ncbi issueshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues2021-10-05T12:21:41Zhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/718Converted files not ingested to BCMS and sent to Load to PMC2021-10-05T12:21:41ZStacy LathropConverted files not ingested to BCMS and sent to Load to PMC@DioneMentis @John.kopanas @jordandc
## Expected behaviour
When converted files complete NCBI XML conversion and are sent to Coko for ingest to BCMS, they should get uploaded to the BCMS and sent to Load to PMC with corresponding stat...@DioneMentis @John.kopanas @jordandc
## Expected behaviour
When converted files complete NCBI XML conversion and are sent to Coko for ingest to BCMS, they should get uploaded to the BCMS and sent to Load to PMC with corresponding status getting correctly updated
## Current behaviour
The status of the Component and Uploaded Source document are stuck at "Converting" though XML conversion completed - see:
![image](/uploads/bc8f3e29860f6b39011420c0b06b387b/image.png)
## Steps to reproduce
https://ncbi.cloud68.co/organizations/014be39d-68ef-4a19-8340-5c044efddfff/bookmanager/74a98c8e-f1e9-42b0-af40-b421fbb1e882/3245a03c-cce7-4d51-98d2-5d4e9e6fc617
1. Upload chapter XML source file without any errors
## Environment
PC Chrome Version 92.0.4515.159 (Official Build) (64-bit)
## Priority
This is a blocker for our testing
1. Resolving this bug is required for migration YSept 02Giannis Kopanasjkopanas@gmail.comGiannis Kopanasjkopanas@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/717BCMS component status and latest source file status are inaccurate2021-10-05T12:21:41ZStacy LathropBCMS component status and latest source file status are inaccurate@DioneMentis @John.kopanas @jordandc
## Expected behaviour
The component status and most recently uploaded file status should be the status of the last completed action (Conversion Errors)
See last TM session with conversion errors s...@DioneMentis @John.kopanas @jordandc
## Expected behaviour
The component status and most recently uploaded file status should be the status of the last completed action (Conversion Errors)
See last TM session with conversion errors says Kafka notification of error passed:
![image](/uploads/3c9458a6edef72fdcff9541ff9c13288/image.png)
## Current behaviour
The component status is that of the previously uploaded source version (which also has that completed status) of previewing
## Steps to reproduce
https://ncbi.cloud68.co/organizations/32d78686-4b9a-46af-b52a-f5d0c4052177/bookmanager/0edd17d6-34fc-458b-b465-fd26a551120d/f011222e-4ab8-4662-b713-8612b5416ee9
1. Upload clean source Word document (V1.1) to point of Previewing
2. Upload source Word document that will cause conversion errors (V1.2)
## Environment
PC Chrome Version 92.0.4515.159 (Official Build) (64-bit)
## Priority
Priority to be able to complete testing - testing is blocked by this
1. Resolving this bug is required for migration YSept 02Giannis Kopanasjkopanas@gmail.comGiannis Kopanasjkopanas@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/716BCMS status indicates "New Upload" although NCBI Word2XML conversion passed a...2021-10-05T12:21:41ZStacy LathropBCMS status indicates "New Upload" although NCBI Word2XML conversion passed and a load to PMC session completed with Preview displaying in BCMS@DioneMentis @jordandc @John.kopanas
## Expected behaviour
The status should be "Previewing" because the uploaded source Word document passed Word conversion and Load to PMC without errors and the preview link shows in the BCMS; also ...@DioneMentis @jordandc @John.kopanas
## Expected behaviour
The status should be "Previewing" because the uploaded source Word document passed Word conversion and Load to PMC without errors and the preview link shows in the BCMS; also all NCBI processing completed without error, see:
![image](/uploads/ac10c3bb44104958f0a424f22ec8066f/image.png)
![image](/uploads/18daf40e44d5745d4406baefdf1d5192/image.png)
## Current behaviour
The status for the Component AND Source and Converted files are all incorrectly "New Upload"
## Steps to reproduce
https://ncbi.cloud68.co/organizations/32d78686-4b9a-46af-b52a-f5d0c4052177/bookmanager/0edd17d6-34fc-458b-b465-fd26a551120d/5a3f8aec-65da-4eea-b645-d9c72460f27f
1. Upload a Word document without errors and press Submit
## Environment
PC Chrome Version 92.0.4515.159 (Official Build) (64-bit)
## Priority
Yes - this is a Blocker to testing and accurate status reporting
1. Resolving this bug is required for migration Y
2. This can be prioritised after migration NSept 02Giannis Kopanasjkopanas@gmail.comGiannis Kopanasjkopanas@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/715updated folder names in dowloaded packaged to match folders in Apex/PDF conve...2021-10-05T12:21:41ZDione Mentisdione@coko.foundationupdated folder names in dowloaded packaged to match folders in Apex/PDF conversion@andynicholson
FYI @John.kopanas
Currently folder names in download packages are as below:
![Screenshot_2021-09-24_at_15.21.11](/uploads/72804c1a9e2ecc21382cfac685d77fd2/Screenshot_2021-09-24_at_15.21.11.png)
Please update the nam...@andynicholson
FYI @John.kopanas
Currently folder names in download packages are as below:
![Screenshot_2021-09-24_at_15.21.11](/uploads/72804c1a9e2ecc21382cfac685d77fd2/Screenshot_2021-09-24_at_15.21.11.png)
Please update the names of the folders to the below:
1. `pdf` --> `display-pdfs`
1. `image` --> `images`
1. `cover` --> `metadata`
1. `comment` --> `review` // only relevant to UI downloads
1. `supplement` --> `suppl`Sept 02Andy NicholsonAndy Nicholsonhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/714Files from converted package (PDF conversion) are duplicated in UI2021-10-05T12:21:41ZDione Mentisdione@coko.foundationFiles from converted package (PDF conversion) are duplicated in UI## Expected behaviour
When Apex (PDF2XML vendor) uploads a converted package to their FTP, its contents should display accurately in the BCMS.
## Current behaviour
All files are duplicated. There are two versions when only one was se...## Expected behaviour
When Apex (PDF2XML vendor) uploads a converted package to their FTP, its contents should display accurately in the BCMS.
## Current behaviour
All files are duplicated. There are two versions when only one was sent.
## Steps to reproduce
See example in [this book](https://ncbidev.cloud68.co/organizations/a2c1e381-f348-41a9-9d76-e4f11f761033/bookmanager/d464525d-82af-40ea-a2fc-9203e9ec9a5e/08a6adfe-517c-4603-a874-d01ecd6fbcb0)
1. Create book, upload source file, and submit.
2. Create a mock vendor conversion package and submit by FTP.
[bcms10000073-ch.zip](/uploads/00c5fe36f7c9f2b2f064b62f9dbaf8bc/bcms10000073-ch.zip)
![Screenshot_2021-09-24_at_14.29.36](/uploads/ea22ccbd8d75e253d80ada8fceae2954/Screenshot_2021-09-24_at_14.29.36.png)
3. In the BCMS I see two versions of each file that was in the conversion package , but only one package was sent.Sept 02Giannis Kopanasjkopanas@gmail.comGiannis Kopanasjkopanas@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/713Add source icon for collection based on collection members2021-10-05T12:21:41ZDione Mentisdione@coko.foundationAdd source icon for collection based on collection members@danjela
The source workflow (PDF/WORD/XML) of a collection is dependent on the books in the collection, so:
1. When collection is created, the "source" is null (show no icon in "source" column in the dashboard)
2. When a book is ad...@danjela
The source workflow (PDF/WORD/XML) of a collection is dependent on the books in the collection, so:
1. When collection is created, the "source" is null (show no icon in "source" column in the dashboard)
2. When a book is added, match collection source to book source
3. If books in collection have more than one source, show no icon (this can be improved later with a icon to show multiple sources)Sept 02Danjela Shehidanjelashehi@gmail.comDanjela Shehidanjelashehi@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/712Show collection status2021-10-05T12:21:40ZDione Mentisdione@coko.foundationShow collection status@danjela
I have added the collection status to the docs [here](https://gitlab.coko.foundation/ncbi/ncbi/-/wikis/Workflows/BCMS-states-and-user-actions#states-of-the-content)
Collection statuses
- When a collection gets created --> "...@danjela
I have added the collection status to the docs [here](https://gitlab.coko.foundation/ncbi/ncbi/-/wikis/Workflows/BCMS-states-and-user-actions#states-of-the-content)
Collection statuses
- When a collection gets created --> "New collection"
- When books in the collection have multiple statuses --> "In production"
- Match the collection status to book status when all books in the collection have the same status.Sept 02Danjela Shehidanjelashehi@gmail.comDanjela Shehidanjelashehi@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/703Part modal versus part page and navigating through books with parts2021-10-05T12:21:40ZDione Mentisdione@coko.foundationPart modal versus part page and navigating through books with parts[Provide a general summary of the issue in the title above]
## Expected behaviour
In chapter-processed books, I should be able to navigate though the components on the order they appear in the book manger
This should work per section:...[Provide a general summary of the issue in the title above]
## Expected behaviour
In chapter-processed books, I should be able to navigate though the components on the order they appear in the book manger
This should work per section:
1. Front
2. Body (including nested components)
3. Back
## Current behaviour
When the Body has parts, components are skipped when I navigate with "next" and "previous" buttons.
## Steps to reproduce
In [this book](https://ncbidev.cloud68.co/organizations/a2c1e381-f348-41a9-9d76-e4f11f761033/bookmanager/709b89aa-5fa3-4736-be37-436f0cfb1d01)
1. Open the first component in the body section
2. Use the "Next >" button to navigate through the components
3. See that components are skipped, instead of navigated in order.
See example video: ![part-navigation-20210920](/uploads/57af6a1e3d7d454c91a3778458b6ab73/part-navigation-20210920.mp4)
## Environment
Mac, Chrome Version 93.0.4577.82, testing on ncbidev
## Possible solution
The part should only be a modal when adding part. Once the part exists, opening the part should take the user to a part page.
## Priority
1. Resolving this bug is required for migration (Y)Sept 02Danjela Shehidanjelashehi@gmail.comSidorela UkuDanjela Shehidanjelashehi@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/702Add part contributors to toc.xml file2021-10-07T08:42:35ZDione Mentisdione@coko.foundationAdd part contributors to toc.xml file@andynicholson
Parts can also have metadata. As you'll see in the UI users can add Editors to a part. This `<contributors>` node should be added to the part `<toc-entry>`, unless it's empty.@andynicholson
Parts can also have metadata. As you'll see in the UI users can add Editors to a part. This `<contributors>` node should be added to the part `<toc-entry>`, unless it's empty.Sept 02Andy NicholsonAndy Nicholsonhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/695Group books by custom group titles in the collection manager UI2021-11-10T04:29:54ZDione Mentisdione@coko.foundationGroup books by custom group titles in the collection manager UI@danjela
There are 2 ways to group books in a collection:
1. Automatically (4 options)
2. by custom group titles
![Screenshot_2021-09-16_at_12.06.00](/uploads/75e6cd33edfe2e534af473d395e5006e/Screenshot_2021-09-16_at_12.06.00.png)
...@danjela
There are 2 ways to group books in a collection:
1. Automatically (4 options)
2. by custom group titles
![Screenshot_2021-09-16_at_12.06.00](/uploads/75e6cd33edfe2e534af473d395e5006e/Screenshot_2021-09-16_at_12.06.00.png)
When books are grouped automatically, this has **no effect** in the collection manger UI. The chosen setting updates the domain and NCBI system creates these groups.
When books are grouped by "custom group titles" the user needs to add these titles and move books into these groups. This is the same functionality as parts in chapter-processed books.
![Collection-manager-V5-groups](/uploads/8c7a6c45ea5f5d22d4f5327fa8ffa9ea/Collection-manager-V5-groups.jpeg)
**Add group modal**
![Add-edit_group](/uploads/d4a8c01390740f8ad38c82b59466e81e/Add-edit_group.jpeg)
**Move to modal**
![Move_books](/uploads/cc341b4a630c01dde1e48fc01dd0c55a/Move_books.jpeg)
Dev tasks:
1. [x] "add groups" button and modal
2. [x] "move to" button and modal
3. [x] drag and drop ordering for groups
4. [x] expand/collapse the groups
5. [x] status column showing the status of the book
6. [x] Click on row to open bookSept 02Danjela Shehidanjelashehi@gmail.comDanjela Shehidanjelashehi@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/690Check collection Agreements when collection member is published2021-10-29T00:15:49ZDione Mentisdione@coko.foundationCheck collection Agreements when collection member is publishedAs in #481 the BCMS must check the collection (parent) agreement when a book that belong to a collection is published.
Refer to #481 description for testingAs in #481 the BCMS must check the collection (parent) agreement when a book that belong to a collection is published.
Refer to #481 description for testingSept 02https://gitlab.coko.foundation/ncbi/ncbi/-/issues/651Unable to fix settings errors2021-11-15T05:30:53ZStacy LathropUnable to fix settings errors@DioneMentis -
cc @ErinS
Based on my testing and frustration of creating books, there are two problems with the current settings design, see attached video - [zoom_0.zip](/uploads/d4807756d8a8e44ba84a1241d737f782/zoom_0.zip)
1. I **V...@DioneMentis -
cc @ErinS
Based on my testing and frustration of creating books, there are two problems with the current settings design, see attached video - [zoom_0.zip](/uploads/d4807756d8a8e44ba84a1241d737f782/zoom_0.zip)
1. I **VERY OFTEN** get the new book settings incorrect when creating new books, and there is no way for me to go back to fix them before approving settings.
1. System admin must have a way to go to the Settings tab of books and fix processing settings like workflow, chapter / book processing, etc. I can guarantee based on testing these issues will happen and we don't want to have many dead books in the database because someone made an error, and then have to migrate to a new book.
I do not think we can go to production with out the second issue addressed - System admin MUST be able to fix mistakes on all settings.Sept 02Dione Mentisdione@coko.foundationDione Mentisdione@coko.foundationhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/631Add last pub date from converted file version2021-10-20T01:21:17ZDione Mentisdione@coko.foundationAdd last pub date from converted file versionThis last item for #582 requires a decision to point 3 in #603
Currently we show the `bookComponentVersionNumber.SourceFileVersion` in the last pub date. This should change to `bookComponent versionNumber.ConvertedFileVersion` because ...This last item for #582 requires a decision to point 3 in #603
Currently we show the `bookComponentVersionNumber.SourceFileVersion` in the last pub date. This should change to `bookComponent versionNumber.ConvertedFileVersion` because it's possible to publish a converted file when a source file does not exist.
**Display in UI**
Use simplified date followed by the version number. For example `3 days ago (V1.4)`. Show the full date on hover, as already dine for the "last updated" date.
* book manager and book component page: `3 days ago (V1.4)`
* Dashboard: `3 days ago` (note: if it's a chapter-processed book then show date for whichever chapter was published most recently)Sept 02Danjela Shehidanjelashehi@gmail.comGiannis Kopanasjkopanas@gmail.comDanjela Shehidanjelashehi@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/598Different versions of a file aren't sorted together in "show history"2021-10-05T12:21:41ZStacy LathropDifferent versions of a file aren't sorted together in "show history"## Expected behaviour
Files should be listed in a consist manner. Show the latest file version when table is collaped. When the tabl is expanded, list each file in decenting order by version number:
```
somefile.pdf V3
somefile.pdf V2...## Expected behaviour
Files should be listed in a consist manner. Show the latest file version when table is collaped. When the tabl is expanded, list each file in decenting order by version number:
```
somefile.pdf V3
somefile.pdf V2
somefile.pdf V1
anotherfile.jpg V2
anotherfile.jpg V1
```
## Current behaviour
When user clicks "show history" on suppl files, the diff versions of a file don't show next to each other as we'd expect - please see:
[127.0.0.2_3390_-_Remote_Desktop_Connection_2021-07-22_13-38-05.zip](/uploads/7bc3944fd0fd11fbfade0ac000a827f8/127.0.0.2_3390_-_Remote_Desktop_Connection_2021-07-22_13-38-05.zip)
## Steps to reproduce
![image2021-7-22_13-41-5](/uploads/6e7d63a059ebac919cc48ea2b19b744d/image2021-7-22_13-41-5.png)
1. upload V1 files to any section (suppl, images, display PDFs)
2. upload V2 files
3. expand to "show all version"
4. see that the files are not ordered togetherSept 02Giannis Kopanasjkopanas@gmail.comSidorela UkuGiannis Kopanasjkopanas@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/539Preview tab lacks notice to check errors after Load to PMC2021-10-23T21:22:21ZStacy LathropPreview tab lacks notice to check errors after Load to PMC!481
## Expected behaviour
There should be an indication that a preview will be available later once content is done processing / errors are fixed.
All use cases:
The preview tab should always display what's relevant to the current ...!481
## Expected behaviour
There should be an indication that a preview will be available later once content is done processing / errors are fixed.
All use cases:
The preview tab should always display what's relevant to the current file. So:
* "new version" and "new upload" --> Submit files for conversion to generate the preview.
* "converting" and "loading preview" --> Preview will display when file loads successfully.
* "previewing" [show preview]
* "conversion errors" and "loading errors" --> Resolve the errors to display the preview.
## Current behaviour
A blank page appears
## Steps to reproduce
Example: ![image](/uploads/430564f0d3fcf5919ad9035bdacb5709/image.png)
Another example: https://ncbi.cloud68.co/organizations/308db55a-21c9-4a64-9a70-d5aa7574726c/bookmanager/96a97d1d-3b7d-403f-9c2f-de3bd2fba297/1e418c5a-ea97-4b1e-b5c5-ea10923fc5f6
1. Run source / converted file
2. When file is processing look at preview page and see it is blank but should have notification
3. Run file with error
4. When file is processing look at preview page and see it is blank but should have notification
## Environment
PC Chrome Version 92.0.4515.159 (Official Build) (64-bit)Sept 02Danjela Shehidanjelashehi@gmail.comDanjela Shehidanjelashehi@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/428book settings changes2021-10-21T15:54:07ZDione Mentisdione@coko.foundationbook settings changesAll settings for books (chapter-processed and wholebooks) are confirmed in the BCMS setting spreadsheet [here](https://docs.google.com/spreadsheets/d/1Xd0vKDbaYrajfnUmYqCnXUY5Ir0znqc7o0KGVp_okg0/edit#gid=725030307&range=I:I).All settings for books (chapter-processed and wholebooks) are confirmed in the BCMS setting spreadsheet [here](https://docs.google.com/spreadsheets/d/1Xd0vKDbaYrajfnUmYqCnXUY5Ir0znqc7o0KGVp_okg0/edit#gid=725030307&range=I:I).Sept 02Dione Mentisdione@coko.foundationDione Mentisdione@coko.foundationhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/421Last published date goes missing on book manager page2021-10-06T15:42:44ZStacy LathropLast published date goes missing on book manager pageThis happens when you update a previous published version component.
See:
![image2021-2-24_15-31-54](/uploads/8a3135651352a88547385749b9ef4687/image2021-2-24_15-31-54.png)This happens when you update a previous published version component.
See:
![image2021-2-24_15-31-54](/uploads/8a3135651352a88547385749b9ef4687/image2021-2-24_15-31-54.png)Sept 02Giannis Kopanasjkopanas@gmail.comSidorela UkuGiannis Kopanasjkopanas@gmail.comhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/390Create, update, apply an Organization settings template2022-07-26T07:04:32ZDione Mentisdione@coko.foundationCreate, update, apply an Organization settings templateUpdated 26 July 2022
Original flow diagrams moved to the BCMS miro board: https://miro.com/app/board/o9J_lEzF9oQ=/
---
**Updated 25 August**
Here's the workflow description and updated design for your review.
## Domain template set...Updated 26 July 2022
Original flow diagrams moved to the BCMS miro board: https://miro.com/app/board/o9J_lEzF9oQ=/
---
**Updated 25 August**
Here's the workflow description and updated design for your review.
## Domain template set up
([View here](https://miro.com/app/board/o9J_l-Nri9c=/?moveToWidget=3074457362753381242&cot=14))
![Create-template-workflow](/uploads/e2264129fabebf189a42995f822e8963/Create-template-workflow.jpeg)
1. NCBI sets up a domain for both book types:
* chapter-processed book - `clonechapterprocess`
* whole-book - `clonebookprocess`
2. These will be used as the default templates in the BCMS (i.e. when creating a book, clone the default until the organization-specific templates are created.)
2. To create the organization-specific templates, the user select one of the defaults, fills in the form, and saves it. (The templates show only some of the settings that are relevant for users to see and change: see the limited set for the initial release on the "Domain Template" tab of the [BCMS settings spreadsheet](https://docs.google.com/spreadsheets/d/1Xd0vKDbaYrajfnUmYqCnXUY5Ir0znqc7o0KGVp_okg0/edit?usp=sharing))
4. Select a template from the dropdown at any stage to edit and update it.
**Wireframe**
![Domain-template-v4](/uploads/5a2c34943a1e8de0f857609e2479f3fc/Domain-template-v4.png)
All settings are in "Domain Template" tab of the [BCMS settings spreadsheet](https://docs.google.com/spreadsheets/d/1Xd0vKDbaYrajfnUmYqCnXUY5Ir0znqc7o0KGVp_okg0/edit?usp=sharing), ordered as they should appear in the from, under these sub-headings:
* Publishing settings
* Landing page: Table of contents
* Display: Content
* Display: Metadata
* Display: Reference citations
## Applying a template
([View here](https://miro.com/app/board/o9J_l-Nri9c=/?moveToWidget=3074457362786547648&cot=14))
When a book is created, the appropriate template is applied depending on the use case:
![apply-template-workflow](/uploads/fc44645118b020bc91588396eabcd0d9/apply-template-workflow.jpeg)
![New-book-modal-V5.2](/uploads/6537d9578994130943f06eed7ac24347/New-book-modal-V5.2.png)Sept 02Dione Mentisdione@coko.foundationDione Mentisdione@coko.foundationhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/373Collections created as PDF or XML supplied ones appear on dashboard incorrect...2021-10-05T12:21:40ZStacy LathropCollections created as PDF or XML supplied ones appear on dashboard incorrectly with Word iconFor example see:
![image2021-1-22_14-50-42](/uploads/e17fcaec4a10d9bbbe0e7939694d18b3/image2021-1-22_14-50-42.png)For example see:
![image2021-1-22_14-50-42](/uploads/e17fcaec4a10d9bbbe0e7939694d18b3/image2021-1-22_14-50-42.png)Sept 02https://gitlab.coko.foundation/ncbi/ncbi/-/issues/114Lock sensitive settings after book is created2021-10-21T19:35:01ZDione Mentisdione@coko.foundationLock sensitive settings after book is created*Updated 8 Sept*
**Use case**
Assuming the user has permission to edit the setting, sensitive settings must be locked to avoid accidentally changing them. The up-to-date information is shown in column K in the [BCMS setting spreadsheet...*Updated 8 Sept*
**Use case**
Assuming the user has permission to edit the setting, sensitive settings must be locked to avoid accidentally changing them. The up-to-date information is shown in column K in the [BCMS setting spreadsheet](https://docs.google.com/spreadsheets/d/1Xd0vKDbaYrajfnUmYqCnXUY5Ir0znqc7o0KGVp_okg0/edit?usp=sharing). This only applies to boolean settings.Sept 02Dione Mentisdione@coko.foundationDione Mentisdione@coko.foundation