Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2018-08-29T10:17:43+02:00https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/273JSP: Accession details page2018-08-29T10:17:43+02:00Matija ObrezaJSP: Accession details pageDepends on #266, #284
On accession page display the list of datasets where this accession is include.
1. Add "List of Datasets” as one of the sections.
1. Display dataset title, number of traits evaluated
Reuse one of the existing d...Depends on #266, #284
On accession page display the list of datasets where this accession is include.
1. Add "List of Datasets” as one of the sections.
1. Display dataset title, number of traits evaluated
Reuse one of the existing display styles to render the list of datasets.
1. Link to https://catalog.genesys-pgr.org/dataset/{uuid}
Update Controller and JSP.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/272JSP: Welcome page2018-07-23T19:20:18+02:00Matija ObrezaJSP: Welcome pageDepends on #266
## Include number of datasets under "number of accessions"
1. Rename "ACCESSION MAP" to “Quick overview”
1. Add “XXX Datasets” with link to Catalog/datasets page at https://catalog.genesys-pgr.org
## Changes to the to...Depends on #266
## Include number of datasets under "number of accessions"
1. Rename "ACCESSION MAP" to “Quick overview”
1. Add “XXX Datasets” with link to Catalog/datasets page at https://catalog.genesys-pgr.org
## Changes to the top navigation bar
1. Remove "Home"
1. Add Datasets menu in header:
Order: About Genesys, Browse, Datasets, Countries, Institutes, My List
Link to https://catalog.genesys-pgr.org/datasets
Update Controller and welcome page JSP.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/271Test sandbox2021-02-15T09:54:45+01:00Matija ObrezaTest sandbox@akirichenko I ran your tester against the upgraded https://sandbox.genesys-pgr.org and things looked pretty much okay.
Because this was a major upgrade of the data model I'm not 100% convinced that everything works and behave as expect...@akirichenko I ran your tester against the upgraded https://sandbox.genesys-pgr.org and things looked pretty much okay.
Because this was a major upgrade of the data model I'm not 100% convinced that everything works and behave as expected.
Can you please test the Sandbox if things behave as they should?2.5Aleksandr KirichenkoAleksandr Kirichenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/268Add picture available column in accessions browser2021-03-11T13:26:17+01:00Nora Castaneda-AlvarezAdd picture available column in accessions browserPlease add a "Picture available" column when browsing for accessions (https://sandbox.genesys-pgr.org/explore).
Accessions with pictures should be flagged with a "yes" or a small icon that indicates that pictures are available. Use this...Please add a "Picture available" column when browsing for accessions (https://sandbox.genesys-pgr.org/explore).
Accessions with pictures should be flagged with a "yes" or a small icon that indicates that pictures are available. Use this as example: https://sandbox.genesys-pgr.org/10.18730/9X2HE2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/267Elasticsearch update2019-11-20T17:25:50+01:00Matija ObrezaElasticsearch updateThe `genesys-catalog` project introduced new approach to indexing with Elasticsearch.
Bring Elasticsearch components into this project and migrate methods implemented in Genesys to the new base code from the Catalog.
You can mass-load...The `genesys-catalog` project introduced new approach to indexing with Elasticsearch.
Bring Elasticsearch components into this project and migrate methods implemented in Genesys to the new base code from the Catalog.
You can mass-load accession passport data into your Genesys database using **Anno** (Genesys uploader) and data from https://eurisco.ipk-gatersleben.de/apex/EURISCO_WEB.download_file?p_id=67 found on https://eurisco.ipk-gatersleben.de/apex/f?p=103:25:::NO::: (right hand side "Download full dataset").
Note that the default OAuth clientId and secret are logged to the console when Genesys starts up with a blank database and uses `auto.createContent=true` -- also echoed on in the log.2.5Alexander PrendetskiyAlexander Prendetskiyhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/266Catalog: merge test2019-11-20T17:25:50+01:00Matija ObrezaCatalog: merge testThe genesys-catalog backend will be merged with Genesys.
This ticket is the first **test merge** where entities, repositories, services and controllers are **copied** into the Genesys project -- but keep the `.catalog.` package names.
...The genesys-catalog backend will be merged with Genesys.
This ticket is the first **test merge** where entities, repositories, services and controllers are **copied** into the Genesys project -- but keep the `.catalog.` package names.
The objective is to identify issues with duplicate classes, Spring configuration problems.
Test this on a new mysql database use a custom `genesys.properties` with:
```
db.hbm2ddl=true
auto.createContent=true
```
This issue is closed when:
1. Tests succeed
1. Database is successfully created on startup
1. http://localhost:8080 launches current Genesys frontend
Please document all problems encountered (and fixed) as comments to this issue.2.5Alexander PrendetskiyAlexander Prendetskiyhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/265ORG page2021-02-15T09:54:10+01:00Matija ObrezaORG pagehttps://www.genesys-pgr.org/org/EURISCO is very slow, see if the query can be updated.https://www.genesys-pgr.org/org/EURISCO is very slow, see if the query can be updated.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/264Remove links from Overview2021-02-15T09:53:54+01:00Matija ObrezaRemove links from OverviewLinks to genera and countries in Overviews suggest that clicking the link would display the actual records.
For example https://www.genesys-pgr.org/project/CWR lists "Most represented Genera" and one would expect to see the 300 *Vicia* ...Links to genera and countries in Overviews suggest that clicking the link would display the actual records.
For example https://www.genesys-pgr.org/project/CWR lists "Most represented Genera" and one would expect to see the 300 *Vicia* accessions of the project when clicking the link.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/263Georef (0, 0) as null2018-07-16T12:33:17+02:00Matija ObrezaGeoref (0, 0) as null`latitude`, `longitude` at **(0, 0)** falls in the ocean and it is very likely that such records are a result of invalid data conversion.
There are currently 51,000 accessions at (0, 0). Genesys should treat georeference (0, 0) as **(nu...`latitude`, `longitude` at **(0, 0)** falls in the ocean and it is very likely that such records are a result of invalid data conversion.
There are currently 51,000 accessions at (0, 0). Genesys should treat georeference (0, 0) as **(null, null)** instead.
1. Add method to Admin pages to update (0, 0) to (null, null)
1. When updating accession data, handle (0, 0) properly
This change should also affect the PDCI score.2.5https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/250Data model cleanup2019-11-20T17:25:50+01:00Matija ObrezaData model cleanupGenesys data model has historically used several database tables for different sections of MCPD: `accession` + `accessioncollect` + `accessionbreeding` + `accessionexchange`, etc. These “section” tables have a 1-to-1 relationship to reco...Genesys data model has historically used several database tables for different sections of MCPD: `accession` + `accessioncollect` + `accessionbreeding` + `accessionexchange`, etc. These “section” tables have a 1-to-1 relationship to records in the core accession table and were originally introduced as a measure to improve database query speeds in view of data sparsity.
This model makes for complicated SQL querying and data export as those additional tables need to be joined to execute the search and need to be loaded to access all passport data for any accession.
The updated data model will undo this database design and bring all columns back to a single table with auxiliary tables for multi-value descriptors: accession names and other identifiers, storage and remarks. These are required for fast and correct querying (e.g. by `STORAGE`).
Instead of generating MCPD-format multi-value strings from sub-tables (e.g. `REMARKS`) we will pre-generate them and store them in a separate passport table (accession_export?) with all data correctly merged using semicolon (;). This table will be kept up-to-date as part of upsert operation.
# Implementation details
This change of the data model affects all aspects of Genesys: the API, JSP pages, querying, elastic search. If possible, we would keep the original `AccessionColl` and other classes and populate them in the service methods so that no change is required to JSPs.
Because of the change in the data model, the filter codes (`coll.collMissId`) may need adjusting.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/179Article templates2021-02-15T09:52:04+01:00Matija ObrezaArticle templatesSome existing **global** articles are actually templates in the system.
Allow for editing of `Article#template` flag only for `ContentService#getDefaultLanguage`. If the flag changes, update all articles with the same `slug` to the sta...Some existing **global** articles are actually templates in the system.
Allow for editing of `Article#template` flag only for `ContentService#getDefaultLanguage`. If the flag changes, update all articles with the same `slug` to the state as set for default language.
Indexing and deleting from ES index was taken care of in 50bc2ad69438f27ae876e587eb526005f10f296e.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/172"In Trust" descriptor2021-02-15T09:51:54+01:00Nora Castaneda-Alvarez"In Trust" descriptorDocument the `InTrust` descriptor, a Genesys extension to MCPD, at https://www.genesys-pgr.org/doc/0/basics#mcpd-genesysDocument the `InTrust` descriptor, a Genesys extension to MCPD, at https://www.genesys-pgr.org/doc/0/basics#mcpd-genesys2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/165Document file management with FTP2021-02-15T09:51:31+01:00Matija ObrezaDocument file management with FTPAdd **asciidoc** on managing files with FTP.Add **asciidoc** on managing files with FTP.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/164Respect institute permissions2021-02-15T09:50:43+01:00Matija ObrezaRespect institute permissionsPermissions must be checked for navigation and files management through FTP.
Related to genesys-pgr/file-repository#22Permissions must be checked for navigation and files management through FTP.
Related to genesys-pgr/file-repository#222.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/162Onboarding / Creating new account2019-11-20T17:25:50+01:00Gregor FrasOnboarding / Creating new account@mobreza
1. Is there really need to be special character(s) in user password? It seems to me that this "rule" is not so common so users can't use their "personal" passwords for Genesys which causes confusion with passwords and problems...@mobreza
1. Is there really need to be special character(s) in user password? It seems to me that this "rule" is not so common so users can't use their "personal" passwords for Genesys which causes confusion with passwords and problems with login.
2. Landing page after user registration is dead-end. We should consider what could be useful links or content on this page. What would we wanted for user to do after registration?
![1](/uploads/d8696a9ea636b31726eed27e445b8db7/1.jpg)
![2](/uploads/d290936f18f1f2cabd84ffc0ef448ad6/2.jpg)2.5Gregor FrasGregor Fras