ncbi issueshttps://gitlab.coko.foundation/ncbi/ncbi/-/issues2024-01-16T18:39:53Zhttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1232publication history allows non-digits in month field2024-01-16T18:39:53ZDiana jordanpublication history allows non-digits in month field@DioneMentis @lathrops1
## Expected behaviour
[Tell us what should happen. Link to the developed feature issue that describles the expected behaviour if possible]
## Current behaviour
chapter based book meta allows non-digits in pub...@DioneMentis @lathrops1
## Expected behaviour
[Tell us what should happen. Link to the developed feature issue that describles the expected behaviour if possible]
## Current behaviour
chapter based book meta allows non-digits in publication history month field
## Steps to reproduce
![image](/uploads/fe50fc3157b97c98a7608e9479b394b2/image.png)
https://ncbi.cloud68.co/organizations/32d78686-4b9a-46af-b52a-f5d0c4052177/bookmanager/6d2f9c57-8078-435b-8bda-f0b0cc9157bf/
1. go to word chapter book meta
2. enter publication history date with letters in month field
3. save (receive no warning and are allowed to save)
## NCBI's priority feedback
Looks like this fix was made and in QA
Going to say needed for deployment - but if we'd get a loading error for this use case, it could wait
## QA Steps
1. go to word chapter book meta
2. On the publication history for both date created and updated try:
a) adding only the year on a non-digit format
b) add the year correctly but the month on a non-digit format
c) add the year and the month correctly but the day on a non digit format.
3. You should not be able to savehttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1231publication date allows unusual syntax2024-01-16T18:20:57ZDiana jordanpublication date allows unusual syntax@DioneMentis @lathrops1
## Expected behaviour
[Tell us what should happen. Link to the developed feature issue that describes the expected behaviour if possible]
## Current behaviour
Publication date for chapter based book and colle...@DioneMentis @lathrops1
## Expected behaviour
[Tell us what should happen. Link to the developed feature issue that describes the expected behaviour if possible]
## Current behaviour
Publication date for chapter based book and collection allows unusual syntax
- letters in day, month, year
- year with more/less than 4 digits
![image](/uploads/4c7d6783ef7c49615e24b50c1004d9c9/image.png)
![image](/uploads/8d2111a16ffeab26b51c8d84d907cf52/image.png)
![image](/uploads/7cc49601d5cb98cc610f2bddf53aeac7/image.png)
![image](/uploads/3188ca0e17cb387cad23376277c19bb3/image.png)
## Steps to reproduce
https://ncbi.cloud68.co/organizations/32d78686-4b9a-46af-b52a-f5d0c4052177/bookmanager/6d2f9c57-8078-435b-8bda-f0b0cc9157bf/
https://ncbi.cloud68.co/organizations/669d427c-32b6-45bf-abd2-c28e7dc65b07/collectionmanager/3d115014-ecba-41c8-a5c8-fb36276b16eb/
1. go to collection meta or word chapter book meta
2. edit publication date with
- letters in day, month, year
- year with more/less than 4 digits
3. save (receive no warning and are allowed to save)
## NCBI's priority feedback
Looks like this fix was made and in QA
Going to say needed for deployment - but if we'd get a loading error for this use case, it could wait
## QA Steps
1. go to collection meta and word/xml/pdf chapter processed book metadata modal
2. edit publication date with
- letters in day, month, year
- year with more/less than 4 digits
- do this for all types of type of publication date print/electronic/range...
- try to check the optional fields like day, month or end date as there where more common the issue of unusual syntax.
3. save (receive no warning and are allowed to save)ChristinaTrompChristinaTromphttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1177Unable to migrate multiple affiliations for chapter-processed book metadata2022-10-31T09:03:58ZStacy LathropUnable to migrate multiple affiliations for chapter-processed book metadata@ChristinaTromp @DioneMentis
## Expected behaviour
NCBI should be able to migrate all of its content from its current CMS to the new BCMS
## Current behaviour
During migration we are losing some contributor affiliations - namely in ...@ChristinaTromp @DioneMentis
## Expected behaviour
NCBI should be able to migrate all of its content from its current CMS to the new BCMS
## Current behaviour
During migration we are losing some contributor affiliations - namely in cases where there is more than one.
Examples on Bookshelf:
EndoText
https://www.ncbi.nlm.nih.gov/books/NBK278943/
```
<contrib-group>
<!--<contrib contrib-type="editor">
<name>
<surname>De Groot</surname>
<given-names>Leslie J</given-names>
</name>
<aff>Research Professor, Cell and Molecular Biology, College of the Environment and
Life Sciences, University of Rhode Island, Kingston, RI</aff>
<role>Editor-in-chief</role>
</contrib>--><!-- removed per 2019010 request -->
<contrib contrib-type="editor">
<name>
<surname>Feingold</surname>
<given-names>Kenneth R</given-names>
</name>
<aff>Emeritus Professor of Medicine, University of California, San Francisco, CA</aff>
<role>Editor-in-chief</role>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Anawalt</surname>
<given-names>Bradley</given-names>
</name>
<aff>Chief of Medicine at the University of Washington Medical Center and Professor and Vice Chair of the Department of Medicine, University of Washington</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Boyce</surname>
<given-names>Alison</given-names>
</name>
<aff>Pediatric Endocrinologist and Associate Research Physician in the Skeletal Diseases and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Chrousos</surname>
<given-names>George</given-names>
</name>
<aff>Professor of Pediatrics and Endocrinology, Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>de Herder</surname>
<given-names>Wouter W</given-names>
</name>
<aff>Professor of Endocrine Oncology, Erasmus MC and Erasmus MC Cancer Center, Rotterdam, the Netherlands</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Dhatariya</surname>
<given-names>Ketan</given-names>
</name>
<aff>Consultant in Diabetes, Endocrinology and General Medicine, Norfolk and Norwich University Hospitals NHS Foundation Trust and University of East Anglia, Norwich, UK</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Dungan</surname>
<given-names>Kathleen</given-names>
</name>
<aff>Professor of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Ohio State University</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Hershman</surname>
<given-names>Jerome M</given-names>
</name>
<aff>Distinguished Professor Emeritus of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA; Endocrinology Consultant, Endocrine Clinic, West Los Angeles VA Medical Center, Los Angeles, CA</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Hofland</surname>
<given-names>Johannes</given-names>
</name>
<aff>Consultant Endocrinologist, Erasmus MC and Erasmus MC Cancer Center, Rotterdam, the Netherlands</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Kalra</surname>
<given-names>Sanjay</given-names>
</name>
<aff>Consultant Endocrinologist, Department of Endocrinology, Bharti Hospital, Karnal, India</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Kaltsas</surname>
<given-names>Gregory</given-names>
</name>
<aff>Professor of General Medicine-Endocrinology, 1st Department of Propaedeutic Medicine, National and Kapodistrian University of Athens, Athens, Greece</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Koch</surname>
<given-names>Christian</given-names>
</name>
<aff>Professor, The University of Tennessee Health Science Center, Memphis, Tennessee</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Kopp</surname>
<given-names>Peter</given-names>
</name>
<aff>Professor of Medicine and Chief of the Division of Endocrinology, Diabetology and Metabolism, University of Lausanne, Switzerland</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Korbonits</surname>
<given-names>Márta</given-names>
</name>
<aff>Professor of Endocrinology and Metabolism, Centre Lead for Endocrinology and Deputy Institute Director, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, England</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Kovacs</surname>
<given-names>Christopher S</given-names>
</name>
<aff>University Research Professor and Professor of Medicine (Endocrinology and Metabolism), Obstetrics & Gynecology, and BioMedical Sciences, at Memorial University of Newfoundland in St. John’s, Newfoundland, Canada</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Kuohung</surname>
<given-names>Wendy</given-names>
</name>
<aff>Director of the Division of Reproductive Endocrinology at Boston Medical Center and an Associate Professor of Obstetrics and Gynecology at the Boston University School of Medicine</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Laferrère</surname>
<given-names>Blandine</given-names>
</name>
<aff>Professor of Medicine, New York Obesity Research Center, Division of Endocrinology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Levy</surname>
<given-names>Miles</given-names>
</name>
<aff>Consultant endocrinologist at University Hospitals of Leicester and Honorary Associate Professor at Leicester University</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>McGee</surname>
<given-names>Elizabeth A</given-names>
</name>
<aff>Professor of Obstetrics and Gynecology at the University of Vermont and Director of the Division of Reproductive Endocrinology and Infertility. Burlington, Vermont</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>McLachlan</surname>
<given-names>Robert</given-names>
</name>
<aff>Director of Clinical Research, Hudson Institute of Medical Research; Consultant Endocrinologist, Monash Medical Centre, Melbourne, Australia</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Morley</surname>
<given-names>John E</given-names>
</name>
<aff>Dammert Professor of Gerontology and Director, Division of Geriatric Medicine and Director of the Division of Endocrinology, Saint Louis University Medical Center</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>New</surname>
<given-names>Maria</given-names>
</name>
<aff>Professor of Pediatrics, Professor of Genetics and Genomic Sciences, and Chief of the Adrenal Steroid Disorders Program, Icahn School of Medicine, Mount Sinai School of Medicine, New York, NY</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Purnell</surname>
<given-names>Jonathan</given-names>
</name>
<aff>Professor of Medicine, Knight Cardiovascular Institute and the Division of Endocrinology, and Associate Director, Bob and Charlee Moore Institute for Nutrition and Wellness, Oregon Health and Science University, Portland, OR</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Sahay</surname>
<given-names>Rakesh</given-names>
</name>
<aff>Professor and Head of Department of Endocrinology, Osmania Medical College and Osmania General Hospital, Hyderabad, India</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Singer</surname>
<given-names>Frederick</given-names>
</name>
<aff>Director of the Endocrine/Bone Disease Program, Saint Johns Cancer Institute at Saint John’s Health Center, Santa Monica, CA; Clinical Professor of Medicine, UCLA School of Medicine, Los Angeles, CA</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Sperling</surname>
<given-names>Mark A</given-names>
</name>
<aff>Professorial Lecturer, Division of Pediatric Endocrinology and Diabetes, Icahn School of Medicine at Mount Sinai, New York, NY. Emeritus Professor and Chair, Department of Pediatrics, University of Pittsburgh</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Stratakis</surname>
<given-names>Constantine A</given-names>
</name>
<aff>CSO, ELPEN, Inc. & Director, Research Institute, Athens, Greece & Senior Investigator, Human Genetics & Precision Medicine, FORTH (ITE), Heraklion, Greece. Emeritus Scientific Director & Senior Investigator, NICHD, NIH, Bethesda, MD, USA</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Trence</surname>
<given-names>Dace L</given-names>
</name>
<aff>Professor of Medicine, Emeritus, University of Washington, Seattle, WA</aff>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Wilson</surname>
<given-names>Don P</given-names>
</name>
<aff>Endowed Chair, Cardiovascular Health and Risk Prevention, Pediatric Endocrinology and Diabetes, Cook Children's Medical Center, Fort Worth, TX</aff>
</contrib>
</contrib-group>
```
Medical Genetics Summaries
https://www.ncbi.nlm.nih.gov/books/NBK61999/
```
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Pratt</surname>
<given-names>Victoria</given-names>
</name>
<xref ref-type="aff" rid="gtrbook.Td.aff1"/>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>McLeod</surname>
<given-names>Howard</given-names>
</name>
<xref ref-type="aff" rid="gtrbook.Td.aff2"/>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Dean</surname>
<given-names>Laura</given-names>
</name>
<xref ref-type="aff" rid="gtrbook.Td.aff3"/>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Malheiro</surname>
<given-names>Adriana</given-names>
</name>
<role>Associate Editor</role>
<xref ref-type="aff" rid="gtrbook.Td.aff4"/>
</contrib>
<contrib contrib-type="editor">
<name>
<surname>Rubinstein</surname>
<given-names>Wendy</given-names>
</name>
<role>Editor-in-chief</role>
<xref ref-type="aff" rid="gtrbook.Td.aff5"/>
</contrib>
</contrib-group>
<aff id="gtrbook.Td.aff1"><institution>Director, Pharmacogenomics and Molecular Genetics
Laboratories, Department of Medical and Molecular Genetics, Indiana University School of
Medicine</institution>
<addr-line>Bloomington, IN 47405</addr-line></aff>
<aff id="gtrbook.Td.aff2"><institution>Medical Director, The DeBartolo Family Personalized Medicine
Institute, Senior Member, Division of Population Sciences, Moffitt Cancer Center</institution>
<addr-line>Tampa, FL 33612</addr-line></aff>
<aff id="gtrbook.Td.aff3"><institution>Senior Medical Writer, Literature Division, National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health</institution>
<addr-line>Bethesda, MD 20894</addr-line></aff>
<aff id="gtrbook.Td.aff4"><institution>Project Lead, Medical Genetics and Human
Variation, National Center for Biotechnology Information (NCBI), National Library of
Medicine, National Institutes of Health</institution>
<addr-line>Bethesda, MD 20894</addr-line></aff>
<aff id="gtrbook.Td.aff5"><institution>Division Director, Clinical Data Management and Curation, CancerLinQ LLC</institution>
<addr-line>Alexandria, VA</addr-line></aff>
```
## Steps to reproduce
Unable to reproduce as it is a migration issue because of lack of functionality in UI.
## Environment
N/A
## Possible solution
Permit more than one affiliation for contributors in chapter processed book metadata, and make affiliations available for other contributors in that same book via a dropdown. The book metadata is then written in the second XML format shown above, where affiliations are de-duplicated, gathered at the end of the contributors XML, and linked to contributors via hrefs and IDs.
## NCBI's priority feedback
Y, for migration
## QA Steps
1. Go to a chapter processed book
2. Open the metadata modal and add editors and authors
![image](/uploads/5bd3f8929e9478a34fd1f43965205d29/image.png)
3. Reload preview of an existing chapter if you can. When the status of the chapter is loading preview download the converted xml and check that all the affiliations are in the xml file.
`<xref ref-type="aff" rid="aff-id-name"/>` -- similar to this will be written on the contrib data for each contributor.
written to the xml it should include the references for the affiliations like this:
``<aff id="aff-id-name">
<institution>Affiliation name</institution>
</aff>``
4. Alternatively you can submit a new chapter and check after the conversion is finished.
5. Once you publish the chapter, and then publish the book's TOC, you can see on the TOC that the affiliations display in a referenced list with a many-to-many relationship from contributors to affiliations, and the affiliations are not duplicated in the referenced list.2022-Jul-BChristinaTrompChristinaTromphttps://gitlab.coko.foundation/ncbi/ncbi/-/issues/1224Permissions refactor and implementation on Book Manager (chapter proccessed)2022-06-09T19:03:17ZDanjela Shehidanjelashehi@gmail.comPermissions refactor and implementation on Book Manager (chapter proccessed)## Implementing Permmisions
1. as Defined in this [sheet here ]( https://docs.google.com/spreadsheets/d/1cJeKIUhkkM_kwQ8Fzh9d2Vw9h2IJcgT3_87sWLiNdNQ/edit#gid=16945569)
wrap all components with permission gate, with appropriate scope <b...## Implementing Permmisions
1. as Defined in this [sheet here ]( https://docs.google.com/spreadsheets/d/1cJeKIUhkkM_kwQ8Fzh9d2Vw9h2IJcgT3_87sWLiNdNQ/edit#gid=16945569)
wrap all components with permission gate, with appropriate scope <br/>
- [x] Upload chapters modal (Bulk upload)
- [x] Team modal
- [x] Settings modal (See readme)
- [x] Metadata modal
- [x] Add part
- Order by drag and drop (when manual ordering is ON) <br/> (This has a fix with issue #1253 )
- [x] TOC page
- [x] Publish TOC
- [x] Submit
- [x] Reload preview
- [x] Publish components
- Download (Not for the first deployment)
- [x] Archive
- [x] Move to and Repeat
<br/>
2. Test all the above UIs for all roles to have the correct access rights <br/>
3. Remove redundant code for permissions in the files where work is done
<br/>
Note:
all elements mentioned above should be wrapped similar to the below example, where parameter `scopes` should have the key-word to check if the user that is logged in has permission
```
<PermissionsGate scopes={['view-or-edit-component-name']}>
<ComponentToBeChecked />
</PermissionsGate>
```
## Testing Permissions
Create users with these roles:
1. System Admin
2. PDF to XML Vendor
Users in Organization no. 1 (can be any title)
3. Organization admin
4. Editor in organization not assigned to any book
5. Editor in organization and assign to book (ex Book no.1 (Word workflow chapter processed) - created in Organization no. 1)
6. Editor in organization and assign to one book component
Users in Organization no. 2 (can be any title)
7. Organization admin for this organization
8. Editor in organization not assigned to any book
9. Editor in organization and assign to book
After created 9 users with above roles , log in as any of them to test if you have correct permissions on the app2022-May-BChristinaTrompChristinaTromp