Genesys Backend issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues2020-01-28T16:52:42+01:00https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/501Admin user can create the same CMS articles;2020-01-28T16:52:42+01:00Kiril MorhalenkoAdmin user can create the same CMS articles;**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/admin/content" as admin user;
2. Click "+" button;
3. Enter to the "Slug" field "test";
4. Enter to the "Language" field "en";
5. Click "Back to article list";
6. Click "+" button;
7. ...**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/admin/content" as admin user;
2. Click "+" button;
3. Enter to the "Slug" field "test";
4. Enter to the "Language" field "en";
5. Click "Back to article list";
6. Click "+" button;
7. Enter to the "Slug" field "test";
8. Enter to the "Language" field "en";
9. Click "Back to article list";
10. Try to open one of created article;
or you can open "https://sandbox.genesys-pgr.org/admin/content/v2LYA5yzWq8" as admin and try to open one of articles;
**Expected result:**
User cann`t create two or more same articles. When user try to create article which already exist he should see snack bar "Article should be unique" or something like this;
**Actual result:**
User can create two or more same articles. Also if user try to open one of them request failed with status code 500;
![image](/uploads/a2fbfea7f5a62eae27be134226b85abc/image.png)
![image](/uploads/8e2e81dd046c7133944bb5a0528380c4/image.png)Maxym 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/499Text search filter doesn't work on the Dashboard catalog`s browse pages;2020-01-27T16:21:14+01:00Kiril MorhalenkoText search filter doesn't work on the Dashboard catalog`s browse pages;**Steps:**
1. Go to any catalog browse page
(
* "https://sandbox.genesys-pgr.org/dashboard/datasets"
or
* "https://sandbox.genesys-pgr.org/dashboard/descriptorlists"
)
2. Enter to the Text search filter some text (e.g. "qwerty");
3....**Steps:**
1. Go to any catalog browse page
(
* "https://sandbox.genesys-pgr.org/dashboard/datasets"
or
* "https://sandbox.genesys-pgr.org/dashboard/descriptorlists"
)
2. Enter to the Text search filter some text (e.g. "qwerty");
3. Click "Apply filters" button;
**Expected result:**
Search results should be match the query;
**Actual result:**
All available items is displayed as search results;
![image](/uploads/d5c5a8ec787708f6a3893955eb7c94f8/image.png)
![image](/uploads/5466910dd8c28f53d1c2daac7b757052/image.png)Maxym BorodenkoMaxym Borodenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/498Genebank can confirm the same request several times;2020-01-27T10:28:12+01:00Kiril MorhalenkoGenebank can confirm the same request several times;**Steps:**
1. Make a request to test genebank;
2. Confirm this request on your email;
3. Go to "https://sandbox.genesys-pgr.org/admin/requests" as admin user;
4. Open your request;
5. Click on the "Resend" button in the "Dispatched to" b...**Steps:**
1. Make a request to test genebank;
2. Confirm this request on your email;
3. Go to "https://sandbox.genesys-pgr.org/admin/requests" as admin user;
4. Open your request;
5. Click on the "Resend" button in the "Dispatched to" block two times;
6. Open genebank`s email (you should have 3 massages from Genesys);
7. Open the first email from Genesys;
8. Click on the link and confirm your request;
9. Open the second email from Genesys;
10. Click on the link and confirm your request;
**Expected result:**
Snack bar with message "Request is already validated or dispatched." should be displayed;
**Actual result:**
Any snack bar isn`t displayed;
![same_request_confirmation](/uploads/e7fb07d6895e4191ad4cac46849e28af/same_request_confirmation.gif)Maxym 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/490Full-text filter doesn`t work;2019-12-05T20:32:07+01:00Kiril MorhalenkoFull-text filter doesn`t work;**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/a";
2. Enter to the "Full-text" filter any text;
3. Apply filters;
**Expected result:**
Filter should be applied;
**Actual result:**
Request is failed
![image](/uploads/a0fb04e87898...**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/a";
2. Enter to the "Full-text" filter any text;
3. Apply filters;
**Expected result:**
Filter should be applied;
**Actual result:**
Request is failed
![image](/uploads/a0fb04e878986c79b067a7143d5dc3cc/image.png)Maxym 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/488DB query performance2020-04-09T15:14:42+02:00Kiril MorhalenkoDB query performanceHaving the default filter `historic: false` affects database query performance.
**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/a/overview";
2. Apply filter "Excluding Holder: GBR140";
3. Click on the "Accessions" tab;
**Expected ...Having the default filter `historic: false` affects database query performance.
**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/a/overview";
2. Apply filter "Excluding Holder: GBR140";
3. Click on the "Accessions" tab;
**Expected result:**
User is on the `/a` page and filters are applied;
**Actual result:**
Request is failed after 19.99 sec;
![requset_is_canceled](/uploads/e5773f2073b8d22b7a455e3655ff8403/requset_is_canceled.gif)Anastasiia KarasAnastasiia Karashttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/487Error "Request failed with status code 500" happens if user apply filters fro...2019-11-25T10:01:44+01:00Kiril MorhalenkoError "Request failed with status code 500" happens if user apply filters from blocks on the /a/overview page;**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/a/overview";
2. Apply filter "Not specified" from block "Type of Germplasm storage" and wait until filters will be applied;
3. Apply filter "India" from block "Provenance of material" ...**Steps:**
1. Go to "https://sandbox.genesys-pgr.org/a/overview";
2. Apply filter "Not specified" from block "Type of Germplasm storage" and wait until filters will be applied;
3. Apply filter "India" from block "Provenance of material" and wait until filters will be applied;
4. Apply filter "Wild" from block "Biological status of accession" and wait until filters will be applied;
![image](/uploads/3f4c87170d2195acecccfd19c03cb7cc/image.png)
**Expected result:**
All applied filter should be applied;
**Actual result:**
Error "Request failed with status code 500" happens
![image](/uploads/89e334fd17ba8ed8af5462efe76b1c1e/image.png)Viacheslav PavlovViacheslav Pavlovhttps://gitlab.croptrust.org/genesys-pgr/genesys-server/-/issues/486Accession: Additional validators2019-12-05T20:54:43+01:00Kiril MorhalenkoAccession: Additional validatorsWe have 23 accessions with incorrect data in Sandbox. You will be able to see this records by link https://sandbox.genesys-pgr.org/a/overview/v2LYdd6b61R:
![image](/uploads/9035f6fb01ddf1b46372d1b720ebeee7/image.png)
## Additional vali...We have 23 accessions with incorrect data in Sandbox. You will be able to see this records by link https://sandbox.genesys-pgr.org/a/overview/v2LYdd6b61R:
![image](/uploads/9035f6fb01ddf1b46372d1b720ebeee7/image.png)
## Additional validation required
Please add data model validation to fields:
- `storage`: https://www.genesys-pgr.org/documentation/basics#mcpd-storage
- `sampStat` https://www.genesys-pgr.org/documentation/basics#mcpd-sampstat
Only the values listed are allowed.
Maxym BorodenkoMaxym Borodenkohttps://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/484Database connection pool empty2019-11-11T15:06:43+01:00Matija ObrezaDatabase connection pool emptySomething is using up all available database connections on https://api.sandbox.genesys-pgr.org
```
2019-11-11T09:47:16.229988776Z Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [qtp1343441044-154] Timeout: Pool empty. U...Something is using up all available database connections on https://api.sandbox.genesys-pgr.org
```
2019-11-11T09:47:16.229988776Z Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [qtp1343441044-154] Timeout: Pool empty. Unable to fetch a connection in 30 seconds, none available[size:50; busy:50; idle:0; lastwait:30000].
2019-11-11T09:47:16.229993290Z at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:674)
2019-11-11T09:47:16.229997383Z at org.apache.tomcat.jdbc.pool.ConnectionPool.getConnection(ConnectionPool.java:188)
2019-11-11T09:47:16.230001418Z at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:128)
2019-11-11T09:47:16.230005637Z at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:139)
2019-11-11T09:47:16.230010020Z at org.hibernate.internal.AbstractSessionImpl$NonContextualJdbcConnectionAccess.obtainConnection(AbstractSessionImpl.java:380)
2019-11-11T09:47:16.230014357Z at org.hibernate.engine.jdbc.internal.LogicalConnectionImpl.obtainConnection(LogicalConnectionImpl.java:228)
2019-11-11T09:47:16.230018580Z ... 140 more
```https://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 Borodenko