Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2018-07-16T12:34:46+02:00https://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/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/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/243Drop-down "Select country" - wrong navigation2018-07-02T16:29:16+02:00Aleksandr KirichenkoDrop-down "Select country" - wrong navigation**Steps:**
1. Go to the "https://sandbox.genesys-pgr.org/org/CGIAR" page;
2. In the drop-down menu select country "Colombia" for example;
**Act.Res.:** Colombia is hidden under the header. See attached video:
![recording_00016](/uplo...**Steps:**
1. Go to the "https://sandbox.genesys-pgr.org/org/CGIAR" page;
2. In the drop-down menu select country "Colombia" for example;
**Act.Res.:** Colombia is hidden under the header. See attached video:
![recording_00016](/uploads/397ab0c41e761d0f5ad0964e18eea49e/recording_00016.gif)Maxim BabichevMaxim Babichevhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/242SCSS for free-text2018-07-02T16:29:16+02:00Matija ObrezaSCSS for free-textDisplay of lists is not styled in user-provided content (`free-text`) at https://www.genesys-pgr.org/wiews/USA1004
![image](/uploads/d574309d69ecd323c03b10cfc0b893e7/image.png)
Please fix the SCSS for `.free-text`:
- lists
- heading ...Display of lists is not styled in user-provided content (`free-text`) at https://www.genesys-pgr.org/wiews/USA1004
![image](/uploads/d574309d69ecd323c03b10cfc0b893e7/image.png)
Please fix the SCSS for `.free-text`:
- lists
- heading sizes should be smaller2.4Maxim BabichevMaxim Babichevhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/237Update documentation2018-07-02T16:29:15+02:00Matija ObrezaUpdate documentationUpdate documentation.Update documentation.2.3Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/246Term of the copywriter has expired.2018-07-02T16:29:15+02:00Aleksandr KirichenkoTerm of the copywriter has expired.![SCR_0072](/uploads/71bc8651a6227becac6ef6130ae06400/SCR_0072.png)![SCR_0072](/uploads/71bc8651a6227becac6ef6130ae06400/SCR_0072.png)2.4Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/247Password reset2018-07-02T16:29:15+02:00Matija ObrezaPassword resetPassword reset stopped working on www.genesys-pgr.org due to user not being authenticated in line 233 of `BasicUserServiceImpl`:
```
@PreAuthorize("hasRole('ADMINISTRATOR') || principal.id == #user.id")
```
![image001](/uploads/2ad4088...Password reset stopped working on www.genesys-pgr.org due to user not being authenticated in line 233 of `BasicUserServiceImpl`:
```
@PreAuthorize("hasRole('ADMINISTRATOR') || principal.id == #user.id")
```
![image001](/uploads/2ad4088ee82273c36796108ec9f06b7a/image001.jpg)
# The update
1. User requests password reset
1. User receives email and opens the link
1. On opening the link, the current security context should be set to that user
1. Setting password works again
2.4Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/219CSS updates for 2.32018-07-02T16:29:14+02:00Matija ObrezaCSS updates for 2.3*This is the placeholder issue for all CSS issues identified for %"2.3"*
1) https://sandbox.genesys-pgr.org/doc/0/apis the `<p>` paragraphs should have top and bottom margins of: `littlebit`**em**. Funny, we have nice margins defined fo...*This is the placeholder issue for all CSS issues identified for %"2.3"*
1) https://sandbox.genesys-pgr.org/doc/0/apis the `<p>` paragraphs should have top and bottom margins of: `littlebit`**em**. Funny, we have nice margins defined for wide screen :-(
2) "Saved lists of accessions" long name or description cause failures
**Steps:**
1. Go to the "https://sandbox.genesys-pgr.org";
2. Click on the "Browse" menu item;
3. Select several Accessions;
4. Click on the "My List" menu item;
5. Navigate to the "Accession List" tab;
6. Fill the "List title" and "List description" fields using long name / description for example 150 characters;
7. Click on the "CREATE NEW LIST" button;
8. Click on the "CLEAR THE LIST" button;
**Act.res.:** See attached screen:
![SCR_0061](/uploads/c4e41a239e70010c4a62f4aef3c4851f/SCR_0061.png)
3) https://sandbox.genesys-pgr.org/content/about/about List items have a color. Links should have css property - color, not list items
4) https://sandbox.genesys-pgr.org/wiews/PHL001 Links should be displayed like block elements, not inline-block.
5) https://sandbox.genesys-pgr.org/registration `.form-group > div` have unnecessary property - min-height.
6) https://sandbox.genesys-pgr.org/welcome The content of 'Quick Links' block has a strange alignment.
7) https://sandbox.genesys-pgr.org/explore The filters panel should be fixed.
8) https://sandbox.genesys-pgr.org/sel There is too much spacing in the tab 1.
9) https://sandbox.genesys-pgr.org/wiews/PHL001 `.row + div` have unnecessary border.
![59b829c179](/uploads/9f92fda892ac4ebac832a7ec9dc240d1/59b829c179.jpg)2.3Aleksandr KirichenkoAleksandr Kirichenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/240Release 2.32018-07-02T16:29:14+02:00Matija ObrezaRelease 2.3Release 2.3Release 2.32.3Matija 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/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/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/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 Borodenkohttps://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/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/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/6Basic BrAPI framework2018-03-26T10:22:24+02:00Matija ObrezaBasic BrAPI frameworkImplement new controller `BrAPIController` mapped onto `/brapi/v1`. It should use the standard OAuth2 authentication that is already implemented for existing `/api/v0`.
http://docs.brapi.apiary.io/#introduction/structure-of-the-response...Implement new controller `BrAPIController` mapped onto `/brapi/v1`. It should use the standard OAuth2 authentication that is already implemented for existing `/api/v0`.
http://docs.brapi.apiary.io/#introduction/structure-of-the-response-object:
# BrAPI response
The response always consists of a "metadata" key that minimally contains the pagination information in a "pagination" key and the status information as well as a "datafiles" key that lists URLs to data files generated by the call.
If the response is a single record that doesn't require pagination, then the value for the "pagination" key is returned with all the keys set to zero. When the results are paginated, the keys "pageSize", "currentPage", "totalCount", "totalPages" contain the appropriate values. Note that pages are zero indexed, so the first page will be page 0 (zero). (For the user interface, this may be adjusted by adding 1).
The status object contains a list of objects with the keys "code" and "message". If no status is reported, the empty list should be returned.
The datafiles key contains a list of strings. The empty list should be returned if no datafiles are present.
The payload data is contained in a key called "result", containing an object with the response. If there is a paginated response, a "data" key will be present, with a list value, which will be paginated over (showing pageSize elements of the currentPage).
Additional documentation is in the GitHub wiki. See especially the [Best Practices and Conventions] (https://github.com/plantbreeding/documentation/wiki/Best-Practices-and-Conventions).Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/241Broken styles2018-01-10T14:03:00+01:00Aleksandr KirichenkoBroken stylesSee attached screen:
![SCR_0070](/uploads/fa566e0bfa47fb84e1191af0bb011b52/SCR_0070.png)
This problem has appeared on the both environments (Sandbox and Prod.)See attached screen:
![SCR_0070](/uploads/fa566e0bfa47fb84e1191af0bb011b52/SCR_0070.png)
This problem has appeared on the both environments (Sandbox and Prod.)Matija ObrezaMatija Obreza