home/xpub/node_modules/objection/lib/model/modelValidate.js:35:20)
at File.$validate (/home/xpub/node_modules/objection/lib/model/Model.js:133:12)
at setJson (/home/xpub/node_modules/objection/lib/model/modelSet.js:28:16)
at File.$setJson (/home/xpub/node_modules/objection/lib/model/Model.js:171:12)
at Function.fromJson (/home/xpub/node_modules/objection/lib/model/Model.js:315:11)
at Function.ensureModel (/home/xpub/node_modules/objection/lib/model/Model.js:583:25)
at UpdateOperation.onAdd (/home/xpub/node_modules/objection/lib/queryBuilder/operations/UpdateOperation.js:21:29)
at QueryBuilder.callOperationMethod (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:353:33)
at QueryBuilder.addOperationUsingMethod (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:389:28)
at QueryBuilder.addOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:380:22)
at writeOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:894:12)
at writeOperation (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:1458:5)
at QueryBuilder.patch (/home/xpub/node_modules/objection/lib/queryBuilder/QueryBuilder.js:891:12), name=ValidationError, type=ModelValidation, manuscriptId=[message=should be string, keyword=type, type=string], statusCode=400
info: PDF conversion: closing connection to the database...