Genesys PGR issueshttps://gitlab.croptrust.org/groups/genesys-pgr/-/issues2024-03-28T10:26:01+01:00https://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1060Reorganize i18n2024-03-28T10:26:01+01:00Matija ObrezaReorganize i18nThe same or similar expressions and phrases appear under different keys (files) making it difficult to consistently translate to other languages.
This ticket is to reorganize i18n files and keys to enable easier translation.
1. `client:...The same or similar expressions and phrases appear under different keys (files) making it difficult to consistently translate to other languages.
This ticket is to reorganize i18n files and keys to enable easier translation.
1. `client:model` namespace needs to contain labels and hints directly linked to the data model. In UI these keys are preferred for form fields, labels, etc.
2. `translations` namespace is the default namespace for i18n of UI components. UI components should use `client:model` whenever referring to the data model.
Originally the `translations.json` files were not detected at folder depths more than 2, but we can now place them deeper in the source code tree, making it easier to identify the translation keys and use them consistently.
The changes will be made in several steps (merge requests):
1. Clean up `client:model` and move model texts from other namespaces to the corresponding `model/.../translations.json`. Update UI to always refer to `client:model`.
2. Break up large `translation.json` into corresponding `subfolder/translation.json` files.2024.2Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/684Citations and literature2024-03-28T10:05:35+01:00Matija ObrezaCitations and literatureThis ticket adds support for citations and literature to Genesys.
## What does this mean?
Researchers often use data from Genesys and refer to Genesys as the source of the data. Genebanks often maintain the list of citations referencin...This ticket adds support for citations and literature to Genesys.
## What does this mean?
Researchers often use data from Genesys and refer to Genesys as the source of the data. Genebanks often maintain the list of citations referencing specific accessions in their collections. Either way, there is a paper published somewhere (with a URL) and a **citation record**. It is these citation records that we wish to include in Genesys.
A `Citation` includes:
- title (text)
- author names (text)
- year of publication (number)
- journal (text)
- type (one of `enum`: Journal article, Book, Book section, Conference proceedings, Preprint, Report, Other)
- article DOI (text, doi, must be unique in the database)
- download URL, if available (text, URL)
- abstract (long text)
- source of citation (one of: `enum` Google Scholar, bioRxiv, genebank, user submission)
- relevance (one or more of: `enum` Genesys cited, Genesys used, Accession referenced, Genesys discussed, Genesys mentioned)
- owner (SID) - user or `Partner` (like in datasets?)
- status (one of `enum`: SUBMITTED, PUBLISHED, DUPLICATE, REJECTED)
- statusText (text) - explanation why submission is not published
- link to valid `Citation` - used for duplicates, otherwise `null`
#### Extra properties (next version)
Additionally we may consider including:
- author OrcIDs and countries/territories/islands of affiliation
- is paper peer reviewed?
- is paper open access?
- subject of research
- source of funding
- countries/territories/islands covered in research
## Detecting duplicates
We'll use our **Similarity** method to detect similar/duplicate submissions. We'll compare the title, journal, year of publication, author names and abstract.
## Linking to Citations
A `Citation` may refer to Genesys in general (Genesys used, discussed, mentioned) or link to specific Accession**s**, Dataset**s**, or Subset**s**. These "links" will then be rendered on corresponding details pages in Genesys.
Other text-based categories could include **crops** and **species names**.
## User submissions
Users (any role) will be able to use a form in Genesys to submit a new citation. Genesys will first search for duplicates and present the matches to the user. If the user still wants to submit their citation, they'll need to include `submitAnyway=true` in the API request.
New submissions will have `status = SUBMITTED` until reviewed and handled by the Genesys team.
Users will be able to see their submitted citations (and their status) in their Dashboard.
## Genebank submissions
In the future, genebanks will be able to push citations related to `Accessions` (with GGCE).
## Managing citations
Users with `CITATION_MANAGER` or `ADMINISTRATOR` role can modify and publish individual citations. The corresponding UI will be in their Dashboard.
They are able to add links to specific Accession**s**, Dataset**s**, or Subset**s**.
> Inspired by https://www.gbif.org/literature-trackingArtem HrybeniukArtem Hrybeniukhttps://gitlab.croptrust.org/genesys-pgr/glis-client/-/issues/36Generating SMTA with Easy-SMTA2024-03-27T14:20:05+01:00Matija ObrezaGenerating SMTA with Easy-SMTAEasy-SMTA provides a new endpoint to generate the SMTA document in PDF format for the provided recipient, language and type of SMTA and list of material. This ticket extends `glis-client` with code to call the new service.
The paramete...Easy-SMTA provides a new endpoint to generate the SMTA document in PDF format for the provided recipient, language and type of SMTA and list of material. This ticket extends `glis-client` with code to call the new service.
The parameters will be the same or similar to those for reporting SMTA.
@mmarsella will provide the details about the new endpoint once it is available, and then the implementation can begin.Vladyslava MokliakVladyslava Mokliakhttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1059Add a message when requesting bean and forage material to notify users of the...2024-03-25T05:51:01+01:00Miguel AcostaAdd a message when requesting bean and forage material to notify users of the contingency where distributions will be enabled by July 2024.Due to internal processes of moving to a new location, the distribution of `Beans `and `Forages `for this first semester is not taking place. The curators of the collections state that to avoid putting all the accessions as not available...Due to internal processes of moving to a new location, the distribution of `Beans `and `Forages `for this first semester is not taking place. The curators of the collections state that to avoid putting all the accessions as not available for distribution (red flag) a measure would be to assign a message to notify the user that the material is available but that the distribution will be from July 2024.
For example, on our web site users can be aware of this situation:
https://alliancebioversityciat.org/future-seeds
So, we consider it pertinent that in Genesys we can also notify users of this contingency.https://gitlab.croptrust.org/genesys-pgr/ui-embedded/-/issues/87Add StringArrFilter support2024-02-29T15:52:31+01:00Matija ObrezaAdd StringArrFilter supportThe fields genus, species and country of origin would benefit from allowing multiple values to be specified.
Please add `<StringArrFilter` support, including `NOT` filters.The fields genus, species and country of origin would benefit from allowing multiple values to be specified.
Please add `<StringArrFilter` support, including `NOT` filters.1.6Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1053Issues for scroll bars on differrent pages2024-02-11T20:27:28+01:00Artem DovhopolenkoIssues for scroll bars on differrent pagesIssues for scroll bars on differrent pages
We are facing some issues with scroll bars on some pages
1. https://sandbox.genesys-pgr.org/a/overview (When user scrolls side bar to the bottom, the main window starts to scroll either)
2.http...Issues for scroll bars on differrent pages
We are facing some issues with scroll bars on some pages
1. https://sandbox.genesys-pgr.org/a/overview (When user scrolls side bar to the bottom, the main window starts to scroll either)
2.https://sandbox.genesys-pgr.org/c/apple (Scroll bar doesn't needed for the page. Issue appears at any page where we have images)Vladyslava MokliakVladyslava Mokliakhttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1052Syntax highlighting2024-02-03T20:30:30+01:00Matija ObrezaSyntax highlightingIf ever we want to add custom query support that allows the user to enter JPA queries with autocompletion then we'll need to explore [codemirror](https://codemirror.net/docs/).
- https://codemirror.net/try/?example=Custom%20completions
...If ever we want to add custom query support that allows the user to enter JPA queries with autocompletion then we'll need to explore [codemirror](https://codemirror.net/docs/).
- https://codemirror.net/try/?example=Custom%20completions
- https://lezer.codemirror.net/docs/Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1049Genesys agrees to request unavailable accessions2024-01-26T05:37:37+01:00Alejandro VelazquezGenesys agrees to request unavailable accessionsOur distribution manager has been receiving requests with accessions that are not available in Genesys
Is it possible to prevent accessions that are not available from being sent?
We have recorded the request:
![Genesys_agrees_to_requ...Our distribution manager has been receiving requests with accessions that are not available in Genesys
Is it possible to prevent accessions that are not available from being sent?
We have recorded the request:
![Genesys_agrees_to_request_unavailable_accessions](/uploads/c66954ede7280e3a6f6ea24e77885988/Genesys_agrees_to_request_unavailable_accessions.mp4)Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1029Do not require PID for making requests2024-01-11T18:48:12+01:00Matija ObrezaDo not require PID for making requests@macosta and collagues from @1cgiar/palmira propose to make it easier for users to make requests for material:
> Allowing users regardless of having a registration in Easy-SMTA, to make a request for material. This is because not all ge...@macosta and collagues from @1cgiar/palmira propose to make it easier for users to make requests for material:
> Allowing users regardless of having a registration in Easy-SMTA, to make a request for material. This is because not all genebanks routinely have the Easy-SMTA system in place and many users are not familiar with the system and registration is not easy to do, in other banks they must help customers to register.
We have support for *Internal requests* that do not require PID and the associated form. This form will become the default form for users to fill out.
## Changes to Genesys
On the UI we treat all requests as `internalRequest` which will skip PID validation on the backend.
![image](/uploads/4ae340250c88dd9269f62a2476bb8c40/image.png)
The form uses `EasySMTAUserData` data model, but it does not reflect the one from the server and needs updating. See https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/blob/main/src/main/java/org/genesys/server/service/EasySMTA.java
1. Convert the form to `react-hook-form`.
1. Force `internalRequest = true` and show the full "Requestor information" form
2. Update form fields:
- Fields: email, first name, last name stay. Move telephone after last name.
- `address` "Address" (required)
- `country` "Country" (required)
- Add radio select `userType` "Type of request": `in` "This is a personal request" and `or` "This request is related to my work"
- If user selected `userType === or`, then enable the section for "Organization" data:
- `orgName` "Organization name" (required if `userType === or`)
- `orgAddress` "Organization address" (required if `userType === or`)
- `orgCountry` "Organization country" (required if `userType === or`)
- Add fields`aoName` and `aoSurname` for name and last name of the "Authorized official"
- Add `aoEmail` "Email of the authorized official"
- Add section "Shipping address":
- If user `userType === or` show a checkbox `useOrgAddress` "Use organization address". When checked, the inputs in this section are disabled.
- If user `userType === in` show checkbox `useMyAddress` "Use my address". When checked, the inputs in this section are disabled.
- Add field `shipAddress` "Shipping address" (3 lines, required)
- Add field `shipCountry` "Country" (required)
- Add field `shipTelephone` "Contact phone number"
3. Convert country code component from autocompleter to a dropdown with all options (active countries only)
4. Require some text to be present in the **Notes** field
3. ~~Add "Direct use" to type of "Use of material"~~
Before the form is sent to the API the following processing must be done:
1. Set `internalRequest = true`
3. If `userType === in` remove `orgAddress`, `orgCountry`, `orgName` from JSON (set them to `undefined`)
2. If `(userType === or && !useOrgAddress) || (userType === in && !useMyAddress)` then set `shipAddrFlag = 'd'` otherwise remove all `shipXxx` fields from JSON2024.1Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1030Updating file repository metadata2023-12-06T05:42:02+01:00Matija ObrezaUpdating file repository metadata@macosta reports he's getting an error message when updating the images metadata with the CSV file:
![image](/uploads/cb6cea39abbcea74b06a126d79ae94c8/image.png)
Please investigate and fix.@macosta reports he's getting an error message when updating the images metadata with the CSV file:
![image](/uploads/cb6cea39abbcea74b06a126d79ae94c8/image.png)
Please investigate and fix.Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/ui-embedded/-/issues/83Upgrade to no-PID request2023-11-11T06:12:16+01:00Matija ObrezaUpgrade to no-PID requestAfter genesys-pgr/genesys-ui!1042 (genesys-pgr/genesys-ui#1029) is deployed to production the requests in Embedded Genesys need to be upgraded for the no-PID functionality.
The MR can be prepared already, but not released to npmjs.After genesys-pgr/genesys-ui!1042 (genesys-pgr/genesys-ui#1029) is deployed to production the requests in Embedded Genesys need to be upgraded for the no-PID functionality.
The MR can be prepared already, but not released to npmjs.1.7Vladyslava MokliakVladyslava Mokliakhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/689Move to OpenSearch2023-10-30T20:10:57+01:00Matija ObrezaMove to OpenSearchhttps://opensearch.org/docs/latest/upgrade-to/upgrade-to/https://opensearch.org/docs/latest/upgrade-to/upgrade-to/Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/4R package to query subsets and trait data2023-10-11T00:21:02+02:00Christelle RabilR package to query subsets and trait dataRequest from CIP, CIAT particiapants in the Spanish CoP to add the possibility to query subsets and trait datasets in Genesys R.Request from CIP, CIAT particiapants in the Spanish CoP to add the possibility to query subsets and trait datasets in Genesys R.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/6Upgrade to /acn/query2023-10-10T16:26:16+02:00Matija ObrezaUpgrade to /acn/queryThe new `.../acn/query` endpoint provides much improved performance compared to `.../acn/query`. Migrate `get_accessions()` to use the new endpoint.The new `.../acn/query` endpoint provides much improved performance compared to `.../acn/query`. Migrate `get_accessions()` to use the new endpoint.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/5Allow get the images with genesysr2023-10-10T16:24:29+02:00Miguel AcostaAllow get the images with genesysrThe objective is to allow a user to download images in bulk using `genesysr`, it can be useful both for users with some programming experience and for those who wish to share filters between users but ensuring an appropriate filter, sinc...The objective is to allow a user to download images in bulk using `genesysr`, it can be useful both for users with some programming experience and for those who wish to share filters between users but ensuring an appropriate filter, since R is a language easy to use for the scientific community.
```
filter_1 <- get_accessions(mcpd_filter(INSTCODE = 'COL003',
GENUS = 'Phaseolus',
SAMPSTAT = c('100','110','120','200'),
IMAGES=T)) # For T or F
```
In **IMAGES**, like boolean attribute use TRUE for get the files and FALSE for not including files. And download in .zip file that contain folders of each images, very similar to normal download by genesys page.https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/685Draft: Deduplicated AccessionRefs2023-09-04T16:41:16+02:00Matija ObrezaDraft: Deduplicated AccessionRefsWe use `SubsetAccessionRef` and `DatasetAccessionRef` to store references to accessions. Each reference may point to an actual `Accession` in Genesys, or has a `null` reference. Each subset and dataset has its own copy of accession refer...We use `SubsetAccessionRef` and `DatasetAccessionRef` to store references to accessions. Each reference may point to an actual `Accession` in Genesys, or has a `null` reference. Each subset and dataset has its own copy of accession references, meaning that when referring to the same accession (for example `inst=NGA039, acce=TMp-419, genu=Manihot, spec=esculenta, doi=...`) we have multiple entries every time the same combination of `instituteCode`, `accessionNumer`, `genus`, ... is referenced.
In this issue we extract `AccessionReference` to a new entity with `@Table("accession_ref")`. Each reference can appear only once in this table. Instead of using `null`, we will use a blank string `""` to enable unique constraint checks in MariaDB.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/997Dark mode2023-07-13T12:06:34+02:00Matija ObrezaDark modeAdd support for **dark mode**.
**Only colors** in CSS can change!
![image](/uploads/769f42ac41c2007df23ab8d9765a397a/image.png)
Figma at https://www.figma.com/file/oXHipxIouyWvGgERlMtcyZ/01-Gynesis_BlogPage?type=design&node-id=1511%3...Add support for **dark mode**.
**Only colors** in CSS can change!
![image](/uploads/769f42ac41c2007df23ab8d9765a397a/image.png)
Figma at https://www.figma.com/file/oXHipxIouyWvGgERlMtcyZ/01-Gynesis_BlogPage?type=design&node-id=1511%3A2649&mode=design&t=wtEAOrFbxiZe7s3t-1Vladyslava MokliakVladyslava Mokliakhttps://gitlab.croptrust.org/genesys-pgr/anno/-/issues/39Sanity checks2023-06-12T11:23:39+02:00Matija ObrezaSanity checksTest that accession numbers are unique in the file. How this works depends on the `uniqueAcceNumbs` of the institute setting in Genesys.Test that accession numbers are unique in the file. How this works depends on the `uniqueAcceNumbs` of the institute setting in Genesys.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/656Draft: NLP queries2023-01-31T19:52:12+01:00Matija ObrezaDraft: NLP queriesAdd support for NLP queries.Add support for NLP queries.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/655Draft: Data translations2023-01-31T19:51:32+01:00Matija ObrezaDraft: Data translationsWe are able to translate Genesys UI and the static labels. The remaining question is: how do we translate data?
More specifically, Subset and Dataset titles and descriptions should be translated to our supported languages and made avail...We are able to translate Genesys UI and the static labels. The remaining question is: how do we translate data?
More specifically, Subset and Dataset titles and descriptions should be translated to our supported languages and made available to users in their preferred language.Matija ObrezaMatija Obreza