Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2020-02-18T16:48:00+01:00https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/505Account expired2020-02-18T16:48:00+01:00Matija ObrezaAccount expiredThere is no mechanism to un-expire a user account:
![image](/uploads/13d8a4dfa628a479117c5e31321a1d34/image.png)
When the account expires I ask users to reset their password. If the password reset is successful, it should also set acco...There is no mechanism to un-expire a user account:
![image](/uploads/13d8a4dfa628a479117c5e31321a1d34/image.png)
When the account expires I ask users to reset their password. If the password reset is successful, it should also set account expiration date to `today + 1 month`.
Add admin API to extend expired account for 3 months.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/504Jetty 9.4.272020-03-02T11:56:31+01:00Matija ObrezaJetty 9.4.27With Jetty `9.4.26.v20200117` the MVC does not render JSPs.
Update pom.xml `<jetty.version>9.4.26.v20200117</jetty.version>` and observe http://localhost:8080/welcome with no content.
```
openjdk version "1.8.0_242"
OpenJDK Runtime Env...With Jetty `9.4.26.v20200117` the MVC does not render JSPs.
Update pom.xml `<jetty.version>9.4.26.v20200117</jetty.version>` and observe http://localhost:8080/welcome with no content.
```
openjdk version "1.8.0_242"
OpenJDK Runtime Environment (build 1.8.0_242-b08)
```
sitemesh3 doesn't work with jetty `>9.4.18` and `<9.4.27`. Wait for **9.4.27** release.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/503Remove documents from ES2020-02-12T06:05:12+01:00Matija ObrezaRemove documents from ESSometimes ES contains invalid documents. Allow admin to remove documents from ES using filters.Sometimes ES contains invalid documents. Allow admin to remove documents from ES using filters.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/502AccessionFilter: add data provider2020-01-30T11:44:32+01:00Matija ObrezaAccessionFilter: add data providerSimilar to PGRFA network, add "partner" filtering (using UUID) that fetches institutes of the `Partner` and lists/overviews accessions like we do for Networks.Similar to PGRFA network, add "partner" filtering (using UUID) that fetches institutes of the `Partner` and lists/overviews accessions like we do for Networks.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/500Sitemap: Add sitemap-genus.xml2020-01-30T11:42:37+01:00Matija ObrezaSitemap: Add sitemap-genus.xmlAdd a new item to the `sitemap.xml` controller to include `sitemap-genus.xml` sitemap.
This XML should list links to all "valid" genera (see below) at `{fontendURL}/t/{genus}` (a new page added to the UI):
```xml
<urlset xsi:schemaLoca...Add a new item to the `sitemap.xml` controller to include `sitemap-genus.xml` sitemap.
This XML should list links to all "valid" genera (see below) at `{fontendURL}/t/{genus}` (a new page added to the UI):
```xml
<urlset xsi:schemaLocation="http://www.sitemaps.org/schemas/sitemap/0.9 http://www.sitemaps.org/schemas/sitemap/0.9/sitemap.xsd">
<url>
<loc>https://www.genesys-pgr.org/t/Arabidopsis</loc>
<changefreq>monthly</changefreq>
<priority>0.4</priority>
</url>
...
```
## The page
The page on the UI will have:
```html
<h1><em>{genus}</em></h1>
<p>Find and request <em>{genus}</em> material for research and breeding from <em>ex-situ</em> collections (genebanks) through Genesys.</p>
<ul>
<li><em>{genus} {species}</em> {spAuthor} <em>{subTaxa}</em>{subtAuthor}</li>
...
```
A click on `h1` should open the accession overview page for the selected genus.
Optional: Each `li` on the website will (onClick) issue a call to list the accessions matching the selected species.
The page needs to retrieve the list of `Taxonomy2` for the selected `genus` from */api/v1/taxonomy* using `{ "genus": "TheGenus" }` filter.
## "Valid" names
A "valid" genus name is one that matches `^[a-zA-Z ]+$` (only ascii chars + space) that can be used as valid URLs.
99% of names match this regular expression, but there are some names that contain `?` and that would cause problems.
## API controller
We need an API endpoint at */api/v[1,2]/taxonomy* that will accept a `TaxonomyFilter` and return a `List<Taxonomy2>` results.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/497JSP Admin OAuth editor2020-01-22T16:59:57+01:00Matija ObrezaJSP Admin OAuth editorPlease update the OAuth client editor in JSP so that all properties can be managed with the JSP version.
![image](/uploads/931c5c824e78607307f6fd3bbdc9a84a/image.png)
At the moment, when the genesys-ui is not able to talk to the backen...Please update the OAuth client editor in JSP so that all properties can be managed with the JSP version.
![image](/uploads/931c5c824e78607307f6fd3bbdc9a84a/image.png)
At the moment, when the genesys-ui is not able to talk to the backend, there is no way to manage the settings of the OAuth client.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/496Database configuration2020-01-22T11:19:49+01:00Matija ObrezaDatabase configurationAdd *wait timeout* to Genesys settings.Add *wait timeout* to Genesys settings.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/495PGR Network accessions2020-01-28T15:11:12+01:00Matija ObrezaPGR Network accessionsThe query to fetch accessions for a PGR Network member is too slow.
Update the `InstituteFilter` so members of the network are loaded by `slug` and passed in as `id`.The query to fetch accessions for a PGR Network member is too slow.
Update the `InstituteFilter` so members of the network are loaded by `slug` and passed in as `id`.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/494Optimize API call /crops2020-05-18T20:14:28+02:00Matija ObrezaOptimize API call /cropsThis call takes too long to execute but is crucial for UI to function.This call takes too long to execute but is crucial for UI to function.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/493JSP menu bug2020-01-07T07:47:26+01:00Matija ObrezaJSP menu bugSteps:
1. Go to https://www.genesys-pgr.org and logout
1. Go to https://api.genesys-pgr.org and observe an Exception thrown
This is because the Authentication object is the OAuth client (from the website) and it has no `.fullName` prop...Steps:
1. Go to https://www.genesys-pgr.org and logout
1. Go to https://api.genesys-pgr.org and observe an Exception thrown
This is because the Authentication object is the OAuth client (from the website) and it has no `.fullName` property.
Update `menu.jsp` so that if authentication object is not `User` it shows the anonymous menu.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/492Detect accessions in Dataset file2021-02-15T09:59:23+01:00Matija ObrezaDetect accessions in Dataset fileData providers generally upload the Excel file with data in Step 2, and then upload accession references in step 3.
Can we add `detectAccessions` function that will use Amphibian to check for `DOI` and `ACCENUMB` headers and automatical...Data providers generally upload the Excel file with data in Step 2, and then upload accession references in step 3.
Can we add `detectAccessions` function that will use Amphibian to check for `DOI` and `ACCENUMB` headers and automatically register accession references?
The user would trigger this function in step 3. So they either copy-paste the list or autodetect it from the file.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/491ES: Text query issue2019-12-17T11:43:33+01:00Matija ObrezaES: Text query issueIf you look at https://www.genesys-pgr.org/a/overview/v2r8eB7XPQw
![image](/uploads/06c6c889cfb91656235fc3c30702920b/image.png)
and then search only for the listed institute codes at https://www.genesys-pgr.org/a/overview/v29Dz9AM6ax ...If you look at https://www.genesys-pgr.org/a/overview/v2r8eB7XPQw
![image](/uploads/06c6c889cfb91656235fc3c30702920b/image.png)
and then search only for the listed institute codes at https://www.genesys-pgr.org/a/overview/v29Dz9AM6ax
![image](/uploads/5f96a184f360b6b024ac1a9d2fd6918c/image.png)
the only difference is the use of full-text search in ES query.
Please check how the text criteria is added to the query built and submitted to ES. It seems to use an "or" operation.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/489SGSV flag2019-11-29T09:46:03+01:00Matija ObrezaSGSV flagThe `Accession#inSvalbard` flag is currently managed by the link to data found in the SGSV database.
As we are not able to reliably link accession numbers between the systems, we use `inSGSV() { return duplSite.contains('NOR051'); }`, ...The `Accession#inSvalbard` flag is currently managed by the link to data found in the SGSV database.
As we are not able to reliably link accession numbers between the systems, we use `inSGSV() { return duplSite.contains('NOR051'); }`, relying on information submitted by data providers.
This value is transient so we cannot use it in our KPI implementation.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/485API v2 for remaining controllers2019-12-18T11:26:31+01:00Matija ObrezaAPI v2 for remaining controllersPlease create API v2 for the remaining v1 controllers.Please create API v2 for the remaining v1 controllers.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/483Accession Filters: historic2019-11-21T09:40:03+01:00Matija ObrezaAccession Filters: historichttps://www.genesys-pgr.org/a/v2yk7BA47YP does not filter the records properly.https://www.genesys-pgr.org/a/v2yk7BA47YP does not filter the records properly.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/482Remove OAuth tokens presistence2019-11-14T14:52:52+01:00Matija ObrezaRemove OAuth tokens presistenceWe're using JWT, can we drop all OAuth token related code?We're using JWT, can we drop all OAuth token related code?2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/481Accession filter: Active records by default2019-11-20T19:46:57+01:00Matija ObrezaAccession filter: Active records by defaultChange behavior of `AccessionFilter` so that only active accessions are included by default.
This requires a new filter field `Set<Boolean> historic` so the user can specify `[true]`, `[false]` or `[true, false]`.
The empty set `[]` sh...Change behavior of `AccessionFilter` so that only active accessions are included by default.
This requires a new filter field `Set<Boolean> historic` so the user can specify `[true]`, `[false]` or `[true, false]`.
The empty set `[]` should convert to `[true]` before any processing takes place. (Maybe this can be done in the constructor?)
`[true, false]` translates to: Don't use filter on `historic`.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/480Descriptor image: Folder permissions2019-10-22T10:40:07+02:00Matija ObrezaDescriptor image: Folder permissionsUploading images for descriptors only works for Administrators.
The folder permissions are not set up properly. How it is done for Dataset files is a good example.Uploading images for descriptors only works for Administrators.
The folder permissions are not set up properly. How it is done for Dataset files is a good example.2.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/479API v2: Subsets and Datasets2019-10-27T09:08:51+01:00Matija ObrezaAPI v2: Subsets and DatasetsUpgrade controllers for subsets and datasets to v2 as described in genesys-pgr/genesys-server#473
Copy and update the unit tests.Upgrade controllers for subsets and datasets to v2 as described in genesys-pgr/genesys-server#473
Copy and update the unit tests.2.5Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/478API v2 /admin2019-11-15T08:25:38+01:00Matija ObrezaAPI v2 /adminUpgrade v1 /admin controllers to v2 using the approach documented in genesys-pgr/genesys-server#473
Copy and update the unit tests.Upgrade v1 /admin controllers to v2 using the approach documented in genesys-pgr/genesys-server#473
Copy and update the unit tests.2.5Maxym BorodenkoMaxym Borodenko