FAIDARE issueshttps://forgemia.inra.fr/urgi-is/faidare/-/issues2023-09-27T17:18:41+02:00https://forgemia.inra.fr/urgi-is/faidare/-/issues/27Follow-up from "Add creation of a log with last indexing informations. GNP-6338"2023-09-27T17:18:41+02:00Raphaël FloresFollow-up from "Add creation of a log with last indexing informations. GNP-6338"The following discussions from !132 should be addressed:
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/132#note_161029): (+2 comments)
> Have you noticed that beta deployed i...The following discussions from !132 should be addressed:
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/132#note_161029): (+2 comments)
> Have you noticed that beta deployed is trigger despite the test failure @raphael.flores ?
- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/132#note_175831):
> Need to enable that again if relevant.Test milestone several projectsRaphaël FloresRaphaël Floreshttps://forgemia.inra.fr/urgi-is/faidare/-/issues/26Follow-up from "Draft: Epic/merge faidare dd"2022-09-21T09:49:54+02:00Cyril PommierFollow-up from "Draft: Epic/merge faidare dd"The following discussion from !82 should be addressed:
- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/82#note_95824): (+4 comments)
> No test at all is checking this ValueObj...The following discussion from !82 should be addressed:
- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/82#note_95824): (+4 comments)
> No test at all is checking this ValueObject at this time?Cyril PommierCyril Pommierhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/25Follow-up from "Fix Export germplasms"2022-09-02T16:37:17+02:00Cyril PommierFollow-up from "Fix Export germplasms"The following discussion from !130 should be addressed:
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/130#note_107798):
> @celia.michotey , I don't remember how those field g...The following discussion from !130 should be addressed:
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/130#note_107798):
> @celia.michotey , I don't remember how those field got supprossed from the export. Does that ring any bell ?
- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/130#note_107894):
> TODO fix.Célia MichoteyCélia Michoteyhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/24Proposal: implement group access verification in Data Discovery2021-10-01T18:09:17+02:00Jean-Baptiste NizetProposal: implement group access verification in Data DiscoveryIn the "old" Faidare application, which was in charge of the searches and of the detailed cards, every access to elastic search targeted one or more indices based on the group IDs of the currently authenticated user.
For reference, thes...In the "old" Faidare application, which was in charge of the searches and of the detailed cards, every access to elastic search targeted one or more indices based on the group IDs of the currently authenticated user.
For reference, these group IDs are obtained by
- looking at the user name in the basic authorization header (in the `AuthenticationFilter`)
- storing it in the `AuthenticationStore` (in a ThreadLocal)
- fetching the group IDs from an in-memory cache, that loads them from an external web service (in `UserGroupsResourceClient`)
Faidare is now split in two separate applications:
- the Faidare flavor of data-discovery, using Spring Data ES
- the Faidare application, still using the same code as the "old" Faidare
Using the same strategy in data-discovery doesn't seem easily doable, because Spring Data considers (and is right to do so, IMHO) that a document belongs to a single index.
So my proposal is
- to keep the Faidare code as is, because changing it is too much a burden for Ninja Squad, and out of our comfort zone anyway.
- to implement access control in a different, simpler way in data-discovery
In details, here's how it would work in data-discovery:
1. The faidare documents would have an additional property of type `int`, named `groupId`. This would have to be populated, as all the other fields, by the ETL
2. In a similar way as in Faidare, the faidare flavor of data-discovery would get the user name from the authorization header, get the user groups for that user, and store them in a cache
3. The FaidareDaoImpl of data-discovery would add a criterion to the queries used for search and aggregation which, in SQL, would be `AND faidare_document.group_id in (:accessibleGroupsOfCurrentUser)`
Note that `accessibleGroupsOfCurrentUser` would always contain the ID `0`, even if the user is not authenticated: 0 is the public group ID.
Please tell if this proposa suits you.Cyril PommierCyril Pommierhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/23Review export2021-09-29T09:41:57+02:00Jean-Baptiste NizetReview exportSee https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/104#note_64782See https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/104#note_64782Célia MichoteyCélia Michoteyhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/21Follow-up from "WIP: Add mcpd developments. Fix GNP-5428."2021-08-20T09:48:59+02:00Célia MichoteyFollow-up from "WIP: Add mcpd developments. Fix GNP-5428."The following discussions from !53 should be addressed:
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/53#note_45203):
> That's just a workaround, it would be needed to ration...The following discussions from !53 should be addressed:
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/53#note_45203):
> That's just a workaround, it would be needed to rationalize the index naming. If it merges like that, which might be better, we need to create a task for the next releaze to make things cleaner. What do you think @celia.michotey @raphael.flores
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/53#note_45207):
> Add many other test to chack that most fields a returned with the right values. Possibly add a deep equals test between germplasm0.json and the returned value.Cyril PommierCyril Pommierhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/20Follow-up from "Feat/implement germplasm result page"2020-08-13T16:18:40+02:00Jérémy DestinFollow-up from "Feat/implement germplasm result page"The following discussions from !46 should be addressed:
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/46#note_18821): (+1 comment)
> The name of this class seems odd to me. S...The following discussions from !46 should be addressed:
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/46#note_18821): (+1 comment)
> The name of this class seems odd to me. Search criterias should be rather generic, not a search criteria by method. I assume that there is no GermplasmGETSearchCriteria ?
> What does it add on top of GermplasmPOSTSearchCriteria ?
> FaidareGermplasmSearchCriteria is strange too. DetailGermplasmSearchCriteria instead ?
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/46#note_18825):
> Redundant with the new method, therefore deprecated no ?
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/46#note_18826):
> Redundant with the new method rigth below that one no ? Shouldn't it be deprecated / removed ?
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/46#note_18849): (+1 comment)
> comment to remove
- [ ] @cyril.pommier started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/-/merge_requests/46#note_18850):
> killJérémy DestinJérémy Destinhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/19Faidare loader improvment2020-03-25T20:27:07+01:00Jérémy DestinFaidare loader improvment- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/merge_requests/21#note_10175): (+1 comment)
> TODO
- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/merge_r...- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/merge_requests/21#note_10175): (+1 comment)
> TODO
- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/merge_requests/21#note_10176): (+1 comment)
> TODO
- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/merge_requests/21#note_10177): (+1 comment)
> TODO
- [ ] @raphael.flores started a [discussion](https://forgemia.inra.fr/urgi-is/faidare/merge_requests/21#note_10196): (+1 comment)
> Is the data directory ever checked in terms of existence, writability, and so on?
>
> In addition, I think the service should take a File/Path parameter and work with that directly instead of transforming the String into a File. The [`IndexController`](https://forgemia.inra.fr/urgi-is/faidare/merge_requests/21/diffs#1e1beed2dbdad9b33679552ae6b4c40c781ce8b3_0_30) should be used to check the input directory is find, then return a relevant HTTP error without having to enter the Service.https://forgemia.inra.fr/urgi-is/faidare/-/issues/18Add a footer2019-06-06T14:15:02+02:00Célia MichoteyAdd a footerAdd a footer, at leat on GPDS search form/result page with Elixir logo.
Exemple on OLS portal : https://www.ebi.ac.uk/ols/indexAdd a footer, at leat on GPDS search form/result page with Elixir logo.
Exemple on OLS portal : https://www.ebi.ac.uk/ols/indexJérémy DestinJérémy Destinhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/17Add an "About Us" page in GPDS2019-07-08T19:56:04+02:00Célia MichoteyAdd an "About Us" page in GPDSCélia MichoteyCélia Michoteyhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/16Responsive: small screen fixes2019-06-06T14:15:02+02:00Guillaume CornutResponsive: small screen fixes- Center accession image horizontally on small screen
=> Add class `justify-content-center` on row https://forgemia.inra.fr/urgi-is/gpds/blob/master/frontend/src/app/germplasm-card/germplasm-card.component.html#L159
- Add non breakable...- Center accession image horizontally on small screen
=> Add class `justify-content-center` on row https://forgemia.inra.fr/urgi-is/gpds/blob/master/frontend/src/app/germplasm-card/germplasm-card.component.html#L159
- Add non breakable space ` ` in result section title (otherwise the`:` wraps to a new line on small screens)
=> `s/Results :/Results :/` https://forgemia.inra.fr/urgi-is/gpds/blob/master/frontend/src/app/result-page/result-page.component.html#L50
- Add space to break text in `Acquisition/Creation date` (otherwise the text overflows in small screens)
=> `s|Acquisition/Creation date|Acquisition / Creation date|` https://forgemia.inra.fr/urgi-is/gpds/blob/master/frontend/src/app/germplasm-card/germplasm-card.component.html#L403
- Fix accession image popover placement on small screen. As-is, it overflows to the right of the screen with no possibility to scroll
- Re-layout the trait widget for small screens (might be difficult!)
Example of accession with an image for the above issues:
http://urgi.versailles.inra.fr/gpds/germplasm?id=ZG9pOjEwLjE1NDU0LzEuNDkyMTc4NTc1ODc5Mzg1M0UxMg%3D%3D
ping @celia.michotey @jeremy.destin @Melanie.Buy @guillaume.cornut https://forgemia.inra.fr/urgi-is/faidare/-/issues/15Improve code GPDS2019-06-11T19:49:47+02:00Jérémy DestinImprove code GPDS* [x] Factorize popover templates for institutes (use parameters ?).
* [x] Use `width: 100%` instead of `max-width: 100%` on `.popover` ? (check if it work correctly everywhere)
* [ ] Simplify code https://forgemia.inra.fr/urgi-is/gpds...* [x] Factorize popover templates for institutes (use parameters ?).
* [x] Use `width: 100%` instead of `max-width: 100%` on `.popover` ? (check if it work correctly everywhere)
* [ ] Simplify code https://forgemia.inra.fr/urgi-is/gpds/merge_requests/14#note_7655.
* [x] Pipe to format from number to string coordinate
* [x] Factorize style card (for link)?
* [x] @guillaume.cornut Add tests for `card-section`, `card-row` and `card-table` that can also be used as documentation (all possible ways to use them)
* [x] Extract photos and logos URL in indexes
* [x] Remove scroll bar in xref table (exemple: https://urgi.versailles.inra.fr/gpds/germplasm?id=ZG9pOjEwLjE1NDU0LzEuNDkyMTc4NjkxMzU3MDE3OEUxMg%3D%3D)
* [x] Add full source name in navbar (exemple: CIRAD TropGENE instead of CIRAD)
* [x] Resize map on cards (to be able to see a little more the identification part).
* [ ] If possible, add an option to show a bigger map.
* [x] Rename "Data source" depending on the current card and set full source name ("Link to this [thematic] in [source]")
* [x] Improve display of external link on result page (change the text and/or pur it beside the object name ?)
* [x] Try to see why IBET and VIB logo are not displayed on cards
* [x] Renamer "Collecting" section in "Collector", "Holding" section in "Depositary"
* [x] Move "Origin site" at the end of the "Identification" section
* [x] Replace link below the photo by its copyright with a link style
* [x] On result page, replace `Results :` by `Results:`
* [x] For emails, replace "@" by " at "
* [x] For panel names, replace all "_" by " "
* [x] Add an "_blank" in xrefs links as it should be opened in a new window (external links)19.1Jérémy DestinJérémy Destinhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/14Center/Zoom map around the whole group of locations not the first location of...2019-05-06T10:27:48+02:00Guillaume CornutCenter/Zoom map around the whole group of locations not the first location of the groupFor now the map centers and zoom around the first location given in an array.
It would be better to have it centered around the whole group of locations.
Center the bottom marker on the point
view :https://forgemia.inra.fr/urgi-is/gnp...For now the map centers and zoom around the first location given in an array.
It would be better to have it centered around the whole group of locations.
Center the bottom marker on the point
view :https://forgemia.inra.fr/urgi-is/gnpis/blob/develop/www/jsp/common/javaScript/geolocation.jsLaterhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/13Fix bug due to the popover link2019-03-06T15:38:29+01:00Jérémy DestinFix bug due to the popover linkWhen the name where the link is on is to big long there is a display a issue.
Example :
http://localhost:4200/gnpis-core/germplasm?id=aHR0cHM6Ly9kb2kub3JnLzEwLjE1NDU0L0ZaWDhLTw%3D%3D
For the breeding instituteWhen the name where the link is on is to big long there is a display a issue.
Example :
http://localhost:4200/gnpis-core/germplasm?id=aHR0cHM6Ly9kb2kub3JnLzEwLjE1NDU0L0ZaWDhLTw%3D%3D
For the breeding instituteJérémy DestinJérémy Destinhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/12Provide data sources in spring properties rather than backend resources2019-06-20T15:33:49+02:00Guillaume CornutProvide data sources in spring properties rather than backend resourcesRemove the data source metadata in the Java backend resources and move them into spring properties (loaded from spring cloud config or application.yml)
* [ ] Move data sources from `datasources.jsonld` to `application.yaml` (update Data...Remove the data source metadata in the Java backend resources and move them into spring properties (loaded from spring cloud config or application.yml)
* [ ] Move data sources from `datasources.jsonld` to `application.yaml` (update DataSourceRepository)
* [ ] Host logos in `gimli:/webfiles/gpds/logo/` and update URL (check for newer logos, resize to same height)
* [ ] Remove logos from java resources
https://urgi.versailles.inra.fr/jira/browse/GNP-5567LaterGuillaume CornutGuillaume Cornuthttps://forgemia.inra.fr/urgi-is/faidare/-/issues/11Manage fields displayed in germplasm card2019-03-19T10:50:37+01:00Jérémy DestinManage fields displayed in germplasm cardDisplay:
* [x] We should display the BRC logo if this accession is part of a BRC.
* [x] Popover for BRC information ?
* [x] Logo for all institutions.
* [x] Parents name for descendants (add other parent).
* [ ] Factorize popover templat...Display:
* [x] We should display the BRC logo if this accession is part of a BRC.
* [x] Popover for BRC information ?
* [x] Logo for all institutions.
* [x] Parents name for descendants (add other parent).
* [ ] Factorize popover templates for institutes (use parameters ?).
* [x] Order of germplasm card sections (by importance).
* [x] Add donorAccessionNumber to Donation section, in third column (after date and institute) or somewhere else.
* [x] (Minor) Siblings links : remove underline.
* [x] Merge ascendants and -descendants- siblings sections, and rename "accession numbers" to "siblings".
* [x] If the distribution status is "EXTERNAL" and the institute has a web site, we should add the link.
* [x] Add informations on the origin site
* [x] Remove collector.germplasmPUI field ?
* [x] In genealogy part, add parent name for self and unknown parent types, but display nothing for for accession 'unknown'
* [x] In population part, add a link on the population name id it is also an accession18.3Mélanie Buymelanie.buy@inra.frMélanie Buymelanie.buy@inra.frhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/10Add display of missing data and improve visual2019-03-07T10:30:37+01:00Célia MichoteyAdd display of missing data and improve visual- [x] In form, rename "Variable" tab in "Trait"
- [x] In frontend code, replace "gnpis-core/*" by "gnpis/gpds/*" in URL stored in indexes (as indexes for gpds and gnpis-core are the same and we want to stay on gpds and not go to the old ...- [x] In form, rename "Variable" tab in "Trait"
- [x] In frontend code, replace "gnpis-core/*" by "gnpis/gpds/*" in URL stored in indexes (as indexes for gpds and gnpis-core are the same and we want to stay on gpds and not go to the old interface)
- [x] Add missing fields in germplasm card ( [Issue 11](https://forgemia.inra.fr/urgi-is/gpds/issues/11) )
- [x] Manage overflow and underline for links in table. ([Issue 13](https://forgemia.inra.fr/urgi-is/gpds/issues/13) )18.3Jérémy DestinJérémy Destinhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/9Bug: fix result page not updating when going back to it2019-02-22T11:38:26+01:00Guillaume CornutBug: fix result page not updating when going back to itPossible solution: use router.events (filtering NavigationStart && navigation on result page) => exec query param parse to criteria &fetch docsPossible solution: use router.events (filtering NavigationStart && navigation on result page) => exec query param parse to criteria &fetch docs18.3Jérémy DestinJérémy Destinhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/8Document deprecated BrAPI fields2019-03-01T14:23:59+01:00Raphaël FloresDocument deprecated BrAPI fields- [ ] For BrAPI field which are deprecated (ie. `backend/src/main/java/fr/inra/urgi/gpds/domain/brapi/v1/data/BrapiLocation.java#getName()` we should add a Javadoc explaining what to do with those fields, ie.:
```java
/**
* Depr...- [ ] For BrAPI field which are deprecated (ie. `backend/src/main/java/fr/inra/urgi/gpds/domain/brapi/v1/data/BrapiLocation.java#getName()` we should add a Javadoc explaining what to do with those fields, ie.:
```java
/**
* Deprecated in favor of {@link #getLocationName()}
*/
@Deprecated
@JsonView(JSONView.BrapiFields.class)
String getName();
```
- [ ] Update code where those deprecated are currently used, ie `backend/src/main/java/fr/inra/urgi/gpds/domain/data/LocationVO.java:150`
- [ ] Update accordingly BrAPI code (ie. VO?) in frontend classes if they still use deprecated code.19.1Jérémy DestinJérémy Destinhttps://forgemia.inra.fr/urgi-is/faidare/-/issues/7Handle both card link and documentationURL links (result page and cards)2019-03-07T09:20:48+01:00Guillaume CornutHandle both card link and documentationURL links (result page and cards)19.1Jérémy DestinJérémy Destin