ncbi issueshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues2024-01-17T06:31:28Zhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1647Invalid TOC XML - repeated chapter tagged twice instead of a PI used2024-01-17T06:31:28ZStacy LathropInvalid TOC XML - repeated chapter tagged twice instead of a PI used<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
TOC XML should be valid to BITS DTD and PMC style checker compliant.
## Current behaviou...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
TOC XML should be valid to BITS DTD and PMC style checker compliant.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
Many TOC XML are invalid because when a repeated chapter is indicated that chapter is getting tagged twice in the TOC XML rather than the correct PI being used in the repeated part.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Validate attached TOC.xml -[TOC_1647.xml](/uploads/5a46b9da648e10c5197ba149224fa558/TOC_1647.xml)
2. See this file is tagged twice completely when it should only have a repeat PI - `<?xml_file epigeneticmechanismscontrollingmesode.xml?>`
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
This is occurring in domain `stembook`. I cannot reproduce it on Coko site. @deniskar can you understand why?
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->P04: Support valid and compliant TOC XML for all migrated Bookshelf contentDenis KaramyshevDenis Karamyshevhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1645Pass metadata and settings PDF2XML vendor for tagging2024-01-16T14:04:18ZStacy LathropPass metadata and settings PDF2XML vendor for tagging<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
Requirements here: https://gitlab.coko.foundation/ncbi/ncbi/-/issues/404
**Package to Apex from BCMS**
Sample package: [BCMS-to-APEX-s...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
Requirements here: https://gitlab.coko.foundation/ncbi/ncbi/-/issues/404
**Package to Apex from BCMS**
Sample package: [BCMS-to-APEX-sample.zip](/ncbi/ncbi/uploads/cc7569dffcc8548c3269b697553699af/BCMS-to-APEX-sample.zip)
**Metadata** Content added in the metadata UI of the relevant book, corresponding to manifest file types:
* cover
And:
* Book meta in json
* Collection meta in json
* settings in json
## Current behaviour
PDF2XML taggers report no metadata or settings are being provided in packages with completed values, per:
**Folder: Metadata** Contains a cover image *only* in the case where the image has been extracted from the source PDF. No metadata is sent back from Apex:
* Wholebook use case: Any metadata sent to Apex is written into the metadata node in the wholebook.xml
* Chapter use case: BCMS writes Book metadata from UI into chapter.xml file prior to load to PMC
Like wholebook XML, following NCBI-specific metadata and settings should be minimally sent to taggers:
Coko will pass the following pieces of NCBI metadata to XML conversion and PDF tagging:
* domain name (required)
* collection id (optional)
* collection title - TBD whether this can be a string or requires formatting and needs to be passed during Load to PMC
* source type (required)
* publisher name (optional)
* publisher location (optional)
All other data or metadata will be in the PDF or support folders.
```
{
"job_id": 9876543210, // Reference ID for the XML conversion job. It's generated by Coko and used by NCBI to report back the status of the conversion.
"user_name": "jordandc", // Name of a user initiating a conversion
"main_xml": "978-3-030-47318-1_Book.xml" // Filename of the primary XML file to use as the conversion entry point.
"domain": "spr9783030473181", // PMCBook domain name of the book being converted
"collection_id": "wtcollect", // PMCBook domain name of the collection that the book being converted belongs to (OPTIONAL)
"collection_title": "Wellcome Monographs", // Title of the collection that the book being converted belongs to (OPTIONAL)
"source_type": "Book", // BCMS assigned "source-type" for the book being converted
"publisher_name": "Springer", // BCMS assigned name of the bibliographic publisher (OPTIONAL)
"publisher_loc": "Cham (CH)", // BCMS assigned publication place (OPTIONAL)
"package": "spr9783030473181.9876543210.2020_05_15-09_25_45.zip", // Name of the package with the XML file, in domain.job_id.timestamp format
"notification_recipients": { // List of emails for NCBI Task Manager (not CoKo) to send notifications to
"success": ["bookshelf@ncbi.nlm.nih.gov","fritz@publisher.org"],
"failure": ["bookshelf@ncbi.nlm.nih.gov"]
}
}
```
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Create a PDF wholebook
2. Enter in source type and publisher name and publisher location using metadata UI
3. Add a collection via settings
4. Check that all above values are sent to Tagging vendor in JSON per provided specifications
5. Check converted XML that all these values are correctly tagged per those provided specifications
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->
Fixing this issue is required for [Priority 1: Deploy MVP](https://gitlab.coko.foundation/groups/ncbi/-/epics/56)P05: Address MVP Files Management and Processing Issues to support all current Bookshelf submitters and NCBI Integration specificationshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1640Invalid TOC XML - id cannot start with a number2024-01-16T21:19:14ZStacy LathropInvalid TOC XML - id cannot start with a number<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
TOC XML should be valid to BITS DTD and PMC style checker compliant.
## Current behaviou...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
TOC XML should be valid to BITS DTD and PMC style checker compliant.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
Many TOC XML are invalid because IDs are beginning with a number when this is not permitted.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Validate attached TOC.xml -[TOC_1640.xml](/uploads/7b815bde8d1f14a1253a39ee594e3e64/TOC_1640.xml)
2. See error -
```
System ID: C:\Users\lathrops\OneDrive - National Institutes of Health\Desktop\Unconfirmed 2202.crdownload
Main validation file: C:\Users\lathrops\OneDrive - National Institutes of Health\Desktop\Unconfirmed 2202.crdownload
Schema: \\fridge\pmcprod\load\converter4\DTD\dtd-niso-z39.96\extensions\bits\2.0\BITS-book2.dtd
Engine name: Xerces
Severity: error
Problem ID: IDInvalidWithNamespaces
Description: Attribute value "17q12foundationbreakgrimesiowa" of type ID must be an NCName when namespaces are enabled.
Start location: 545:1993
End location: 545:2025
```
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
This is occurring in domain `gene`. I cannot reproduce it on Coko site. @deniskar can you understand why? Affiliations should not get tagged in TOC.XML but they are in content in NCBI deployment but not Coko deployment.
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->P04: Support valid and compliant TOC XML for all migrated Bookshelf contentDenis KaramyshevDenis Karamyshevhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1639Invalid TOC XML - duplicate aff ids are not valid2024-01-16T21:17:42ZStacy LathropInvalid TOC XML - duplicate aff ids are not valid<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
TOC XML should be valid to BITS DTD and PMC Style Checker compliant.
## Current behaviou...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
TOC XML should be valid to BITS DTD and PMC Style Checker compliant.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
TOC XML is invalid in numerous cases because duplicate aff ids are tagged.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Validate attached TOC.xml [TOC_1639.xml](/uploads/7924fbba1cc8ad7dd108e4f36fe4d919/TOC_1639.xml)
2. See error -
```
System ID: C:\Users\lathrops\Downloads\Unconfirmed_2202.crdownload
Main validation file: C:\Users\lathrops\Downloads\Unconfirmed_2202.crdownload
Schema: \\fridge\pmcprod\load\converter4\DTD\dtd-niso-z39.96\extensions\bits\2.0\BITS-book2.dtd
Engine name: Xerces
Severity: error
Problem ID: IDNotUnique
Description: Attribute value "seattlevamedicalcenterbreakdepartmentsofneurologyandmedicinebreakuniversityofwashingtonbreakseattlewashington" of type ID must be unique within the document.
Start location: 4684:169
End location: 4684:280
```
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
This is occurring in domain `gene`. I cannot reproduce it on Coko site. @deniskar can you understand why? Affiliations should not get tagged in TOC.XML but they are in content in NCBI deployment but not Coko deployment.
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->P04: Support valid and compliant TOC XML for all migrated Bookshelf contentDenis KaramyshevDenis Karamyshevhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1637Selected PIs do not remain selected after user saves them and moves from the ...2024-01-16T08:02:00ZStacy LathropSelected PIs do not remain selected after user saves them and moves from the UI page<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
When a user selects and saves a PI in the BCMS book metadata UI, it remains selected and ...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
When a user selects and saves a PI in the BCMS book metadata UI, it remains selected and saved until the user intentionally deselects it.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
After user saves successfully with all PIs selected (or checked), when the user opens the UI again the checkboxes are unchecked. Same bug in Word metadata modal & pdf chapter metadata modal.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Go to any chapter-processed book
2. Open the book metadata modal
3. Select and save all available PIs
4. Move away form metadata modal
5. Reopen same book's metadata modal and notice PIs are no longer selected
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->P03: Support valid and compliant metadata for all migrated Bookshelf contenthttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1630Support files are not getting ingested to BCMS Support folders for completed ...2024-01-16T16:32:47ZStacy LathropSupport files are not getting ingested to BCMS Support folders for completed Word conversions<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
The `*.extylesOutput.xml` and `*-extyles.doc` files returned in Word converted returned ....<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
The `*.extylesOutput.xml` and `*-extyles.doc` files returned in Word converted returned .zip packages should be uploaded to the Support folder so users can troubleshoot issues and fix styling that requires codes in the tagged Word files.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
The `*.extylesOutput.xml` and `*-extyles.doc` files are not getting uploaded to the Support folders leaving GeneReviews and other power users no way to fix some reference citation errors without intervention from Bookshelf System Admin causing production delays.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Go to: https://ncbi.cloud68.co/organizations/6c4d37c4-b9f2-4962-9080-b3e29a37dfbd/bookmanager/7f099bb1-3379-4beb-bc4b-aeca26884a47/2ca956af-c1ca-449f-8b54-8c512c1e1f55#undefined
2. Note the attached file[bcms1086.lathosterolosis.docx.09b875.2023_11_29-07_53_21.output.zip](/uploads/1e4ad97e361542004f776149e50ad140/bcms1086.lathosterolosis.docx.09b875.2023_11_29-07_53_21.output.zip) that NCBI posted to: `/am/ftp-private/bookshelf/coko/convert/word/out/bcms1086.lathosterolosis.docx.09b875.2023_11_29-07_53_21.output.zip`
3. It contains `lathosterolosis.eXtylesOutput.xml` and 'lathosterolosis-eXtyles.doc`
4. Go to Support folder in BCMS Book Manager link in #1 - see files in #3 are not available for download from this folder
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->P05: Address MVP Files Management and Processing Issues to support all current Bookshelf submitters and NCBI Integration specificationshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1627Can save metadata without contributor validations2023-10-10T16:40:53ZYannis BarlasCan save metadata without contributor validationsThere is a bug with other extra sections, that have required fields, that now I can save without filling those. The following issues are only for the case of Word Book Complete.
More specifically:
- Contributors, if you click to add the...There is a bug with other extra sections, that have required fields, that now I can save without filling those. The following issues are only for the case of Word Book Complete.
More specifically:
- Contributors, if you click to add them some fields are required to be filled and should look like below, but it's not like that currently:
![image](/uploads/8d7b23eefe01cb9942e4c4adafc8817b/image.png)
- Permission: If the setting for open access license is set to true, the `license type` and `license statement` should become required.
![image](/uploads/487cf2b80f59646868c6ad833a609105/image.png)
- Notes: If you add a note `type` and `description` are required
![image](/uploads/6f1289cfde3b4fdc2a0f30fd871ce28f/image.png)
Currently I can save metadata without filling none of those.Yannis BarlasYannis Barlashttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1626Cannot save Metadata of Word complete books2023-10-10T16:20:15ZBela TociCannot save Metadata of Word complete books## Expected behaviour
User should be able to save the Metadata of Word complete books after filling in the required fields.
## Current behaviour
After filling in the required fields in `Metadata`, when clicking Save nothing happens. ...## Expected behaviour
User should be able to save the Metadata of Word complete books after filling in the required fields.
## Current behaviour
After filling in the required fields in `Metadata`, when clicking Save nothing happens. However, there is an error in the console.
![image](/uploads/d808ad7a0e4a93c4ccdc3aaa73f1e734/image.png)
Since user cannot save "Book source type" which is a required field in the metadata, user cannot submit new Word complete books.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Go to any Word complete book, e.g. [this one](https://ncbidev.cloud68.co/organizations/cdc8efc4-c964-47ca-9637-6234f7affc5c/bookmanager/05357fe7-77bf-41c3-b0b8-2487f7cde4e0)
2. Fill in all the required fields
3. Click Save
4. Check the error in the console and that nothing happens
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->https://gitlab.coko.foundation/ncbi/ncbi/-/issues/1625Unable to upload file in wholebook source folder when source files are conver...2024-01-16T17:10:26ZStacy LathropUnable to upload file in wholebook source folder when source files are conversion errors and converted files are stuck in converting status<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
User should be able to upload source files to any book when in status Conversion Errors t...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
User should be able to upload source files to any book when in status Conversion Errors to fix those errors and Submit it again to conversion.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
In an chapter-processed XML book with component and source file in Conversion Errors and converted file in Converting, users is unable to upload source XML file.
User should be able to upload source files to any book when in status Conversion Errors to fix those errors and Submit it again to conversion.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Go to: https://ncbi.cloud68.co/organizations/e704f821-3ce6-45cf-b3f4-407c4b5fa73d/bookmanager/5f91eec8-b8a0-4192-9b8d-95778ecb865b/64d17010-3a4a-458c-8ec7-396bd49cd73b#undefined
2. Download source XML file
3. Upload source XML file
4. Notice you get this error: "Could not upload file"
This is from a real production use case. For now for this participant to work we need to create a new test conversion book that won't be possible in production, so a fix is required for BCMS MVP.
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->P05: Address MVP Files Management and Processing Issues to support all current Bookshelf submitters and NCBI Integration specificationshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1623Can't see or scroll to see all components on Book Manager Search results page...2023-10-10T16:04:50ZStacy LathropCan't see or scroll to see all components on Book Manager Search results page when filter is applied@DioneMentis - @rorris FYI
<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
User should see or be able to scroll to see all components that meet a filter / search query on the returned...@DioneMentis - @rorris FYI
<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
User should see or be able to scroll to see all components that meet a filter / search query on the returned Book Manager search results page.
<!-- Required. Tell us what should happen -->
## Current behaviour
User cannot scroll to see all returned search results on a Book Manager search results page when a filter is applied.
<!-- Required. Tell us what happens instead of the expected behaviour -->
## Steps to reproduce
Go to a book with 15 or more results on a PC and Chrome browser with a monitor width of about 20-24 in. See that there is no scroll bar to see all results.
Attached video of my experience here:
![Stacy_Lathrop_s_Personal_Room_2023-09-26-11-38-50](/uploads/cee2e35c7c95dd23e5200b2407088290/Stacy_Lathrop_s_Personal_Room_2023-09-26-11-38-50.mp4)
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->https://gitlab.coko.foundation/ncbi/ncbi/-/issues/1621Need to reload to see changes after repeat2024-01-16T18:01:57ZYannis BarlasNeed to reload to see changes after repeatWe need to refetch the division and the relevant component children, like we do for moving.We need to refetch the division and the relevant component children, like we do for moving.P09: Book Manager and other MVP BCMS improvements and Lower Priority Bug Fixeshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1620Converted file failed to upload because of validation error on metadata2023-09-26T10:09:57ZSidorela UkuConverted file failed to upload because of validation error on metadataSteps to reproduce:
- In the book component [linked here](https://ncbidev.cloud68.co/organizations/480042fa-f26a-49dd-a9d3-fc016d4e705e/bookmanager/2f3874a1-3a7c-402a-b8d3-aeff794a8ba6/9214d65e-2395-410c-ac6b-3d973c47eec3#undefined) I d...Steps to reproduce:
- In the book component [linked here](https://ncbidev.cloud68.co/organizations/480042fa-f26a-49dd-a9d3-fc016d4e705e/bookmanager/2f3874a1-3a7c-402a-b8d3-aeff794a8ba6/9214d65e-2395-410c-ac6b-3d973c47eec3#undefined) I download the converted file and tried to upload it again.
- During upload the converted file [dup7q11_23.xml](/uploads/35e1b05664a24e8bb8458a02bf64679d/dup7q11_23.xml) throws an error that file is not correct or parsing failed.
When I try it locally the following error is in the terminal:
```
server_1 | message: 'metadata.author[0].affiliation: should be array,null, metadata.author[1].affiliation: should be array,null, metadata.author[2].affiliation: should be array,null, metadata.author[3].affiliation: should be array,null, metadata.author[4].affiliation: should be array,null',
server_1 | stack: 'ValidationError: metadata.author[0].affiliation: should be array,null, metadata.author[1].affiliation: should be array,null, metadata.author[2].affiliation: should be array,null, metadata.author[3].affiliation: should be array,null, metadata.author[4].affiliation: should be array,null\n' +
server_1 | ' at Function.createValidationError (/home/node/app/node_modules/objection/lib/model/Model.js:363:12)\n' +
server_1 | ' at parseValidationError (/home/node/app/node_modules/objection/lib/model/AjvValidator.js:189:21)\n' +
server_1 | ' at AjvValidator.validate (/home/node/app/node_modules/objection/lib/model/AjvValidator.js:78:19)\n' +
server_1 | ' at validate (/home/node/app/node_modules/objection/lib/model/modelValidate.js:35:20)\n' +
server_1 | ' at BookComponent.$validate (/home/node/app/node_modules/objection/lib/model/Model.js:97:12)\n' +
server_1 | ' at setJson (/home/node/app/node_modules/objection/lib/model/modelSet.js:28:16)\n' +
server_1 | ' at BookComponent.$setJson (/home/node/app/node_modules/objection/lib/model/Model.js:135:12)\n' +
server_1 | ' at Function.fromJson (/home/node/app/node_modules/objection/lib/model/Model.js:286:11)\n' +
server_1 | ' at Function.ensureModel (/home/node/app/node_modules/objection/lib/model/Model.js:614:25)\n' +
server_1 | ' at UpdateOperation.onAdd (/home/node/app/node_modules/objection/lib/queryBuilder/operations/UpdateOperation.js:21:29)\n' +
server_1 | ' at QueryBuilder.callOperationMethod (/home/node/app/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:379:33)\n' +
server_1 | ' at QueryBuilder.addOperationUsingMethod (/home/node/app/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:410:28)\n' +
server_1 | ' at QueryBuilder.addOperation (/home/node/app/node_modules/objection/lib/queryBuilder/QueryBuilderOperationSupport.js:401:22)\n' +
server_1 | ' at /home/node/app/node_modules/objection/lib/queryBuilder/QueryBuilder.js:999:12\n' +
server_1 | ' at writeOperation (/home/node/app/node_modules/objection/lib/queryBuilder/QueryBuilder.js:1679:5)\n' +
server_1 | ' at QueryBuilder.patch (/home/node/app/node_modules/objection/lib/queryBuilder/QueryBuilder.js:996:12)',
server_1 | name: 'ValidationError',
server_1 | type: 'ModelValidation',
server_1 | data: {
server_1 | 'metadata.author[0].affiliation': [
server_1 | {
server_1 | message: 'should be array,null',
server_1 | keyword: 'type',
server_1 | params: { type: 'array,null' }
server_1 | }
server_1 | ],
server_1 | 'metadata.author[1].affiliation': [
server_1 | {
server_1 | message: 'should be array,null',
server_1 | keyword: 'type',
server_1 | params: { type: 'array,null' }
server_1 | }
server_1 | ],
server_1 | 'metadata.author[2].affiliation': [
server_1 | {
server_1 | message: 'should be array,null',
server_1 | keyword: 'type',
server_1 | params: { type: 'array,null' }
server_1 | }
server_1 | ],
server_1 | 'metadata.author[3].affiliation': [
server_1 | {
server_1 | message: 'should be array,null',
server_1 | keyword: 'type',
server_1 | params: { type: 'array,null' }
server_1 | }
server_1 | ],
server_1 | 'metadata.author[4].affiliation': [
server_1 | {
server_1 | message: 'should be array,null',
server_1 | keyword: 'type',
server_1 | params: { type: 'array,null' }
server_1 | }
server_1 | ]
server_1 | },
server_1 | statusCode: 400,
server_1 | modelClass: [class BookComponent extends BaseModel]
server_1 | }
server_1 | 2023-09-25T14:50:17.772Z - error: The converted file you uploaded is not correct OR parsing failed with error: Error: Running command: Chapter Update Command Failed
server_1 | {
server_1 | error: {
server_1 | message: 'The converted file you uploaded is not correct OR parsing failed with error: Error: Running command: Chapter Update Command Failed ',
server_1 | locations: [ { line: 2, column: 3 } ],
server_1 | path: [ 'uploadConvertFiles' ],
server_1 | extensions: {
server_1 | code: 'INTERNAL_SERVER_ERROR',
server_1 | exception: {
server_1 | stacktrace: [
server_1 | 'Error: The converted file you uploaded is not correct OR parsing failed with error: Error: Running command: Chapter Update Command Failed ',
server_1 | ' at /home/node/app/server/api/graphql/bookComponent/bookComponent.resolvers.js:403:15',
server_1 | ' at processTicksAndRejections (node:internal/process/task_queues:96:5)'
server_1 | ]
server_1 | }
server_1 | }
server_1 | }
server_1 | }
```Giannis Kopanasjkopanas@gmail.comGiannis Kopanasjkopanas@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1619Selecting all chapters in a part messes with buttons being enabled / disabled2023-09-25T17:07:42ZYannis BarlasSelecting all chapters in a part messes with buttons being enabled / disabledAs it stands currently, selecting all chapters in a part will also select the part.
This however, can mean that eg. the repeat button is not enabled as there is one component (the part) that does not pass the criteria for the button be...As it stands currently, selecting all chapters in a part will also select the part.
This however, can mean that eg. the repeat button is not enabled as there is one component (the part) that does not pass the criteria for the button being enabled, even though all its children might.Yannis BarlasYannis Barlashttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1617Repeat a chapter in the body division2023-09-27T12:33:26ZYannis BarlasRepeat a chapter in the body division<!-- Required. Provide a general summary of the issue in the title above -->
Given a chapter that exists inside a part, trying to repeat it in the body does nothing.
## Expected behaviour
<!-- Required. Tell us what should happen -->
...<!-- Required. Provide a general summary of the issue in the title above -->
Given a chapter that exists inside a part, trying to repeat it in the body does nothing.
## Expected behaviour
<!-- Required. Tell us what should happen -->
A copy of that chapter should appear in the body.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
Nothing happens.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Start with a chapter that only exists inside a part
2. Open the repeat modal
3. Check "body" without unchecking the existing checked part
4. Click save
## Possible solution
The client sends an array of ids. Each id there could potentially be the body id (a division id), even though the other items in the array are part ids (book component ids). The sent division id needs to be handled and the `division.bookComponents` array updated.
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->Stacy LathropStacy Lathrophttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1614Search by "new upload" status finds "Part" in results even though "Parts" cur...2024-01-16T17:47:49ZDione Mentisdione@coko.foundationSearch by "new upload" status finds "Part" in results even though "Parts" currently have no Status displaying in these components<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
All Components can be filtered correctly by displayed component status.
## Current behav...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
All Components can be filtered correctly by displayed component status.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
Parts don't have statuses currently and are retrieved when a user Filters by "New Upload" status
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1.
2.
3.
4.
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
To be scoped with #1455
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->P07 - Support Current Bookshelf Chapter-Processed contents with Parts with Bodyhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1573Current statuses and details of components / files do not display and user is...2024-01-16T17:19:00ZStacy LathropCurrent statuses and details of components / files do not display and user is forced to refresh pages to see them<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
Users can expect to see accurate statuses and details of their components / files when th...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
Users can expect to see accurate statuses and details of their components / files when they are working in the BCMS.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
BCMS is not automatically updating component / file statuses and details and the user is forced to refresh BCMS pages using their Browser refresh to see them.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
See attached video - this is not a one off but consistent BCMS behavior after 20230822 release
![video1312790282](/uploads/03bf91b5f92ff96cab265be0f27984c1/video1312790282.mp4)
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->
For #1496 and #1497 to be useful this issue must be addressed, so I propose this be scheduled for Files Management Milestone.P05: Address MVP Files Management and Processing Issues to support all current Bookshelf submitters and NCBI Integration specificationshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1572Contributors are not getting written in to TOC XML2024-01-16T16:13:28ZStacy LathropContributors are not getting written in to TOC XML<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
All metadata from converted XML should be accurately written into chapter-processed TOC XML. If there are contribs in the chapter-proces...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
All metadata from converted XML should be accurately written into chapter-processed TOC XML. If there are contribs in the chapter-processed book metadata they should always without exception be tagged in the chapter-processed TOC XML no matter what other siblings or children/grandchildren are in the contrib-group.
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
Contributors are sometimes not getting written into chapter-processed TOC XML.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
* Testing done in book: https://ncbi.cloud68.co/organizations/d400f251-44e8-44f4-9c27-58d25a09f849/bookmanager/37de885b-91ab-406a-a380-275df5ec66f5
* Example chapter component in the book: https://ncbi.cloud68.co/organizations/d400f251-44e8-44f4-9c27-58d25a09f849/bookmanager/37de885b-91ab-406a-a380-275df5ec66f5/7f9b6220-3b92-440f-b372-ec1d67df6f8c#c4af838d-02f0-4854-bf30-2b71d5184b34
1. Reload Preview or publish a chapter that has a converted file (example above)
2. See that the contributors metadata within the `book-part-meta` (copied below) does not display in the metadata UI
![Screenshot_2023-09-04_at_10.15.05](/uploads/a137140bdc83e75615348d1b9250859d/Screenshot_2023-09-04_at_10.15.05.png)
Note there are contributors in the book part metadata in attached file:
[RB-0020-Saavedra.bxml](/uploads/2c358355b60d30500a8b78387a7ba631/RB-0020-Saavedra.bxml)
```xml
<contrib-group>
<contrib contrib-type="author" rid="RB-0020-Saavedra.bio1"><name><surname>Saavedra</surname><given-names>Lissette M.</given-names></name></contrib>
<contrib contrib-type="author" rid="RB-0020-Saavedra.bio2"><name><surname>Morgan-Lopez</surname><given-names>Antonio A.</given-names></name></contrib>
<contrib contrib-type="author" rid="RB-0020-Saavedra.bio3"><name><surname>Yaros</surname><given-names>Anna C.</given-names></name></contrib>
<contrib contrib-type="author" rid="RB-0020-Saavedra.bio4"><name><surname>Buben</surname><given-names>Alex</given-names></name></contrib>
<contrib contrib-type="author" rid="RB-0020-Saavedra.bio5"><name><surname>Trudeau</surname><given-names>James V.</given-names></name></contrib>
<bio id="RB-0020-Saavedra.bio1"><p><bold>Lissette M. Saavedra</bold>, PhD, is a research psychologist in the Mental Health, Risk and Resilience Research Program at RTI International.</p></bio>
<bio id="RB-0020-Saavedra.bio2"><p><bold>Antonio A. Morgan-Lopez</bold>, PhD, is a Fellow in quantitative psychology in the Substance Use, Prevention, Evaluation and Research Program at RTI International.</p></bio>
<bio id="RB-0020-Saavedra.bio3"><p><bold>Anna C. Yaros</bold>, PhD, is the program manager of the Mental Health, Risk, and Resilience Research Program at RTI International.</p></bio>
<bio id="RB-0020-Saavedra.bio4"><p><bold>Alex Buben</bold>, BA, is a public health analyst in the Substance Use, Prevention, Evaluation and Research Program at RTI International.</p></bio>
<bio id="RB-0020-Saavedra.bio5"><p><bold>James V. Trudeau</bold>, PhD, is a chief scientist in the Applied Justice Research at RTI International.</p>
</bio>
</contrib-group>
```
3. Go to TOC and download TOC.XML and see that these contributors are not tagged in the TOC XML as they should be
[TOC__58_.xml](/uploads/8a97517bbcbbfcd6c02707190e8a853a/TOC__58_.xml)
```xml
<toc-entry>
<title>Provider Resistance to Evidence-Based Practice in Schools: Why It Happens and How to Plan for It in Evaluations</title>
<?epub 20190501?>
<nav-pointer>
<related-object document-id="RB-0020-Saavedra" document-type="chapter">
<?xml_file RB-0020-Saavedra.bxml?>
<?version 1?>
</related-object>
</nav-pointer>
<toc-entry>
<title>Future Research: Steps Toward Rapprochement</title>
<nav-pointer>
<related-object document-id="RB-0020-Saavedra" document-type="chapter" object-id="RB-0020-Saavedra.sec4" object-type="sec"/>
</nav-pointer>
</toc-entry>
</toc-entry>
```
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
Best guess without checking the code is that `<bio></bio>` tags within `<contrib-group></contrib-group>` are not supported by the BCMS yet.
https://jats.nlm.nih.gov/extensions/bits/tag-library/2.1/element/contrib-group.html
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->P04: Support valid and compliant TOC XML for all migrated Bookshelf contenthttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1492Not all suppl files are sent to PMC ingest when multiple files with same base...2024-01-08T22:59:34ZStacy LathropNot all suppl files are sent to PMC ingest when multiple files with same base name but different file extension<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
All suppl files uploaded to BCMS UI should be packaged and sent to PMC ingest to avoid loading errors.
## Current behaviour
When multi...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
All suppl files uploaded to BCMS UI should be packaged and sent to PMC ingest to avoid loading errors.
## Current behaviour
When multiple suppl files are upload to BCMS UI with same base name but different extensions not all of them are package and sent to PMC for ingest causing loading errors.
## Steps to reproduce
1. Go to: https://ncbi.cloud68.co/organizations/3c48a8ec-05e4-465c-b9ea-b1cb93c688ac/bookmanager/797a661f-eab3-4c6c-a970-7e66bbdca49e -note loading error
2. Look at all files in suppl folder in UI
3. See that not all files were sent in package sent to ingest attached - [bcms6774.640b1a.2023_02_23-03_30_17.zip](/uploads/b0079d8d2ce25880b7a810697eae7877/bcms6774.640b1a.2023_02_23-03_30_17.zip)
4.
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->
- [ x] This issue is blocking current user testing
- [ ] This issue is blocking current migration testing
- [ x] Fixing this issue is required for [Priority 1: Deploy MVP](https://gitlab.coko.foundation/groups/ncbi/-/epics/56)
- [ ] This issue should be triaged into later epics in the PM weekly meetingP05: Address MVP Files Management and Processing Issues to support all current Bookshelf submitters and NCBI Integration specificationshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1491Not all section titles are written into TOC.xml as required2024-01-16T17:36:48ZStacy LathropNot all section titles are written into TOC.xml as required
## Expected behaviour
Per TOC.xml writing specifications, all sections / parts should be written into the TOC.xml
## Current behaviour
Some sections are not getting written into TOC.xml per migration testing.
## Steps to reproduce
...
## Expected behaviour
Per TOC.xml writing specifications, all sections / parts should be written into the TOC.xml
## Current behaviour
Some sections are not getting written into TOC.xml per migration testing.
## Steps to reproduce
1. Go to: https://ncbi.cloud68.co/organizations/308db55a-21c9-4a64-9a70-d5aa7574726c/bookmanager/ec697f80-db87-4094-8af3-cd796e8049c1/toc/25d90194-0a0a-44c0-aa99-04e839a9afc3
2. Go to TOC Preview: see:
![Screenshot_2023-10-11_at_09.55.18](/uploads/5f2330bec03ee686c89d517c8a4c30c9/Screenshot_2023-10-11_at_09.55.18.png)
3. Download TOC.XML and see only that section was tagged:
[TOC__47_.xml](/uploads/e70dae0fd766652752365dd9bf2c5ca7/TOC__47_.xml)
4. Compare to chapter XML which has many more sections that should have been tagged in TOC.xml: https://ncbi.cloud68.co/organizations/308db55a-21c9-4a64-9a70-d5aa7574726c/bookmanager/ec697f80-db87-4094-8af3-cd796e8049c1/8a23e0b0-801d-41b6-ab33-f3b6ebc5c742#5ccc8109-867a-4df9-8b96-83b08dd353e4 - [wt605742_ch7__1_.xml](/uploads/de650a3018605e77ecaa613a737e3601/wt605742_ch7__1_.xml)
![Screenshot_2023-10-11_at_09.57.39](/uploads/8b5b49d001dceb19c10779f30ac5188c/Screenshot_2023-10-11_at_09.57.39.png)
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->
- [ ] This issue is blocking current user testing
- [ x] This issue is blocking current migration testing
- [ x] Fixing this issue is required for [Priority 1: Deploy MVP](https://gitlab.coko.foundation/groups/ncbi/-/epics/56)
- [ ] This issue should be triaged into later epics in the PM weekly meetingP04: Support valid and compliant TOC XML for all migrated Bookshelf contenthttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1490Loading error because both source and converted XML sent in ingest package2024-01-08T22:59:34ZStacy LathropLoading error because both source and converted XML sent in ingest package@DioneMentis @douglassue
## Expected behaviour
Ingests should load without error if converted XML is valid and meets Bookshelf tagging guidelines.
## Current behaviour
Ingests are failing for chapters because both source and convert...@DioneMentis @douglassue
## Expected behaviour
Ingests should load without error if converted XML is valid and meets Bookshelf tagging guidelines.
## Current behaviour
Ingests are failing for chapters because both source and converted XML are sent in ingest packages and system does not know which file of same name and extension to read.
## Steps to reproduce
1. Go to: https://ncbi.cloud68.co/organizations/308db55a-21c9-4a64-9a70-d5aa7574726c/bookmanager/7fb00b76-dd57-4ce8-881c-d503ac6249c5/80b6a22a-1468-44a4-8e19-6d0e093f20f9#0b681b1c-5fe7-47e7-a8e7-548b07d238e9
2. See attached ingest package that shows both source and converted files are sent: [bcms7148.chapter7.1.6b95d0.2023_04_27-04_54_46.zip](/uploads/26ec461fce3492a3e3c87fc45aa0b47a/bcms7148.chapter7.1.6b95d0.2023_04_27-04_54_46.zip)
## Possible solution
Only send converted files for ingests.
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->
## QA Steps
[To be completed by Coko once dev is done]
## Scheduling
<!-- Select all the relevant options -->
- [ ] This issue is blocking current user testing
- [x] This issue is blocking current migration testing
- [x] Fixing this issue is required for [Priority 1: Deploy MVP](https://gitlab.coko.foundation/groups/ncbi/-/epics/56)
- [ ] This issue should be triaged into later epics in the PM weekly meetingP05: Address MVP Files Management and Processing Issues to support all current Bookshelf submitters and NCBI Integration specifications