Genesys Website issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues2024-01-08T18:30:46+01:00https://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1040Bug: Histogram bin not displayed2024-01-08T18:30:46+01:00Matija ObrezaBug: Histogram bin not displayedhttps://www.genesys-pgr.org/datasets/ae9cac23-86c8-4aef-b67b-0a99cfc067d8/overview has 1780 accessions for one bin, but the bin is not rendered (it is, but it has a width of `0`).
![image](/uploads/23dc994d7b6709539e10a4f6e3a8cf94/image...https://www.genesys-pgr.org/datasets/ae9cac23-86c8-4aef-b67b-0a99cfc067d8/overview has 1780 accessions for one bin, but the bin is not rendered (it is, but it has a width of `0`).
![image](/uploads/23dc994d7b6709539e10a4f6e3a8cf94/image.png)
![image](/uploads/77c8d588ad7494c28c4087ac4abcea37/image.png)Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1039WIEWS code MKD007 not found in Sandbox but is available in Production2024-01-08T15:08:50+01:00Christelle RabilWIEWS code MKD007 not found in Sandbox but is available in ProductionI'm uploading WP4 data in Sandbox and getting an error for MKD007, the page is present in Production but shows this in Sandbox:
![Screenshot_2024-01-08_at_14.24.36](/uploads/01213906b608ece883b3761eca2f3a52/Screenshot_2024-01-08_at_14.2...I'm uploading WP4 data in Sandbox and getting an error for MKD007, the page is present in Production but shows this in Sandbox:
![Screenshot_2024-01-08_at_14.24.36](/uploads/01213906b608ece883b3761eca2f3a52/Screenshot_2024-01-08_at_14.24.36.png)Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1038Upgrade dependencies2024-01-08T11:20:09+01:00Maksym TishchenkoUpgrade dependenciesupgrade dependencies with `yarn upgrade`upgrade dependencies with `yarn upgrade`Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1037Accession images: download passport data2024-01-10T18:06:42+01:00Matija ObrezaAccession images: download passport data@erojas suggests two features in Genesys for “Accession Images” for example for the case of:
https://www.genesys-pgr.org/a/images/v2m8a7gl063
- Add total of images not only total of accessions (in first red arrow)
- Add Download MCPD...@erojas suggests two features in Genesys for “Accession Images” for example for the case of:
https://www.genesys-pgr.org/a/images/v2m8a7gl063
- Add total of images not only total of accessions (in first red arrow)
- Add Download MCPD accessions for the images of the list not only Download Images (second red arrow).
![image](/uploads/dfad40321e2a6771f120d38f5dd0741b/image.png)2024.1Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1036Removing image from descriptor in draft2024-01-10T07:43:27+01:00Christelle RabilRemoving image from descriptor in draftAfter uploading an image to a descriptor (for example: https://sandbox.genesys-pgr.org/dashboard/descriptors/ebea3288-59d9-4857-9139-219418b14d0a/edit ) we cannot then remove it, and an error message shows:
![Screenshot_2023-12-13_at_10...After uploading an image to a descriptor (for example: https://sandbox.genesys-pgr.org/dashboard/descriptors/ebea3288-59d9-4857-9139-219418b14d0a/edit ) we cannot then remove it, and an error message shows:
![Screenshot_2023-12-13_at_10.22.47](/uploads/b84c4e47b5ab8f52b5cc28abe267fb2f/Screenshot_2023-12-13_at_10.22.47.png)Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1035Curation Type filters2023-12-14T10:17:44+01:00Christelle RabilCuration Type filtersPlease add the Curation Type filters in the filters pane. Note that Historical is already a Yes/No filter category, and also an entry of Curation Type.Please add the Curation Type filters in the filters pane. Note that Historical is already a Yes/No filter category, and also an entry of Curation Type.Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1034Institute: Include KPI2023-12-13T17:51:52+01:00Matija ObrezaInstitute: Include KPIWe currently display KPI charts and tables in the dashboard and admin pages. In this issue we make some of the KPIs directly accessible on Institute pages. The idea is that when user opens an [institute page](https://www.genesys-pgr.org/...We currently display KPI charts and tables in the dashboard and admin pages. In this issue we make some of the KPIs directly accessible on Institute pages. The idea is that when user opens an [institute page](https://www.genesys-pgr.org/wiews/NGA039) there is a button that replaces the page contents with a display of KPIs (similar to how "Find similar" accessions works).
## Displayed metrics
For every metric we only show values only for **active accessions** (i.e. `historic == false`).
For every metric we show: (4) the latest values, (3) start of this `year`, (2) start of `year - 1` and (1) start of `year - 2`. We do this type of display when **comparing KPI runs**:
![image](/uploads/a0e7ded89d764c4b20255fefce6cc406/image.png)
Using the example above, `institute.code` and `accession.historic` columns are our filters and are not included in tables.
The following KPIs (available in sandbox and production) are displayed:
### Number of accessions `accession.states`
This summarizes numbers by `crop` and has columns for: `crop`, 1 Jan `year - 2`, 1 Jan `year - 1`, 1 Jan `year`, `today`.
### Fully curated accessions `accessions.curation`
Same table as above: `institute.code`, `accession.historic == false`, and with filter for `curation == FULL`.
### Number of accessions available for distribution (using `accession.states`)
The filters are: `institute.code`, `accession.historic == false`, `mls == true`, `availability == true`.
Summarizes numbers by `crop` and has columns for: `crop`, 1 Jan `year - 2`, 1 Jan `year - 1`, 1 Jan `year`, `today`.
### Safety-duplication of seed accessions `accession.seed.duplsite`
Sandbox data:
![image](/uploads/e29b2d96514cfa5c08f32619c0583360/image.png)
### Safety-duplication of clonal accessions `accession.clonal.duplsite`
Same as one up.
### PDCI table
The filters are: `institute.code`, `accession.historic == false`.
Table display is the same as above: crop + four columns for time.
### Number of requests from Genesys `institute.requests.annual`
The filter is: `institute.code` only. Table displays: `state` + the four columns for time.
Note: `institute.requests.annual` is a new KPI, data before today is not available (will be 0).2024.1Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1033Editing descriptor in review2023-11-30T16:49:41+01:00Christelle RabilEditing descriptor in reviewYonas reported this message after pressing the edit buttuon on descriptors in review :
>Something went wrong
>
>A bug caused this rapid unscheduled disassembly of Genesys. Please refresh the page and retry your action. If that does not ...Yonas reported this message after pressing the edit buttuon on descriptors in review :
>Something went wrong
>
>A bug caused this rapid unscheduled disassembly of Genesys. Please refresh the page and retry your action. If that does not help, please contact Genesys support and let them know about the problem.
>
>Error: Cannot be un-published. More than 24 hours have passed since the publication.
>URL: https://www.genesys-pgr.org/descriptors/41d610d1-b1ba-4aae-8f1d-da38ee12f37f
(I also tried on my side, and after clearing cache but also same message as above)
cc: @mobrezaVladyslava MokliakVladyslava Mokliakhttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1032Dataset stepper: List of traits2023-11-28T11:00:43+01:00Matija ObrezaDataset stepper: List of traitsIn the step "6. Organize trait descriptors" please add a button "Check for unmapped descriptors". The button call the API that:
1. Checks which descriptors are mapped for this dataset in Amphibian (gets their `uuid`s)
2. Removes descrip...In the step "6. Organize trait descriptors" please add a button "Check for unmapped descriptors". The button call the API that:
1. Checks which descriptors are mapped for this dataset in Amphibian (gets their `uuid`s)
2. Removes descriptors from the Dataset that are not in Amphibian
3. Adds descriptors that are in Amphibian to the Dataset2023.9Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1031Curation Type overviews2023-12-06T11:42:28+01:00Matija ObrezaCuration Type overviewshttps://sandbox.genesys-pgr.org/a/overview/v285k6eKJq0 shows overviews for Curation Type:
- PARTIAL .. 7
- ARCHIVED .. 6
- FULL .. 6
- HISTORICAL .. 4
- Not specified .. 30,422
Clicking any of the numbers does not seem to work correctl...https://sandbox.genesys-pgr.org/a/overview/v285k6eKJq0 shows overviews for Curation Type:
- PARTIAL .. 7
- ARCHIVED .. 6
- FULL .. 6
- HISTORICAL .. 4
- Not specified .. 30,422
Clicking any of the numbers does not seem to work correctly. Please investigate and fix.Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1030Updating file repository metadata2023-12-06T05:42:02+01:00Matija ObrezaUpdating file repository metadata@macosta reports he's getting an error message when updating the images metadata with the CSV file:
![image](/uploads/cb6cea39abbcea74b06a126d79ae94c8/image.png)
Please investigate and fix.@macosta reports he's getting an error message when updating the images metadata with the CSV file:
![image](/uploads/cb6cea39abbcea74b06a126d79ae94c8/image.png)
Please investigate and fix.Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1029Do not require PID for making requests2024-01-11T18:48:12+01:00Matija ObrezaDo not require PID for making requests@macosta and collagues from @1cgiar/palmira propose to make it easier for users to make requests for material:
> Allowing users regardless of having a registration in Easy-SMTA, to make a request for material. This is because not all ge...@macosta and collagues from @1cgiar/palmira propose to make it easier for users to make requests for material:
> Allowing users regardless of having a registration in Easy-SMTA, to make a request for material. This is because not all genebanks routinely have the Easy-SMTA system in place and many users are not familiar with the system and registration is not easy to do, in other banks they must help customers to register.
We have support for *Internal requests* that do not require PID and the associated form. This form will become the default form for users to fill out.
## Changes to Genesys
On the UI we treat all requests as `internalRequest` which will skip PID validation on the backend.
![image](/uploads/4ae340250c88dd9269f62a2476bb8c40/image.png)
The form uses `EasySMTAUserData` data model, but it does not reflect the one from the server and needs updating. See https://gitlab.croptrust.org/genesys-pgr/genesys-server/-/blob/main/src/main/java/org/genesys/server/service/EasySMTA.java
1. Convert the form to `react-hook-form`.
1. Force `internalRequest = true` and show the full "Requestor information" form
2. Update form fields:
- Fields: email, first name, last name stay. Move telephone after last name.
- `address` "Address" (required)
- `country` "Country" (required)
- Add radio select `userType` "Type of request": `in` "This is a personal request" and `or` "This request is related to my work"
- If user selected `userType === or`, then enable the section for "Organization" data:
- `orgName` "Organization name" (required if `userType === or`)
- `orgAddress` "Organization address" (required if `userType === or`)
- `orgCountry` "Organization country" (required if `userType === or`)
- Add fields`aoName` and `aoSurname` for name and last name of the "Authorized official"
- Add `aoEmail` "Email of the authorized official"
- Add section "Shipping address":
- If user `userType === or` show a checkbox `useOrgAddress` "Use organization address". When checked, the inputs in this section are disabled.
- If user `userType === in` show checkbox `useMyAddress` "Use my address". When checked, the inputs in this section are disabled.
- Add field `shipAddress` "Shipping address" (3 lines, required)
- Add field `shipCountry` "Country" (required)
- Add field `shipTelephone` "Contact phone number"
3. Convert country code component from autocompleter to a dropdown with all options (active countries only)
4. Require some text to be present in the **Notes** field
3. ~~Add "Direct use" to type of "Use of material"~~
Before the form is sent to the API the following processing must be done:
1. Set `internalRequest = true`
3. If `userType === in` remove `orgAddress`, `orgCountry`, `orgName` from JSON (set them to `undefined`)
2. If `(userType === or && !useOrgAddress) || (userType === in && !useMyAddress)` then set `shipAddrFlag = 'd'` otherwise remove all `shipXxx` fields from JSON2024.1Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1028Uploading descriptor definitions as CSV2023-11-13T10:04:13+01:00Christelle RabilUploading descriptor definitions as CSVWhen admins try to copy-paste descriptor definitions from the Genesys catalog template, an error message shows, and the descriptors do not get uploaded:
![image](/uploads/a44f4506396cc98d23845134e857d44a/image.png)
This is in Dashboard...When admins try to copy-paste descriptor definitions from the Genesys catalog template, an error message shows, and the descriptors do not get uploaded:
![image](/uploads/a44f4506396cc98d23845134e857d44a/image.png)
This is in Dashboard > Catalog > Descriptor lists > add new one > Step 2
cc: @mobrezaMaksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1027Webpack 52024-03-04T12:10:17+01:00Matija ObrezaWebpack 5We're ready for `webpack@5` -- the migration was done previously for `ggce-web`, so this should be quite straightforward.We're ready for `webpack@5` -- the migration was done previously for `ggce-web`, so this should be quite straightforward.2023.8Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1026Browsing accessions with no images2023-10-27T16:55:29+02:00Matija ObrezaBrowsing accessions with no imagesWhen there are **no images** matching the filters, Genesys displays:
![image](/uploads/1282408b15a9cff8f1385b84820a3332/image.png)
Please include an `<Alert` saying `No accession images available for your filters.`When there are **no images** matching the filters, Genesys displays:
![image](/uploads/1282408b15a9cff8f1385b84820a3332/image.png)
Please include an `<Alert` saying `No accession images available for your filters.`2023.8Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1025Accession filters with suggested country2023-12-12T17:42:54+01:00Matija ObrezaAccession filters with suggested country`AccessionFilters` demands an ISO-3 code for the country of holding instute:
![image](/uploads/929ab443d8a0a683358119fb09662c8e/image.png)
## Improvement
Use the autocompleter endpoint (@ahrybeniuk can advise) to retrieve the list of ...`AccessionFilters` demands an ISO-3 code for the country of holding instute:
![image](/uploads/929ab443d8a0a683358119fb09662c8e/image.png)
## Improvement
Use the autocompleter endpoint (@ahrybeniuk can advise) to retrieve the list of options **for currently applied filters** and render a dropdown with country names.
It might make sense to display `<code>{ code3 }</code> { name }` in the dropdown to help users understand the ISO3 country codes.
We are already doing this for *Provenance of material*:
![image](/uploads/1074ab54b8ffe8b7facaf7dcaf1f98e3/image.png)2023.9Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1024Institute names as labels for INSTCODE2023-12-05T15:13:35+01:00Matija ObrezaInstitute names as labels for INSTCODEThis ticket is to use **Institute names** instead of `INSTCODE`, or in addition to `INSTCODE`: `<code>{ code }</code> { name }`
## Filters
The accession filters should display user-friendly institute names:
![image](/uploads/29827eaa1...This ticket is to use **Institute names** instead of `INSTCODE`, or in addition to `INSTCODE`: `<code>{ code }</code> { name }`
## Filters
The accession filters should display user-friendly institute names:
![image](/uploads/29827eaa151ec26a6587b152f94d8345/image.png)
We already have a *decoder* in `ui-express/src/actions/decoder.ts` that takes care of partner names and we are taking care of **country code > name**.
Can we use the same approach for `INSTCODE`?
Don't change the field label *Institute code* in the filter.
## Overviews
We are already decoding `institute.code3` to country names in the **Overview**:
![image](/uploads/74be354612891f9e59f24bf0aa8e8548/image.png)
Please use the same logic to convert `INSTCODE` to `<code>{ code }</code> { name }`.
# Implementation
The decoder **must not** make 100s of requests (one for each institute). It is based on Redux and has to be implemented so that
it collects the codes, then makes a single request to retrieve institute data for those codes and put the mappings to state.
Any other missing mappings need to be handled in a separate request, maybe a timeout-based approach will work best.
If a code can't be decoded, then just use `INSTCODE`.2023.8Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1023Country page bugs2023-12-04T10:16:37+01:00Matija ObrezaCountry page bugsThe "Country details" page (e.g. https://sandbox.genesys-pgr.org/iso3166/AUS) does not render overviews provided by the API and only renders the species:
![image](/uploads/88ff767af8e4b625bc37547d6657a819/image.png)
```json
{
"overvie...The "Country details" page (e.g. https://sandbox.genesys-pgr.org/iso3166/AUS) does not render overviews provided by the API and only renders the species:
![image](/uploads/88ff767af8e4b625bc37547d6657a819/image.png)
```json
{
"overview": {
"taxonomy.genusSpecies": {
"terms": [
{
"term": "Triticum aestivum",
"count": 8135
},
{
"term": "Trifolium sp.",
"count": 3401
},
{
"term": "Hordeum vulgare",
"count": 2396
},
{
"term": "Medicago sp.",
"count": 1927
},
{
"term": "Pisum sativum",
"count": 1108
},
{
"term": "Avena sativa",
"count": 1095
},
{
"term": "Festuca sp.",
"count": 873
},
{
"term": "Glycine max",
"count": 806
},
{
"term": "Lotus sp.",
"count": 729
},
{
"term": "Zea mays",
"count": 524
}
],
"total": 53756,
"other": 32762,
"missing": null
},
"institute.code": {
"terms": [
{
"term": "AUS167",
"count": 13428
},
{
"term": "AUS165",
"count": 10997
},
{
"term": "GBR004",
"count": 8473
},
{
"term": "RUS001",
"count": 3031
},
{
"term": "KEN212",
"count": 2137
},
{
"term": "USA029",
"count": 1819
},
{
"term": "USA033",
"count": 1076
},
{
"term": "USA016",
"count": 941
},
{
"term": "TWN001",
"count": 865
},
{
"term": "LBN002",
"count": 814
}
],
"total": 53756,
"other": 10175,
"missing": null
},
"institute.country.code3": {
"terms": [
{
"term": "AUS",
"count": 24425
},
{
"term": "GBR",
"count": 9648
},
{
"term": "USA",
"count": 6047
},
{
"term": "RUS",
"count": 3031
},
{
"term": "KEN",
"count": 2176
},
{
"term": "TWN",
"count": 865
},
{
"term": "LBN",
"count": 814
},
{
"term": "ETH",
"count": 772
},
{
"term": "MEX",
"count": 694
},
{
"term": "ITA",
"count": 548
}
],
"total": 53756,
"other": 4736,
"missing": null
},
"mlsStatus": {
"terms": [
{
"term": "true",
"count": 17900
},
{
"term": "false",
"count": 9742
}
],
"total": 53756,
"other": 0,
"missing": 26114
},
"available": {
"terms": [
{
"term": "true",
"count": 13491
},
{
"term": "false",
"count": 6338
}
],
"total": 53756,
"other": 0,
"missing": 33927
},
"taxonomy.genus": {
"terms": [
{
"term": "Triticum",
"count": 8708
},
{
"term": "Trifolium",
"count": 4405
},
{
"term": "Medicago",
"count": 2804
},
{
"term": "Glycine",
"count": 2599
},
{
"term": "Hordeum",
"count": 2537
},
{
"term": "Avena",
"count": 1647
},
{
"term": "Pisum",
"count": 1122
},
{
"term": "Acacia",
"count": 1062
},
{
"term": "Festuca",
"count": 924
},
{
"term": "Vigna",
"count": 855
}
],
"total": 53756,
"other": 27093,
"missing": null
}
}
}
```
## Buttons
Also add "Browse" and "Overview" buttons like on Network/Institute pages (see #1021):
![image](/uploads/3eb1f805732583db2e02a225b9c40d0d/image.png)2023.8Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1022My List as Table2023-10-27T16:59:04+02:00Matija ObrezaMy List as TableAdd the option to use `<Table` for **My List** of accessions. Also introduce FAB as described in #1020.
**Only the "Request for material"** button must remain in the header. It should have the primary color (as "Download ZIP" now).
![i...Add the option to use `<Table` for **My List** of accessions. Also introduce FAB as described in #1020.
**Only the "Request for material"** button must remain in the header. It should have the primary color (as "Download ZIP" now).
![image](/uploads/4bfd07d1d4b5dfe09d66bc3ee37068b7/image.png)
The default display (table or cards) needs to work the same as for `/a` and use the same setting.
When rows are selected, the FAB action is "Remove".
Take note that highligting of rows in `/sel` must work differently (because they are all `selected`!) -- see commit 5d198fff.
~~And make sure that the top navigation uses the **wide display** on `/sel`.~~ Sorry, that's done.2023.8Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1021Browse and overview buttons for data provider2023-10-26T18:28:40+02:00Matija ObrezaBrowse and overview buttons for data providerPlease add "Browse" and "Overview" buttons to the Data Provider page:
![image](/uploads/510b4864161911a04b82aa1cc9a1740e/image.png)
They should look the same as for a single Institute:
![image](/uploads/3e860e98638fb942b82aa02b19c3b8d...Please add "Browse" and "Overview" buttons to the Data Provider page:
![image](/uploads/510b4864161911a04b82aa1cc9a1740e/image.png)
They should look the same as for a single Institute:
![image](/uploads/3e860e98638fb942b82aa02b19c3b8d0/image.png)
We apparently already have this button for Networks, but not for **Crops** where "Overview" is missing. Please add it:
![image](/uploads/83a8e3a77da8e5728ac9ccdde9da510f/image.png)2023.8Maksym TishchenkoMaksym Tishchenko