Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2018-08-27T10:06:08+02:00https://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 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/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/244Subsets2018-08-22T12:48:12+02:00Matija ObrezaSubsetsWe're introducing a new "list of accessions", similar to current implementation of *AccessionList*.
# Model
Add a new entity `Subset` to *..model.impl*:
```java
public class Subset extends AuditedVersionedModel implements AclAware {
...We're introducing a new "list of accessions", similar to current implementation of *AccessionList*.
# Model
Add a new entity `Subset` to *..model.impl*:
```java
public class Subset extends AuditedVersionedModel implements AclAware {
@Type(type = "uuid-binary")
protected UUID uuid;
protected boolean published;
// other strings, only description is @Lob
// dateCreated as string -- it's not the same as createdDate (from Auditing)
protected String title, description, publisher, rights, dateCreated, publisher;
@ManyToMany(cascade = {}, fetch = FetchType.LAZY)
@JoinTable(name = "SubsetAccessions", joinColumns = @JoinColumn(name = "subsetId"), inverseJoinColumns = @JoinColumn(name = "acceId"))
private List<AccessionId> accessionIds;
}
```
1. Add JPA repository
1. Implement service
# Controller and JSP
Add a new `SubsetController` at */subset* with the following methods
1. GET */subset/* `listSubsets()` that renders the list of Subsets where `published == true`.
1. GET */subset/{uuid}* `subset()` that renders all properties of the Subset + the passport data of accessions in the subset. It should use the components from *browse*.
# REST API controller
New controller at */api/v1/subset* with endpoints:
1. POST */list* `Page<Subset> list(@RequestBody SubsetFilters filter`)
1. GET */{uuid}* `Subset get(@PathVariable UUID uuid)`
1. POST */create* `Subset create(@RequestBody Subset subset)`
1. POST */update* `Subset update(@RequestBody Subset subset)`
1. DELETE */{uuid},{version}* `Subset delete(@PathVariable UUID uuid, @PathVariable int version)`2.4Maxym BorodenkoMaxym Borodenkohttps://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/235CSS for printing2017-12-22T16:57:46+01:00Matija ObrezaCSS for printingSeems that the CSS at this moment somehow allows only for printing a single page from the Browser.
Steps to reproduce:
1. Open https://sandbox.genesys-pgr.org/explore
1. Press `Cmd+P` or whatever
1. Observe the print preview with a si...Seems that the CSS at this moment somehow allows only for printing a single page from the Browser.
Steps to reproduce:
1. Open https://sandbox.genesys-pgr.org/explore
1. Press `Cmd+P` or whatever
1. Observe the print preview with a single page
[Accession_browser.pdf](/uploads/f6aaf788f5a7e7e3ed8a904743f52099/Accession_browser.pdf)
Printing from the Browser should print entire contents of the page. Make sure it is tested on
https://sandbox.genesys-pgr.org/doc/0/basics and https://sandbox.genesys-pgr.org/doc/0/brapi
Must also work when in mobile view.2.4Maxim BabichevMaxim Babichevhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/234Wrong navigation through the links in the Table of Contents2017-12-22T16:54:05+01:00Aleksandr KirichenkoWrong navigation through the links in the Table of Contents**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/doc/0/brapi" page;
2. Click on the "Germplasm" link in the Table of contents;
See attached video:
![recording_00013](/uploads/1fcec4b71cf69633ef7f00609653e540/recording_00013.gif)
*...**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/doc/0/brapi" page;
2. Click on the "Germplasm" link in the Table of contents;
See attached video:
![recording_00013](/uploads/1fcec4b71cf69633ef7f00609653e540/recording_00013.gif)
**This also applies to "Tables of Contents" on the pages: "Genesis API" and "Accession passport data"**2.4Maxim BabichevMaxim Babichevhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/215"Saved lists of accessions" long name or description2017-11-07T21:11:21+01:00Aleksandr Kirichenko"Saved lists of accessions" long name or description"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. Na..."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)2.4Nina Tkachenkon.tkachenko@aimprosoft.comNina Tkachenkon.tkachenko@aimprosoft.comhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/155Pagination buttons aren't disabled2018-07-23T07:11:25+02:00Aleksandr KirichenkoPagination buttons aren't disabledWhen there is only one page in the results, the pagination buttons are not disabled
**Steps:**
1. Go to browse page "https://sandbox.genesys-pgr.org/explore";
2. Add several accessions in My List 3 for example;
3. Click on the "My List"...When there is only one page in the results, the pagination buttons are not disabled
**Steps:**
1. Go to browse page "https://sandbox.genesys-pgr.org/explore";
2. Add several accessions in My List 3 for example;
3. Click on the "My List" menu item;
4. Click on the ">" Next page button
Act.res.: ">" Next page button is enabled, and transition to the 2nd page is performed; See attached video
[rec_017.avi](/uploads/c4ff45f05ec2caa8a97484108fc3567a/rec_017.avi)
![SCR_0048](/uploads/70a01f567c8081bb3140632e4aa79ca4/SCR_0048.png)
This also applies to any pagination on the site except search. In the search it is implemented as needed. For example, watch the video: [rec_018.avi](/uploads/785e41edc7d6d6bda744c5a0629250de/rec_018.avi)2.4Maxym BorodenkoMaxym Borodenko