Genesys Website issueshttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues2023-09-05T11:26:35+02:00https://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1013Accession Traits tab updates2023-09-05T11:26:35+02:00Matija ObrezaAccession Traits tab updatesThe order of descriptor categories must be:
```
PASSPORT: Passport data,
ENVIRONMENT: Environment and site,
MANAGEMENT: Management data,
CHARACTERIZATION: Characterization,
EVALUATION: Evaluation,
ABIOTICSTRESS: Abiotic stress,
BIOTICS...The order of descriptor categories must be:
```
PASSPORT: Passport data,
ENVIRONMENT: Environment and site,
MANAGEMENT: Management data,
CHARACTERIZATION: Characterization,
EVALUATION: Evaluation,
ABIOTICSTRESS: Abiotic stress,
BIOTICSTRESS: Biotic stress,
MOLECULAR: Molecular marker,
```
1. Fix order of descriptor categories
1. Please check and update the **Traits** tab on mobile devices.2023.6Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1012Check if <ErrorBoundary works correctly2023-09-04T19:44:06+02:00Maksym TishchenkoCheck if <ErrorBoundary works correctlyThis is from discussion on https://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/merge_requests/1019#note_80419
Make sure that `<ErrorBoundary` behaves correctly and it properly catches all child component errors.This is from discussion on https://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/merge_requests/1019#note_80419
Make sure that `<ErrorBoundary` behaves correctly and it properly catches all child component errors.Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1011Overviews with Curation Type2023-09-02T06:28:40+02:00Matija ObrezaOverviews with Curation TypeThis is a simple ticket to add more overview groups to Geneys.
1. Add "Curation type" overview to Overview `/a/overview`.
2. Update institute details page `/wiews/XXXyyy` with additional Overviews:
- Biological status of accession
...This is a simple ticket to add more overview groups to Geneys.
1. Add "Curation type" overview to Overview `/a/overview`.
2. Update institute details page `/wiews/XXXyyy` with additional Overviews:
- Biological status of accession
- Provenance of material
- Type of Germplasm storage
- Curation type
- FAO WIEWS code of donor institute
- Breeder code
- Site of safety duplication
- Safety duplicated in Svalbard
- ITGPRFA Multi-lateral system
- Available for distribution2023.5Yevhenii PykhovYevhenii Pykhovhttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1010Bug in loading page of one accession2023-08-23T10:48:13+02:00Christelle RabilBug in loading page of one accessionWhen clicking of permalink of a single accession, an arror 404 is showing: https://www.genesys-pgr.org/a/e7fa695c-ea43-4608-a812-626b4da31085When clicking of permalink of a single accession, an arror 404 is showing: https://www.genesys-pgr.org/a/e7fa695c-ea43-4608-a812-626b4da31085Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1009Bug in Admin: Users2023-08-18T09:23:57+02:00Matija ObrezaBug in Admin: UsersI can't access Admin > Users on Sandbox. Please check.I can't access Admin > Users on Sandbox. Please check.2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1008Accession trait data2023-09-01T19:20:14+02:00Matija ObrezaAccession trait dataAdd a new tab "Traits" to accession browser. The tab **is only enabled** if the current filter includes one of `institute.code`, `taxonomy.genus` or `crop`. The tab does not have SSR support.
The new component first executes an API call...Add a new tab "Traits" to accession browser. The tab **is only enabled** if the current filter includes one of `institute.code`, `taxonomy.genus` or `crop`. The tab does not have SSR support.
The new component first executes an API call to */api/v1/datasets/accessions-datasets* with the existing accession filter in the request body. This returns a set of dataset `uuid`s. Next the code looks up the information of these datasets using */api/v1/datasets/list*. For each dataset, it fetches descriptor details using */api/v1/descriptor/list/details*. This allows us to build a `datasetDescriptors: Map<uuid, List<Descriptor>>` and a `descriptorDatasets: Map<uuid, List<Dataset>>` for lookups.
## Selecting trait descriptors
All available trait descriptors are displayed and can be toggled on and off, similar to configuring the *Subsetting Tool*:
![image](/uploads/d6df8cbec377c781a4c24a42d1bbdba2/image.png)
The body of each descriptor section displays (1) the names of datasets where descriptor is present and (2) the descriptor filter:
![image](/uploads/6cccd93fd59975e3c7a3e74f0e593333/image.png)
## Table
Below the descriptor selection we display a `<Table`. The table `configuration` uses the selected descriptors (toggled on) for columns and their renderers. The "My list" and "Accession" columns are always included, same as in our [searchable datasets](https://sandbox.genesys-pgr.org/datasets/ecfca747-36bd-478e-82f5-fd2d70911306/view).
## Loading table data
"Apply trait filters" button is in the section where descriptors are selected (above the table). No data is loaded until trait filters are applied.
The button fetches trait data from */api/v1/datasets/data* and submits the trait data filter in the body. This filter includes the accession filters:
```json
{
"accession": <ACCESSION FILTER>,
"observations": <TRAIT FILTERS>
}
```2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1007Quick download2023-09-01T19:49:06+02:00Matija ObrezaQuick downloadgenesys-pgr/genesys-server!799 adds a new endpoint to download a **CSV file** of the filtered accessions. It accepts a HTTP POST to `/api/v1/a/query` with the following form parameters:
- `_access_token` is the user's access token
- `se...genesys-pgr/genesys-server!799 adds a new endpoint to download a **CSV file** of the filtered accessions. It accepts a HTTP POST to `/api/v1/a/query` with the following form parameters:
- `_access_token` is the user's access token
- `select` the columns to include in the file
- `filter` the filter JSON object (as text)
The download limit is 1,000,000 records.
## UI
Add a button "Quick download". Please make all download buttons available only to logged in users.
When "Quick download" clicked, it opens a dialog with:
- Title: Download passport data for {} accessions in CSV format
- Body
- A list of labels with checkboxes for `uuid`, `instCode` (disabled, always on), `accessionNumber` (always on), `doi` (always on), `storage`, `duplSite`, `taxonomy.genus`, `taxonomy.species`
- The labels should reuse existing `t` names from `model:Accession`!
- The standard Download disclaimer
- Footer: "Download" button
"Download" must be placed in a HTML `<form method="POST" target=".../api/v1/a/query">` with the form parameters listed above.2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1006Datasets: Analyze tab2023-08-19T07:28:30+02:00Matija ObrezaDatasets: Analyze tabThe **Analyze** tab now shows all combinations of traits automatically. We need to give user more control over what to analyze.
On the **Analyze** tab, we need to prompt the user to pick the traits to compare. Let's add a new component ...The **Analyze** tab now shows all combinations of traits automatically. We need to give user more control over what to analyze.
On the **Analyze** tab, we need to prompt the user to pick the traits to compare. Let's add a new component `CompareTraits` that lets the user to **Select two traits to analyze** with two dropdowns that list (relevant) descriptors.
As the user changes their selection (as long as they select two descriptors), the chart comparing the two is displayed as it is displayed now. If the user picks "Row number/lateral florets" and "Lemma awn/hood" they get:
![image](/uploads/e1bd56758b88cf97f7966127feb8c2f8/image.png)
If only one descriptor is selected, then we display just the histogram of that trait.
## ... and while we're at it
Clicking on the heatmap chart should apply the **two** filters for that area.2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1005Datasets: Filter title t-function2023-08-11T12:12:34+02:00Matija ObrezaDatasets: Filter title t-functionThe component rendering filters applies `t` to the title provided. When that `title` contains a `:` as in the example below, the full title is no longer displayed.
Notice how **Awns:** is missing from the filter section:
![image](/upl...The component rendering filters applies `t` to the title provided. When that `title` contains a `:` as in the example below, the full title is no longer displayed.
Notice how **Awns:** is missing from the filter section:
![image](/uploads/4bef96c2e308b145959e27a13ef08851/image.png)
Please remove the use of `t(title)` and **make sure** the title coming to the component is already translated.2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1004Datasets: Chart legend2023-08-11T12:14:47+02:00Matija ObrezaDatasets: Chart legendThe screenshot from `https://sandbox.genesys-pgr.org/datasets/ecfca747-36bd-478e-82f5-fd2d70911306/overview` shows how the labels overflow the available space:
![image](/uploads/7fe16b37ef90ab41e1da0fc95a479e5d/image.png)
The better di...The screenshot from `https://sandbox.genesys-pgr.org/datasets/ecfca747-36bd-478e-82f5-fd2d70911306/overview` shows how the labels overflow the available space:
![image](/uploads/7fe16b37ef90ab41e1da0fc95a479e5d/image.png)
The better display would use a **Chart legend** that renders the **displayed** codes below the chart like we do for **scale descriptors**:
![image](/uploads/b4f5f967614d9ce40e445f2c572d6e31/image.png)
## Summary
The chart uses codes on X axis and they are displayed without slanting (just normal), and then **below the chart** we display the coding table for scale and for coded descriptors.
## And while we're at it
Please relabel "Count" on Y axis to "Accessions".2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1003Datasets: Click to apply a filter2023-08-14T20:28:07+02:00Matija ObrezaDatasets: Click to apply a filterAs I explore the data of `https://sandbox.genesys-pgr.org/datasets/ecfca747-36bd-478e-82f5-fd2d70911306/overview` I'd like to click a category (bar) and Genesys should apply the filter for the criteria I selected.
For example: in these ...As I explore the data of `https://sandbox.genesys-pgr.org/datasets/ecfca747-36bd-478e-82f5-fd2d70911306/overview` I'd like to click a category (bar) and Genesys should apply the filter for the criteria I selected.
For example: in these charts (one a histogram, one categorical)
![image](/uploads/2283d5aad15fdc8190f5f1978d74408f/image.png)
... so that when I click on a green bar of the histogram or chart, Genesys should apply that filter and show me the results (staying on the same page).
## While we're at it
If the `Descriptor` has `uom` (unit of measure) then it should be displayed in the chart and card as `The title and then in square brackets [${uom$}]`.
## Cards of the same size
![image](/uploads/55b64a29e664c1273e59ccacab6e0172/image.png)
The screenshot shows that the two `Card`s are not of the same height. Please fix that.2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1002Accession Curation type2023-08-04T19:29:19+02:00Matija ObrezaAccession Curation typegenesys-pgr/genesys-server!793 adds `curationType: string` to `Accession`.
Please add `<PropertyItem` before "Availability for distribution" to AccessionDetails.
Use the following translations of the `enum`:
- `FULL`: Fully curated
- ...genesys-pgr/genesys-server!793 adds `curationType: string` to `Accession`.
Please add `<PropertyItem` before "Availability for distribution" to AccessionDetails.
Use the following translations of the `enum`:
- `FULL`: Fully curated
- `PARTIAL`: Partly curated
- `ARCHIVED`: Archived
- `HISTORICAL`: Historical2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1001Ingest: Upgrade preview filters2023-08-03T10:04:07+02:00Matija ObrezaIngest: Upgrade preview filtersUpgrade Ingest Preview filters to react-hook-form. The same was done in genesys-pgr/genesys-ui!1008 for the public part.
The API supports a new `PreviewFilter#isAccessionMapped?: boolean` flag. Please add it to the ingest filters and us...Upgrade Ingest Preview filters to react-hook-form. The same was done in genesys-pgr/genesys-ui!1008 for the public part.
The API supports a new `PreviewFilter#isAccessionMapped?: boolean` flag. Please add it to the ingest filters and use the `AccessionHistoricFilter` (just allow for specifying different labels).2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/1000Overviews with TreeMap2023-07-27T13:47:49+02:00Matija ObrezaOverviews with TreeMapAdd `TreeMap` charts to **all** Overviews (accession, dataset, subset) like we do in Embedded Genesys. Also replace the `<PieCharts` on Insitute page with `<TreeMap`.
![image](/uploads/87729f614cba41c76eff7a9e7ae98b7b/image.png)
For ex...Add `TreeMap` charts to **all** Overviews (accession, dataset, subset) like we do in Embedded Genesys. Also replace the `<PieCharts` on Insitute page with `<TreeMap`.
![image](/uploads/87729f614cba41c76eff7a9e7ae98b7b/image.png)
For extra points add a click handler that adds the selected category to `filters` -- or in the case of institute page, opens the accessions of that category.2023.5Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/999Accession details with trait observations2023-07-24T18:44:28+02:00Matija ObrezaAccession details with trait observationsgenesys-pgr/genesys-server!776 implements a new endpoint to fetch trait observations for one accession.
After the `AccessionDetails` page loads, try to load observations, and if they are available, display a new section "Trait data" and...genesys-pgr/genesys-server!776 implements a new endpoint to fetch trait observations for one accession.
After the `AccessionDetails` page loads, try to load observations, and if they are available, display a new section "Trait data" and display the observations. If there is no trait data, then the section is not rendered.
In the first implementation, each observation is displayed as a simple `<div` that shows:
- trait descriptor title
- observation value (render depends on descriptor type)
- descriptor description
- dataset?2023.4Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/998Adding ACCENUMB as a filter of the trait datasets2023-08-15T06:22:17+02:00Christelle RabilAdding ACCENUMB as a filter of the trait datasetsIs it possible to add this as a filter directly, or if the genebanks add it twice in 2 column in the Excel file, then does one pick up as ACCENUMB and another one as a regular trait data descriptor that can be filtered as a text or numbe...Is it possible to add this as a filter directly, or if the genebanks add it twice in 2 column in the Excel file, then does one pick up as ACCENUMB and another one as a regular trait data descriptor that can be filtered as a text or number? That's what Miguel from CIAT tried to do in the latest COL003 dataset publication.2023.5Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/996Download Amphibian data2023-07-22T12:28:52+02:00Matija ObrezaDownload Amphibian datagenesys-pgr/genesys-server!782 adds support to generate Excel on the server. Please replace the current javascript-based "Download" of Amphibian data with a call to the API.genesys-pgr/genesys-server!782 adds support to generate Excel on the server. Please replace the current javascript-based "Download" of Amphibian data with a call to the API.2023.4Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/995Request: Copy accession data to clipboard2023-07-24T18:44:28+02:00Matija ObrezaRequest: Copy accession data to clipboardIn Dashboard, users would like to copy the requested accessions of one Subrequest to clipboard and bring the data to Excel.
Please add a "Copy to clipboard" button .In Dashboard, users would like to copy the requested accessions of one Subrequest to clipboard and bring the data to Excel.
Please add a "Copy to clipboard" button .Maksym TishchenkoMaksym Tishchenkohttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/994Admin: Adding a new OAuth client2023-07-06T15:16:07+02:00Matija ObrezaAdmin: Adding a new OAuth clientI am not able to `+` a new OAuth client:
![image](/uploads/c1c8d1e314e6268e5c07386c0ee7adb8/image.png)I am not able to `+` a new OAuth client:
![image](/uploads/c1c8d1e314e6268e5c07386c0ee7adb8/image.png)Yevhenii PykhovYevhenii Pykhovhttps://gitlab.croptrust.org/genesys-pgr/genesys-ui/-/issues/993Sandbox bug: genebank pages not loading or showing "undefined" error2023-07-17T10:33:42+02:00Christelle RabilSandbox bug: genebank pages not loading or showing "undefined" error![image](/uploads/a049cdb3e0d8f63ba3becba987bf087d/image.png)
![image](/uploads/b1e3c79f8eca904161cebde0b6c4c741/image.png)![image](/uploads/a049cdb3e0d8f63ba3becba987bf087d/image.png)
![image](/uploads/b1e3c79f8eca904161cebde0b6c4c741/image.png)Maksym TishchenkoMaksym Tishchenko