Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2018-09-02T19:21:04+02:00https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/304FTP: uploading fails2018-09-02T19:21:04+02:00Matija ObrezaFTP: uploading failsIRRI is trying to upload images and documents to genesys sandbox but there's an error, please see below:
![image](/uploads/765b568bc7b71c10d5c4a667e21d9954/image.png)
The issue relates to permission checks on RepositoryService.IRRI is trying to upload images and documents to genesys sandbox but there's an error, please see below:
![image](/uploads/765b568bc7b71c10d5c4a667e21d9954/image.png)
The issue relates to permission checks on RepositoryService.2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/302Google Auth fails2018-08-23T13:19:51+02:00Matija ObrezaGoogle Auth fails#283 and the corresponding !175 break authentication using Google+ on https://genesys.demo.genesys-pgr.org/login
- **/google/verify-token** returns the old-fashioned UUID access token
- **/oauth/check_token** doesn't understand it.#283 and the corresponding !175 break authentication using Google+ on https://genesys.demo.genesys-pgr.org/login
- **/google/verify-token** returns the old-fashioned UUID access token
- **/oauth/check_token** doesn't understand it.2.4Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/301Accession listIds not in ES2018-08-22T18:13:47+02:00Matija ObrezaAccession listIds not in ESOverviews for CWR project-related accessions show no data -- ES has no information on listIds?Overviews for CWR project-related accessions show no data -- ES has no information on listIds?2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/300InstituteFilter: accessions2018-08-22T14:37:57+02:00Matija ObrezaInstituteFilter: accessionsExtend `InstituteFilter` with:
```
public Boolean accessions;
```
If the `accessions` value is not `null`:
```java
if (accessions != null) {
if (accessions == true)
and.and(institute.accessionCount.gt(0));
else
and.and(insti...Extend `InstituteFilter` with:
```
public Boolean accessions;
```
If the `accessions` value is not `null`:
```java
if (accessions != null) {
if (accessions == true)
and.and(institute.accessionCount.gt(0));
else
and.and(institute.accessionCount.eq(0));
}
```2.4Alexander PrendetskiyAlexander Prendetskiyhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/299OOM reindexing Accessions2018-08-21T17:45:53+02:00Matija ObrezaOOM reindexing Accessions2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/295Accession overview API2018-08-03T05:07:05+02:00Matija ObrezaAccession overview API2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/294InstituteController v12018-08-04T12:33:53+02:00Matija ObrezaInstituteController v1Add a new API controller `v1.InstituteController` with these methods:
## `/details`
Loads basic `FaoInstitute` data and if not `null` it adds:
- ES termStatistics on `crop.shortName`, `cropName`, `taxonomy.genus`, `taxonomy.genusSpeci...Add a new API controller `v1.InstituteController` with these methods:
## `/details`
Loads basic `FaoInstitute` data and if not `null` it adds:
- ES termStatistics on `crop.shortName`, `cropName`, `taxonomy.genus`, `taxonomy.genusSpecies`
- PDCI statistics for the institute
- Last updates of passport data for the institute
```java
@GetMapping("/{wiewsCode}")
public InstituteDetails details(...) {
InstituteDetails details = new InstituteDetails();
details.stats = elasticsearchService....
details.blurb = ...
...
return details;
}
// New class
public static class InsituteDetails {
public FaoInstitute institute;
public Article blurb;
public ? lastUpdates;
public ? stats; // for term statistics
}
}
```
Using InstituteDetails class will also help with API docs generation.2.4Alexander PrendetskiyAlexander Prendetskiyhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/293Dataset location and timing2018-08-03T15:25:21+02:00Matija ObrezaDataset location and timingThe `DatasetLocation` now holds data on **where** the plant material was evaluated, but does not tell us **when** that happened.
Add `String startDate` and `endDate` fields to this class. `@Column(length = 8)`
## Date format
We need t...The `DatasetLocation` now holds data on **where** the plant material was evaluated, but does not tell us **when** that happened.
Add `String startDate` and `endDate` fields to this class. `@Column(length = 8)`
## Date format
We need to keep this as `String` because the exact month or day of the dates may not be known. We will use the `YYYYMMDD` format and the setter should test with `MCPDUtils.isMcpdDate()` method if the value is valid.
## Update MCPDUtils
Update `MCPDUtils.isMcpdDate()` method to test that the values for **DD** and **MM** are:
- DD: -- or 00 or valid month value from 1 to 12
- MM: -- or 00 or valid day in the month of the year (if provided)
## Dataset
Update `Dataset` class and add `String startDate` and `endDate` fields to `Dataset`. `@Column(length = 8)`
In `@PrePersist/@PreUpdate` get the minimum and maximum start and end dates from all dataset locations.
```java
if (dataset.locations != null) {
this.startDate = dataset.locations.stream().map(ds -> ds.startDate).sorted(/* ascending */).findFirst().orElse(null);
this.endDate = ... /* descending */
}
```
You may need to update methods for saving locations to also trigger an update on the dataset.
## After merge
When this is done, file a ticket in the **catalog-ui** project to update the forms and display of DatasetLocations.2.4Viacheslav PavlovViacheslav Pavlovhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/280Bug: CWR page 5002018-08-27T10:06:08+02:00Matija ObrezaBug: CWR page 500- Go to the https://sandbox.genesys-pgr.org/welcome
- Click on the CWR Project link;
## Overviews
The page is fixed in 78739c47, but the overviews do not show up. Fix the overviews.- Go to the https://sandbox.genesys-pgr.org/welcome
- Click on the CWR Project link;
## Overviews
The page is fixed in 78739c47, but the overviews do not show up. Fix the overviews.2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/279Bug: Latitude filter fails2018-07-20T22:33:07+02:00Matija ObrezaBug: Latitude filter fails- Go to the "Browse" page
- Open Latitude filter
- Input some value in the filter fields- Go to the "Browse" page
- Open Latitude filter
- Input some value in the filter fields2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/278Bug: Create new list functionality2018-07-21T10:54:28+02:00Matija ObrezaBug: Create new list functionalityCreating new list fails with 500 server error. Steps to reproduce:
- Go to the https://sandbox.genesys-pgr.org/welcome
- Login as admin;
- Go to the "Browse" page;
- Add some accessions to the list;
- Go to the "My List" page;
- Go to t...Creating new list fails with 500 server error. Steps to reproduce:
- Go to the https://sandbox.genesys-pgr.org/welcome
- Login as admin;
- Go to the "Browse" page;
- Add some accessions to the list;
- Go to the "My List" page;
- Go to the "Accession List" tab;
- Fill the fields and click on the "CREATE NEW LIST" button.2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/270Debug upsert2018-07-16T12:34:46+02:00Matija ObrezaDebug upsertPosting
```json
{"acceName":["ajda","","èrna"],"coll":{"collNumb":"Ivan Kreft","collDate":null,"collCode":null,"collName":null,"collSite":"Kranj","collInstAddress":null,"collMissId":null,"collSrc":50},"geo":{"latitude":46.2333,"longitu...Posting
```json
{"acceName":["ajda","","èrna"],"coll":{"collNumb":"Ivan Kreft","collDate":null,"collCode":null,"collName":null,"collSite":"Kranj","collInstAddress":null,"collMissId":null,"collSrc":50},"geo":{"latitude":46.2333,"longitude":14.3667,"elevation":357.0,"uncertainty":null,"datum":null,"method":null},"sampStat":500,"ancest":null,"donorCode":null,"donorNumb":"Dr. T. Tajnšek","donorName":null,"otherNumb":["RUS001:106","unknown:106"],"duplSite":null,"storage":null,"acceUrl":null,"remarks":null,"instituteCode":"SVN018","accessionNumber":"SRGB 2080","acquisitionDate":null,"breederCode":null,"origCty":"SVN","taxonomy":{"genus":"Fagopyrum","species":"esculentum","spAuthor":null,"subtaxa":null,"subtAuthor":null}}
```
fails with
```
16:27:59,579 qtp1156060786-409 WARN o.g.s.s.c.r.AccessionController:251 - Upsert failed due to: could not execute statement; SQL [n/a]; constraint [null]; nested exception is org.hibernate.exception.ConstraintViolationException: could not execute statement data=...
2018-07-15T16:27:59.591979430Z sandbox_server.1.i0duijjbjwbj@genesys3 | org.springframework.dao.DataIntegrityViolationException: could not execute statement; SQL [n/a]; constraint [null]; nested exception is org.hibernate.exception.ConstraintViolationException: could not execute statement
```2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/269Invalid JSON2018-07-15T12:02:14+02:00Matija ObrezaInvalid JSONSome code is generating invalid JSON:
```
{"lastModifiedDate":["2014-7-23"],+"institute.code":["UKR028"]}
```
There is a space `+` where there should't be.Some code is generating invalid JSON:
```
{"lastModifiedDate":["2014-7-23"],+"institute.code":["UKR028"]}
```
There is a space `+` where there should't be.2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/260Increased page size for API calls2018-06-12T18:21:44+02:00Matija ObrezaIncreased page size for API callsThe `pageSize` for API responses is limited to 50. Increase this to 1000 for API calls.The `pageSize` for API responses is limited to 50. Increase this to 1000 for API calls.2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/259Upgrade appblocks2018-05-18T00:35:40+02:00Matija ObrezaUpgrade appblocksUpgrade to latest app-blocksUpgrade to latest app-blocks2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/255Rename model2018-05-03T20:46:16+02:00Matija ObrezaRename modelThe **DS2** model `Descriptor` does not follow the usual `DS2Descriptor` naming. Rename model and database table.The **DS2** model `Descriptor` does not follow the usual `DS2Descriptor` naming. Rename model and database table.2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/254FTP password2018-04-26T14:58:20+02:00Matija ObrezaFTP passwordUsers are not able to generate FTP password.Users are not able to generate FTP password.2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/252Delete user account2018-04-28T13:12:52+02:00Matija ObrezaDelete user accountAllow users to delete their Genesys user account.
The User/SID is linked to many entities. It is best if we replace all personal information with:
1. `email`: Used for logging in and must be unique. Replace with `deleted@${timestamp}` ...Allow users to delete their Genesys user account.
The User/SID is linked to many entities. It is best if we replace all personal information with:
1. `email`: Used for logging in and must be unique. Replace with `deleted@${timestamp}` (e.g. `deleted@2134523311`)
1. `fullName`: Displayed in various places, replace with `Account removed`
1. `accountType`: Add `DELETED` option and use that.
1. `enabled`: Set to `false`.2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/251Excel corrupted2018-04-24T19:04:23+02:00Matija ObrezaExcel corruptedLarge datasets (~70K rows) break Excel 2016, 2013 limit on number of hyperlinks.
https://support.office.com/en-us/article/excel-specifications-and-limits-1672b34d-7043-467e-8e27-269d656771c3
> Hyperlinks in a worksheet: 66,530 hyperlinksLarge datasets (~70K rows) break Excel 2016, 2013 limit on number of hyperlinks.
https://support.office.com/en-us/article/excel-specifications-and-limits-1672b34d-7043-467e-8e27-269d656771c3
> Hyperlinks in a worksheet: 66,530 hyperlinks2.4Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/249Data download2018-05-01T11:10:24+02:00Nora Castaneda-AlvarezData downloadRegistered and un-registered users can download data in ZIP format:
![Screen_Shot_2018-04-11_at_09.38.47](/uploads/e54250b20ff9e515150e1329c7cac921/Screen_Shot_2018-04-11_at_09.38.47.png)
This ZIP often contains six files: coll.csv, co...Registered and un-registered users can download data in ZIP format:
![Screen_Shot_2018-04-11_at_09.38.47](/uploads/e54250b20ff9e515150e1329c7cac921/Screen_Shot_2018-04-11_at_09.38.47.png)
This ZIP often contains six files: coll.csv, core.csv, geo.csv, meta.xml, names.csv and README.txt.
The file `core.csv` is missing some columns. These columns need to be included: `SPAUTHOR`, `SUBTAUTHOR`, `SUBTAXA`, coming from **Taxonomy2** table.
2.4Maxym BorodenkoMaxym Borodenko