Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2021-02-15T09:50:43+01:00https://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/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/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/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/232Adjust CI deployments2021-02-15T09:52:56+01:00Matija ObrezaAdjust CI deploymentsCI deployment for this project must use a single hostname and the application needs to run under a virtual path.
This addresses the issue of too many requests for certificates to LetsEncrypt.CI deployment for this project must use a single hostname and the application needs to run under a virtual path.
This addresses the issue of too many requests for certificates to LetsEncrypt.Matija ObrezaMatija Obrezahttps://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/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/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/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/296Replace all @Query with DSL2021-02-15T09:55:34+01:00Matija ObrezaReplace all @Query with DSLThe "text" mode `@Query` syntax in JPA repositories is impossible to maintain as the data models are updated and changed.
Migrate all cases where `@Query` is used to QueryDSL. Use the following approach:
1. If the query is used from a ...The "text" mode `@Query` syntax in JPA repositories is impossible to maintain as the data models are updated and changed.
Migrate all cases where `@Query` is used to QueryDSL. Use the following approach:
1. If the query is used from a single service method, implement the query in the service method
1. If the query is used from multiple service methods, implement the query in a `...CustomImpl` and extend the repository with a `...Custom` interface2.5Vladyslava MokliakVladyslava Mokliakhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/344Invalid incoming JSON2021-02-15T09:55:50+01:00Matija ObrezaInvalid incoming JSONCan we URLDecode the incoming string without breaking anything?
```java
2018-09-26T09:46:44.962667827Z 09:46:44,961 qtp485815673-3398 ERROR o.g.s.s.c.UserControllerAdvice:89 - Unexpected character ('+' (code 43)): was expecting double-q...Can we URLDecode the incoming string without breaking anything?
```java
2018-09-26T09:46:44.962667827Z 09:46:44,961 qtp485815673-3398 ERROR o.g.s.s.c.UserControllerAdvice:89 - Unexpected character ('+' (code 43)): was expecting double-quote to start field name
2018-09-26T09:46:44.962707242Z at [Source: {"taxonomy.genus":["Trifolium"],+"taxonomy.species":["sp."]}; line: 1, column: 34] on GET http://www.genesys-pgr.org/fr/explore
2018-09-26T09:46:44.962718755Z com.fasterxml.jackson.core.JsonParseException: Unexpected character ('+' (code 43)): was expecting double-quote to start field name
2018-09-26T09:46:44.962725480Z at [Source: {"taxonomy.genus":["Trifolium"],+"taxonomy.species":["sp."]}; line: 1, column: 34]
2018-09-26T09:46:44.962732556Z at com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1581)
2018-09-26T09:46:44.962739545Z at com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:533)
2018-09-26T09:46:44.962745777Z at com.fasterxml.jackson.core.base.ParserMinimalBase._reportUnexpectedChar(ParserMinimalBase.java:462)
2018-09-26T09:46:44.962751962Z at com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddName(ReaderBasedJsonParser.java:1502)
2018-09-26T09:46:44.962758374Z at com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:624)
2018-09-26T09:46:44.962765522Z at org.genesys2.server.service.impl.FilterHandler$AppliedFilters$Deserializer.deserialize(FilterHandler.java:415)
2018-09-26T09:46:44.962772316Z at org.genesys2.server.service.impl.FilterHandler$AppliedFilters$Deserializer.deserialize(FilterHandler.java:244)
2018-09-26T09:46:44.962778623Z at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:3736)
2018-09-26T09:46:44.962784635Z at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:2726)
2018-09-26T09:46:44.962791177Z at org.genesys2.server.servlet.controller.ExplorerController.viewFiltered(ExplorerController.java:207)
```2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/370Case-sensitive Taxonomy2021-02-15T09:56:05+01:00Matija ObrezaCase-sensitive TaxonomyTaxonomy lookups and updates should be case sensitive:
> had the species authors in capital letters `((AUBL.) SW.)`. This was corrected in the updated data `((Aubl.) Sw.)`, but the author remains in capital letters in Genesys.Taxonomy lookups and updates should be case sensitive:
> had the species authors in capital letters `((AUBL.) SW.)`. This was corrected in the updated data `((Aubl.) Sw.)`, but the author remains in capital letters in Genesys.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/413DB: AccessionId updated2021-02-15T09:56:35+01:00Matija ObrezaDB: AccessionId updatedThere's something wrong with AccessionId. When pushing data I see a bunch of:
```
update acce set active=0, version=2, lastModifiedBy=1273, lastModifiedDate='2019-02-05 16:34:34',
collId=3152251, geoId=null, imageCount=0, pdciId=616925...There's something wrong with AccessionId. When pushing data I see a bunch of:
```
update acce set active=0, version=2, lastModifiedBy=1273, lastModifiedDate='2019-02-05 16:34:34',
collId=3152251, geoId=null, imageCount=0, pdciId=616925, folderId=null where id=3794549 and version=1
update acce set active=0, version=5, lastModifiedBy=1273, lastModifiedDate='2019-02-05 16:34:40',
collId=3151926, geoId=3092359, imageCount=0, pdciId=616587, folderId=null where id=3794214 and version=4
update acce set active=0, version=2, lastModifiedBy=1273, lastModifiedDate='2019-02-05 16:34:33',
collId=3152255, geoId=3091876, imageCount=0, pdciId=616929, folderId=null where id=3794553 and version=1
update acce set active=0, version=7, lastModifiedBy=985, lastModifiedDate='2019-02-05 16:34:41',
collId=null, geoId=null, imageCount=0, pdciId=1583595, folderId=null where id=734501 and version=6
update acce set active=0, version=5, lastModifiedBy=1273, lastModifiedDate='2019-02-05 16:34:39',
collId=3151736, geoId=3091975, imageCount=0, pdciId=616395, folderId=null where id=3794024 and version=4
```
- why is `active` updated (and to **0**)?
- `imageCount` ok... I guess.
- `collId`, `geoId` and `pdciId` should be updated when needed
ExploreMatija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/420Spatial data2021-02-15T09:56:52+01:00Matija ObrezaSpatial dataWe'd like to make spatial (polygon) queries for accessions in Genesys.
## Use case
https://www.genesys-pgr.org/explore/map has the **Select area** that allows user to select a rectangle (`min&max` for accession collecting site `latitu...We'd like to make spatial (polygon) queries for accessions in Genesys.
## Use case
https://www.genesys-pgr.org/explore/map has the **Select area** that allows user to select a rectangle (`min&max` for accession collecting site `latitude&longitude`). If we allow user to select a polygon (https://leafletjs.com/reference-1.4.0.html#polygon), can the API make a query to the database to find accessions where `accessionGeo` is **inside** the selected polygon?
- https://mariadb.com/kb/en/library/geographic-geometric-features/
- https://www.baeldung.com/hibernate-spatial
## Other cases
- `FaoInstitute` location has `lat&long`2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/245Map isn't displayed on the /org/CGIAR/map page2021-02-15T09:58:38+01:00Aleksandr KirichenkoMap isn't displayed on the /org/CGIAR/map page**Steps:**
1. Go to the "https://sandbox.genesys-pgr.org/org/CGIAR" page;
2. Click on the VIEW MAP button;
**Expected result:** Map is displayed.
**Actual result:** Map isn't displayed. See attached screen:
![SCR_0071](/uploads/47da0d1...**Steps:**
1. Go to the "https://sandbox.genesys-pgr.org/org/CGIAR" page;
2. Click on the VIEW MAP button;
**Expected result:** Map is displayed.
**Actual result:** Map isn't displayed. See attached screen:
![SCR_0071](/uploads/47da0d15aa5382f7b45e3a7f5cec01b6/SCR_0071.png)https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/248Impossibility to remove filter label in iOs2021-02-15T09:58:49+01:00Aleksandr KirichenkoImpossibility to remove filter label in iOsSteps:
* go to the Browse page
* open crop name filter
* select crop
* remove label
Act result: Impossibility to remove filter label in iOs
![CBD4B78C-6C2D-48D1-A06E-724AAE1E9AB7](/uploads/4c6ad1d06845271360aa0b6cf392da0f/CBD4B78C-...Steps:
* go to the Browse page
* open crop name filter
* select crop
* remove label
Act result: Impossibility to remove filter label in iOs
![CBD4B78C-6C2D-48D1-A06E-724AAE1E9AB7](/uploads/4c6ad1d06845271360aa0b6cf392da0f/CBD4B78C-6C2D-48D1-A06E-724AAE1E9AB7.jpeg)Vladyslava MokliakVladyslava Mokliakhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/492Detect accessions in Dataset file2021-02-15T09:59:23+01:00Matija ObrezaDetect accessions in Dataset fileData providers generally upload the Excel file with data in Step 2, and then upload accession references in step 3.
Can we add `detectAccessions` function that will use Amphibian to check for `DOI` and `ACCENUMB` headers and automatical...Data providers generally upload the Excel file with data in Step 2, and then upload accession references in step 3.
Can we add `detectAccessions` function that will use Amphibian to check for `DOI` and `ACCENUMB` headers and automatically register accession references?
The user would trigger this function in step 3. So they either copy-paste the list or autodetect it from the file.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/521Connection reset by peer2021-02-15T09:59:53+01:00Kiril MorhalenkoConnection reset by peer@mobreza Please have a look that sometimes happens the situations when request is failed. It happens not all the time, but I think it will be annoying for users.
It happens in the cases when user download any page and try to open anoth...@mobreza Please have a look that sometimes happens the situations when request is failed. It happens not all the time, but I think it will be annoying for users.
It happens in the cases when user download any page and try to open another or if he applying filters and click to another one (on the `/a/overview` page).
So should we heed to do something with this issue from our side?
![image](/uploads/1e670df8730c9fdfeb1ee8e2b1391b2d/image.png)
![image](/uploads/055f29e4a9707b275610af96749bd626/image.png)Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/542Synonymy search2021-02-15T10:00:19+01:00Matija ObrezaSynonymy searchThe current TaxonomyFilter supports search by *current GRIN names*. Search for *Solanum lycopersicum* (a current name) includes *Solanum lycopersicum*, *Lycopersicon esculentum* and *Lycopersicon lycopersicum*.
Searching for *Lycopers...The current TaxonomyFilter supports search by *current GRIN names*. Search for *Solanum lycopersicum* (a current name) includes *Solanum lycopersicum*, *Lycopersicon esculentum* and *Lycopersicon lycopersicum*.
Searching for *Lycopersicon esculentum* on the other hand does not include *Solanum lycopersicum*.
Update `TaxonomyFilter` to extend the search:
1. Find all *Lycopersicon esculentum* in `Taxonomy2` and use their **currentTaxonomySpecies**
1. Find all *Lycopersicon esculentum* in GRIN taxonomy and use their **currentTaxonomySpecies**?2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/544Elastic Search configuration;2021-02-15T10:19:34+01:00Kiril MorhalenkoElastic Search configuration;@mobreza Now I can't to found descriptor list by contained in it descriptor using Full-text query filter. Is it ok? because in previous versions it's working fine;
![image](/uploads/38bbe7381a3bb79f8231832862631c57/image.png)
![image](/...@mobreza Now I can't to found descriptor list by contained in it descriptor using Full-text query filter. Is it ok? because in previous versions it's working fine;
![image](/uploads/38bbe7381a3bb79f8231832862631c57/image.png)
![image](/uploads/5809652d92c54d1d5a9bfe3563da08e9/image.png)
![image](/uploads/3a5e1d40245dc4c3bcbb4ae440c13861/image.png)Matija ObrezaMatija Obreza