Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2017-10-27T15:41:31+02:00https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/185KML exhausts memory2017-10-27T15:41:31+02:00Aleksandr KirichenkoKML exhausts memoryThe `MappingServiceImpl#filteredKml` is generating the KML in memory and returns a `String`. This exhausts memory on the server.
Please add a test and allow execution if filters give **<= 200,000** records to
1. `mappingService.filtere...The `MappingServiceImpl#filteredKml` is generating the KML in memory and returns a `String`. This exhausts memory on the server.
Please add a test and allow execution if filters give **<= 200,000** records to
1. `mappingService.filteredGeoJson`
1. `mappingService.filteredKml`
Throw exception if filter produces over 200,000 records.
Next, convert the filteredGeoJson to accept the response `OutputStream` and write the KML directly to the response stream, not a `String` buffer.
## Exhausting memory on the server
1. Go to "https://sandbox.genesys-pgr.org/welcome";
2. Click on the map area;
3. Click on the "DOWNLOAD KML" button;
4. On the Download pop-up click "cancel" button;
5. Click on the "DOWNLOAD KML" button again;
The reproducibility of the error is unstable, and it can take several repetitions.
2.3Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/183User can't generate FTP password2017-10-14T17:49:23+02:00Matija ObrezaUser can't generate FTP passwordUsers with role `VETTED_USER` see button "Generate FTP password". After clicking, the password is not displayed.Users with role `VETTED_USER` see button "Generate FTP password". After clicking, the password is not displayed.2.2Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/182Institute files permissions2017-10-20T19:47:22+02:00Matija ObrezaInstitute files permissionsUsers can see the links to manage institute (and accession) files, but opening the link gives `Access denied`.Users can see the links to manage institute (and accession) files, but opening the link gives `Access denied`.2.2Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/1814042017-10-14T17:49:23+02:00Matija Obreza404A 404 (like https://sandbox.genesys-pgr.org/asdasdsda) results in a Jetty error message:
```
HTTP ERROR 404
Problem accessing /asdasdsda. Reason:
Not Found
Powered by Jetty:// 9.4.5.v20170502
```
Make it use our pretty HTML error.A 404 (like https://sandbox.genesys-pgr.org/asdasdsda) results in a Jetty error message:
```
HTTP ERROR 404
Problem accessing /asdasdsda. Reason:
Not Found
Powered by Jetty:// 9.4.5.v20170502
```
Make it use our pretty HTML error.2.2Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/180Normalize class names in ..spring.config package2017-10-14T17:49:22+02:00Matija ObrezaNormalize class names in ..spring.config packageRemove `Spring` prefix from class names in `org.genesys2.spring.config` package.Remove `Spring` prefix from class names in `org.genesys2.spring.config` package.2.2Matija 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/178Article slugs without dot2017-10-21T19:37:41+02:00Matija ObrezaArticle slugs without dotArticle slugs cannot contain `.` character because they cannot be submitted to Transifex for translation.
Genesys relies on some default articles from `src/main/resources/default-articles`. These should be renamed to not use the `.`, bu...Article slugs cannot contain `.` character because they cannot be submitted to Transifex for translation.
Genesys relies on some default articles from `src/main/resources/default-articles`. These should be renamed to not use the `.`, but `-` instead, and references in code to such articles must be CONSTANTS in ContentService -- there should be no String `"user.password-reset"` anywhere in the code.2.2Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/177Logging fixed2017-10-18T09:56:46+02:00Matija ObrezaLogging fixedUsing string concatenation `"foo=" + bar + " x=" + x"` in logging is horribly bad. The SLF4J avoids that by creating the log message string on demand (if current log level must be logged).
Replace **ALL** loggers with `org.slf4j.Logger`...Using string concatenation `"foo=" + bar + " x=" + x"` in logging is horribly bad. The SLF4J avoids that by creating the log message string on demand (if current log level must be logged).
Replace **ALL** loggers with `org.slf4j.Logger` and make sure they are called `LOG`:
```java
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
...
Logger LOG = LoggerFactory.getLogger(...
```
Replace all string concatenation in calls to `LOG.info`, `LOG.debug`, etc. with message format logging:
```java
LOG.info("Test value=" + value + " other=" + other);
// must be
LOG.info("Test value={} other={}", value, other);
```2.2Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/175Genesys CI2017-10-06T11:51:42+02:00Matija ObrezaGenesys CIGenesys branches should automatically deploy to Docker so that testing can begin without clicking buttons.Genesys branches should automatically deploy to Docker so that testing can begin without clicking buttons.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/174OAuth Client Credentials Grant2017-10-06T20:21:06+02:00Matija ObrezaOAuth Client Credentials GrantImplement Client Credentials grant in Genesys to allow system-to-system communication. Test that permissions on institutes work.
Document the use of this grant type in the API docs `/docs/0/api`.Implement Client Credentials grant in Genesys to allow system-to-system communication. Test that permissions on institutes work.
Document the use of this grant type in the API docs `/docs/0/api`.2.2Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/173Clear DOIs2017-10-06T11:07:03+02:00Matija ObrezaClear DOIsDOIs are in testing phase and data providers may provide test values.
Implement an admin operation to clear all accession DOIs from the database.
- Add the **Clear DOIs** button to `/admin`
- On submit, execute the action that clears t...DOIs are in testing phase and data providers may provide test values.
Implement an admin operation to clear all accession DOIs from the database.
- Add the **Clear DOIs** button to `/admin`
- On submit, execute the action that clears the DOI: `update Accession set doi = null where doi is not null`
No other GUI required.2.2https://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/171Requesting germplasm JSP error2017-09-26T13:02:58+02:00Matija ObrezaRequesting germplasm JSP error1. Add ITC00002 to the list
1. Click "Request for germplasm"
```
javax.el.PropertyNotFoundException: Property 'acceNumb' not found on type org.genesys2.server.model.genesys.Accession
```1. Add ITC00002 to the list
1. Click "Request for germplasm"
```
javax.el.PropertyNotFoundException: Property 'acceNumb' not found on type org.genesys2.server.model.genesys.Accession
```Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/170Article#template2017-10-19T09:32:12+02:00Matija ObrezaArticle#templateTemplates used by Genesys to send emails and display other information are using the `Article` entity. This automatically indexes their contents in Elasticsearch and also displays these templates to end users:
- https://sandbox.genesys-...Templates used by Genesys to send emails and display other information are using the `Article` entity. This automatically indexes their contents in Elasticsearch and also displays these templates to end users:
- https://sandbox.genesys-pgr.org/acn/search2?q=email§ion=article
- https://sandbox.genesys-pgr.org/content/smtp.email-verification
Add new property `boolean template` to `Article` entity.
Change Genesys code to:
- Not include in ES articles with `template == true`
- Only display such articles to users with roles ADMINISTRATOR and CONTENTMANAGER, return 404 otherwise
- Content of template articles is not HTML santitized2.2https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/169Move institute files to /wiews/INSTCODE2017-09-28T15:23:33+02:00Matija ObrezaMove institute files to /wiews/INSTCODEThe `InstituteFilesServiceImpl` now uses `/accessions/INSTCODE/acn/ACCENUMB` for accession image galleries. This makes it inconvenient to test permissions and support other institute files.
Change the path to `/wiews/INSTCODE/acn/ACCENU...The `InstituteFilesServiceImpl` now uses `/accessions/INSTCODE/acn/ACCENUMB` for accession image galleries. This makes it inconvenient to test permissions and support other institute files.
Change the path to `/wiews/INSTCODE/acn/ACCENUMB`.
At the same time, automatically create image galleries when a file is uploaded to `/wiews/INSTCODE/acn/ACCENUMB`.2.2Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/168Upload repository metadata for institutes2017-12-23T09:22:08+01:00Matija ObrezaUpload repository metadata for institutesDepends on #167.
Allow ADMINISTRATOR and Institute ADMINISTRATOR to upload a CSV file with updated metadata for institute files.
Sample file as generated by #167 is attached: [ETH013_files_metadata__6_.csv](/uploads/e6a11f96b134c982382...Depends on #167.
Allow ADMINISTRATOR and Institute ADMINISTRATOR to upload a CSV file with updated metadata for institute files.
Sample file as generated by #167 is attached: [ETH013_files_metadata__6_.csv](/uploads/e6a11f96b134c9823826f2fc9eb6b6e6/ETH013_files_metadata__6_.csv)
The users will
1. Upload files to the server
1. Download metadata CSV and make local changes to the file
1. Upload modified CSV file
Genesys will update RepositoryFile metadata based on the `uuid` -- `version` can be ignored for now. Only the following fields will be updated from CSV:
* title
* subject
* description
* creator
* created
* rightsHolder
* accessRights
* license
* bibliographicCitation
2.3https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/167Download repository metadata2017-10-24T11:07:02+02:00Matija ObrezaDownload repository metadataAfter #166 is implemented, add function to download metadata for all repository files and its subclasses belonging to an institute.
Export data in CSV format, using `tab` as separator, `"` as quote char and `\` as escape char.
The func...After #166 is implemented, add function to download metadata for all repository files and its subclasses belonging to an institute.
Export data in CSV format, using `tab` as separator, `"` as quote char and `\` as escape char.
The function should be available to users with ADMINISTRATOR permissions on the institute record.2.2https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/166File management for institutes2017-10-14T17:49:22+02:00Matija ObrezaFile management for institutesAdd **Manage files** link to institute page, displayed for users with ADMIN permissions on the institute record. For [BEL084](https://sandbox.genesys-pgr.org/wiews/BEL084) the link would be https://sandbox.genesys-pgr.org/wiews/BEL084/fi...Add **Manage files** link to institute page, displayed for users with ADMIN permissions on the institute record. For [BEL084](https://sandbox.genesys-pgr.org/wiews/BEL084) the link would be https://sandbox.genesys-pgr.org/wiews/BEL084/files/
File management UI and most logic can be copied from existing https://sandbox.genesys-pgr.org/admin/r/files/ (accessible to ADMINISTRATORS).
Institute files are stored at repository paths:
- ~~`/accessions/INSTCODE`~~
- `/wiews/INSTCODE`
2.2https://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/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 Obreza