Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2018-04-28T13:12:52+02:00https://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/250Data model cleanup2019-11-20T17:25:50+01:00Matija ObrezaData model cleanupGenesys data model has historically used several database tables for different sections of MCPD: `accession` + `accessioncollect` + `accessionbreeding` + `accessionexchange`, etc. These “section” tables have a 1-to-1 relationship to reco...Genesys data model has historically used several database tables for different sections of MCPD: `accession` + `accessioncollect` + `accessionbreeding` + `accessionexchange`, etc. These “section” tables have a 1-to-1 relationship to records in the core accession table and were originally introduced as a measure to improve database query speeds in view of data sparsity.
This model makes for complicated SQL querying and data export as those additional tables need to be joined to execute the search and need to be loaded to access all passport data for any accession.
The updated data model will undo this database design and bring all columns back to a single table with auxiliary tables for multi-value descriptors: accession names and other identifiers, storage and remarks. These are required for fast and correct querying (e.g. by `STORAGE`).
Instead of generating MCPD-format multi-value strings from sub-tables (e.g. `REMARKS`) we will pre-generate them and store them in a separate passport table (accession_export?) with all data correctly merged using semicolon (;). This table will be kept up-to-date as part of upsert operation.
# Implementation details
This change of the data model affects all aspects of Genesys: the API, JSP pages, querying, elastic search. If possible, we would keep the original `AccessionColl` and other classes and populate them in the service methods so that no change is required to JSPs.
Because of the change in the data model, the filter codes (`coll.collMissId`) may need adjusting.2.5Matija 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/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/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/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/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/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/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 Obrezahttps://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/239"Type of Germplasm storage" filter2018-08-28T17:37:10+02:00Aleksandr Kirichenko"Type of Germplasm storage" filter@mobreza Hi Matija, I have a question about filtering by "Type of Germplasm storage" filter if user on the Overview page "https://sandbox.genesys-pgr.org/explore/overview?".
So, when I choose "Long term seed collection" option for examp...@mobreza Hi Matija, I have a question about filtering by "Type of Germplasm storage" filter if user on the Overview page "https://sandbox.genesys-pgr.org/explore/overview?".
So, when I choose "Long term seed collection" option for example, in the "Type of Germplasm storage" section I expect to see only this option displayed, but instead of this I see other options such as:
- "Medium term seed collection";
- "Seed collection";
- "Short term seed collection" etc.
Is this correct behaviour or this is bug?
Screen-shots examples:
![SCR_0068](/uploads/2dbf4bf64fe0ccfd1c090b247affaf1a/SCR_0068.png)
![SCR_0069](/uploads/fd5579e3138b0530b970e01a818157aa/SCR_0069.png)Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/238Scrollbar slider is hidden under the header2018-01-02T14:33:59+01:00Aleksandr KirichenkoScrollbar slider is hidden under the headerThis problem is most noticeable when the page content is long
For example go to the "https://www.genesys-pgr.org/doc/0/apis"
See attached video:
![recording_00015](/uploads/a535b09e3b937d5e8e29539043bd6f3e/recording_00015.gif)
I think t...This problem is most noticeable when the page content is long
For example go to the "https://www.genesys-pgr.org/doc/0/apis"
See attached video:
![recording_00015](/uploads/a535b09e3b937d5e8e29539043bd6f3e/recording_00015.gif)
I think that the header should be aligned along the edge of the Scrollbar.Nina Tkachenkon.tkachenko@aimprosoft.comNina Tkachenkon.tkachenko@aimprosoft.comhttps://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/236ACL SID updated2017-12-18T19:31:03+01:00Matija ObrezaACL SID updatedApplication Blocks has changed `#sid` property from UUID to `email` of the user in
in application-blocks@e23f2c1c16c1188d9eb5fff43586dd603e5193cb
Update liquibase to migrate data.Application Blocks has changed `#sid` property from UUID to `email` of the user in
in application-blocks@e23f2c1c16c1188d9eb5fff43586dd603e5193cb
Update liquibase to migrate data.2.3Matija ObrezaMatija Obrezahttps://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/233Inconsistency of filtering results.2018-08-29T13:58:50+02:00Aleksandr KirichenkoInconsistency of filtering results.**Steps**:
1. Go to "https://www.genesys-pgr.org/explore?";
2. Open "***ITPGRFA Art. 15 accession***" filter;
3. Remember the number of accessions near the option "No" (15952);
4. Click on the "Apply button"
**Act.res.:** Number of res...**Steps**:
1. Go to "https://www.genesys-pgr.org/explore?";
2. Open "***ITPGRFA Art. 15 accession***" filter;
3. Remember the number of accessions near the option "No" (15952);
4. Click on the "Apply button"
**Act.res.:** Number of results shown does not match with the number of accessions near the option "No".
See attached video
![recording_00012](/uploads/f8eed3c0ff527f6521e658d37166c252/recording_00012.gif)
@mobreza I suspect that this is a incorrect behaviour, isn't it?Maxym BorodenkoMaxym Borodenko