Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2018-08-22T18:32:13+02:00https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/283JWT OAuth tokens2018-08-22T18:32:13+02:00Matija ObrezaJWT OAuth tokensBring in the JWT token converter from the catalog-server.
Test if Genesys Uploader (Anno) works with JWT.Bring in the JWT token converter from the catalog-server.
Test if Genesys Uploader (Anno) works with JWT.2.5Alexander PrendetskiyAlexander Prendetskiyhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/282Accession APIv1 /filter2018-07-24T23:34:42+02:00Matija ObrezaAccession APIv1 /filterAdd **/filter** endpoint to `org.genesys2.server.api.v1.AccessionController` (depends on #281).
Method (based on `DatasetController#list`:
```java
@PostMapping(value = "/filter")
public FilteredPage<Accession> filter(@RequestParam(name...Add **/filter** endpoint to `org.genesys2.server.api.v1.AccessionController` (depends on #281).
Method (based on `DatasetController#list`:
```java
@PostMapping(value = "/filter")
public FilteredPage<Accession> filter(@RequestParam(name = "p", required = false, defaultValue = "0") final int page,
@RequestParam(name = "l", required = false, defaultValue = "50") final int pageSize,
@RequestParam(name = "d", required = false, defaultValue = "ASC") final Sort.Direction direction,
@RequestParam(name = "s", required = false, defaultValue = "id") final String[] sort, @RequestBody final DatasetFilter filter) {
if (StringUtils.isNotBlank(filterCode)) {
filter = shortFilterService.filterByCode(filterCode, DatasetFilter.class);
} else {
filterCode = shortFilterService.getCode(filter);
}
return new FilteredPage<>(filterCode, filter, genesysService.filter(filter, new PageRequest(page, Integer.min(pageSize, 100), direction, sort)));
}
```2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/281Model filters2018-08-03T14:51:44+02:00Matija ObrezaModel filtersIn the Catalog we developed a good approach to providing filter data to the backend.
Add model filters to `org.genesys2.server.model.filters` package:
- `AccessionFilter` for `Accession` (and `AccessionData` and `AccessionId`)
- `Insti...In the Catalog we developed a good approach to providing filter data to the backend.
Add model filters to `org.genesys2.server.model.filters` package:
- `AccessionFilter` for `Accession` (and `AccessionData` and `AccessionId`)
- `InstituteFilter` for `FaoInstitute`2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/277Updating controlled vocabularies fails2018-10-26T17:00:47+02:00Matija ObrezaUpdating controlled vocabularies failsTrying to update vocabularies from
- https://catalog.demo.genesys-pgr.org/proxy/api/v0/wiews/update
- https://catalog.demo.genesys-pgr.org/proxy/api/v0/lang/update
- https://catalog.demo.genesys-pgr.org/proxy/api/v0/geo/update
Depends ...Trying to update vocabularies from
- https://catalog.demo.genesys-pgr.org/proxy/api/v0/wiews/update
- https://catalog.demo.genesys-pgr.org/proxy/api/v0/lang/update
- https://catalog.demo.genesys-pgr.org/proxy/api/v0/geo/update
Depends on #266 Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/276COORDDATUM support2021-03-11T13:27:48+01:00Matija ObrezaCOORDDATUM supportAdd support for different datum used in coordinates. See what is supported by the library.Add support for different datum used in coordinates. See what is supported by the library.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/275Extend Recent activity 22018-07-26T09:32:03+02:00Matija ObrezaExtend Recent activity 2Similar to #274, but include display of:
- Last 5 Datasets published (depends on #266)
Include a link to https://catalog.genesys-pgr.org at the bottom.
Update Controller and JSP.Similar to #274, but include display of:
- Last 5 Datasets published (depends on #266)
Include a link to https://catalog.genesys-pgr.org at the bottom.
Update Controller and JSP.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/274Extend Recent activity2018-09-27T22:35:31+02:00Matija ObrezaExtend Recent activityOn the Welcome page, in recent activity section add a "post" that displays
- Last 5 updates from https://www.genesys-pgr.org/acn/updates
Display date, institute name and number of records updated.
Include a link to https://www.genes...On the Welcome page, in recent activity section add a "post" that displays
- Last 5 updates from https://www.genesys-pgr.org/acn/updates
Display date, institute name and number of records updated.
Include a link to https://www.genesys-pgr.org/acn/updates at the bottom.
Draft the UI based on current “activity post” design.
Update Controller and JSP.2.5Maxym BorodenkoMaxym Borodenkohttps://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/262Hazelcast misbehaving with Docker2021-02-15T09:53:43+01:00Matija ObrezaHazelcast misbehaving with Dockerhttps://github.com/bitsofinfo/hazelcast-docker-swarm-discovery-spi
Genesys (production) is now configured as two separate services (`server` and `standby`) that try to expose the correct names using service names. While this works most ...https://github.com/bitsofinfo/hazelcast-docker-swarm-discovery-spi
Genesys (production) is now configured as two separate services (`server` and `standby`) that try to expose the correct names using service names. While this works most of the time, we have a **cluster brain-split** every few weeks, causing `403` HTTP errors as `_crsf` tokens are out of sync.
Maybe the best approach would be to add another Hazelcast instance (to 3 in total) as a docker service. This may prevent issues with merging after a brain split.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/261"Rebuild" button leads to the 404 error.2018-08-29T10:17:40+02:00Aleksandr Kirichenko"Rebuild" button leads to the 404 error.**Steps:**
1. Go to the "https://sandbox.genesys-pgr.org/welcome" Welcome page;
2. Login as administrator;
3. Click on the "Rebuild" button
**Act. res.:** 404 - Not found
**Exp. res.:** unknown
See attached video:
![recording_00020](/up...**Steps:**
1. Go to the "https://sandbox.genesys-pgr.org/welcome" Welcome page;
2. Login as administrator;
3. Click on the "Rebuild" button
**Act. res.:** 404 - Not found
**Exp. res.:** unknown
See attached video:
![recording_00020](/uploads/a1f629942ac8df04224250b64b3ebe3b/recording_00020.gif)Alexander PrendetskiyAlexander Prendetskiyhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/258"FORGOT PASSWORD" functionality is not available2018-05-15T08:27:22+02:00Aleksandr Kirichenko"FORGOT PASSWORD" functionality is not available**Steps:**
* Go to the Login "https://sandbox.genesys-pgr.org/login" page;
* Click on the forgot password button.
**Exp.res.:** user is on the forgot password page "https://sandbox.genesys-pgr.org/profile/forgot-password"
**Act.res....**Steps:**
* Go to the Login "https://sandbox.genesys-pgr.org/login" page;
* Click on the forgot password button.
**Exp.res.:** user is on the forgot password page "https://sandbox.genesys-pgr.org/profile/forgot-password"
**Act.res.:** forgot password page isn't opened. See attached video:
![recording_00019](/uploads/4c2e65f030072378a81835f43de28f29/recording_00019.gif)Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/257"First Page" (pugination) button does not work2018-08-22T13:29:07+02:00Aleksandr Kirichenko"First Page" (pugination) button does not work**Steps:**
* Go to the Institutes "https://sandbox.genesys-pgr.org/wiews/active" page;
* Click on the "Last" pagination button;
* Click on the "First" pagination button.
**Expected result:** First page is opened, content from the fi...**Steps:**
* Go to the Institutes "https://sandbox.genesys-pgr.org/wiews/active" page;
* Click on the "Last" pagination button;
* Click on the "First" pagination button.
**Expected result:** First page is opened, content from the first page is displayed.
**Actual result:** First page isn't opened. See attached video:
![recording_00018](/uploads/c0b0985556ffe4f0b6e9f66198947f1c/recording_00018.gif)Viacheslav PavlovViacheslav Pavlov