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updated docs for specimen and search
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@SachinPawaskarUNO
SachinPawaskarUNO committed Jan 1, 2024
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46 changes: 45 additions & 1 deletion docs/user-guide/modules/specimens/specimens.md
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Expand Up @@ -45,7 +45,31 @@ Once these details are filled and the specimen is saved, a new specimen with an
1. The toolbar shows the options to the Edit/Save button and the Expand/Collapse button.
2. The Details button lists all specimen associations.

![](media/specimen-view.png)
![View and Edit Specimen](media/specimen-view.png)

> The screen fields are shown below. Fields in bold are required.
Attributes |Data Type |Size | Validation Rule | Required/Optional
--------------------|---------------|-----------|------------------------------------------------------------------------------| -------------
**Accession** |String |32 chars |Can only contain letters, numbers, dash and space and should have min 3 chars | Required
Provenance1 |String |32 chars |Can only contain letters, numbers, dash and space | Optional
Provenance2 |String |32 chars |Can only contain letters, numbers, dash and space | Optional
**Designator** |Alphanumeric |32 chars |Can only contain letters and numbers | Required
**Bone** |Id |id |valid bones via dropdown | Required
**Side** |String |8 chars |valid sides via dropdown (Left, Right, Middle, Unsided) | Required
**Completeness** |String |8 chars |valid completeness via dropdown (Complete, Incomplete) | Required
Measured |Boolean | |true/false toggle | Optional
DNA Sampled |Boolean | |true/false toggle | Optional
Isotope Sampled |Boolean | |true/false toggle | Optional
Inventory Completed |Boolean | |true/false toggle | Optional
Reviewed |Boolean | |true/false toggle | Optional
CT Scanned |Boolean | |true/false toggle | Optional
X-ray Scanned |Boolean | |true/false toggle | Optional
3D Scanned |Boolean | |true/false toggle | Optional
Individual Number |String |32 chars |can only contain letters, numbers, dash and space | Optional
Remain Status |String |16 chars |valid sides via dropdown (In Lab, Released) | Optional

Click "Save" When you are done making changes.

A specimen can be deleted by clicking on the delete icon and then confirming the deletion in the pop-up.

Expand Down Expand Up @@ -81,6 +105,26 @@ The fields to create a new bone group are:
- Taphonomy

The bolded fields are required. Once you have created a new bone group, you can edit the fields and click "Save" to update the bone group.

Attributes |Data Type |Size |Validation Rule | Required/Optional
------------------------| ------------- | --------------|------------------------------------------------------------------------------| -------------
Bone Group |String |64 chars |can only contain letters | Required
Bone Group Id |String |64 chars |valid UUID, auto generated | Required
**Side** |String |8 chars |valid sides via dropdown (Left, Right, Middle, Unsided) | Required
**Completeness** |String |8 chars |valid completeness via dropdown (Complete, Incomplete) | Required
**Accession** |String |32 chars |can only contain letters, numbers, dash and space and should have min 3 chars | Required
Provenance1 |String |32 chars |can only contain letters, numbers, dash and space | Optional
Provenance2 |String |32 chars |can only contain letters, numbers, dash and space | Optional
**Starting Designator** |Alphanumeric |32 chars |can only contain letters and numbers | Required
**Bone** |Id |id |valid bones via dropdown | Required

Once you have created a new bone group, you can edit the fields and click "Save" to update the bone group.

!!! tip

When creating specimens via bone groups, you only have to specify the starting designator and CoRA will automatically create the specimens
with that starting designator and increment it for subsequent specimens within the bone group.


![](media/create-new-bone-group.gif)

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72 changes: 72 additions & 0 deletions docs/user-guide/search/index.md
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Expand Up @@ -34,6 +34,78 @@ the user with the most appropriate or valid search options for the selected proj

## Specimen Search

The easiest way to search for specimens is to use the top search bar in the nav bar.
To complete a search, first select the project you wish to search on the left-most select field, you will only be able to view projects which are assigned to your user profile.

![SE Search](../../assets/screenshots/specimens/topNavBar.png)

![SE Project Categories](../../assets/screenshots/specimens/projectCategories.png)

By default, "Bone" is selected as the search option. Select the desired search category before typing your search text into the search bar. Then click the magnifying glass to execute your search.

![SE Search Categories](../../assets/screenshots/specimens/searchCategories.png)

Once you complete your search, you are taken to the Specimens search screen. The following columns are visible for all the specimens search:

- Key
- Bone
- Side
- Bone Group
- Individual Number
- DNA Sampled
- Mito Sequence Number
- Measured
- Isotope Sampled
- Clavicle Triage
- CT Scanned
- Xray Scanned

There are some columns which are not displayed at the screen but can be made visible by checking the column visibility section. The names of those columns are given below:
- Inventoried
- Reviewed
- Inventoried By
- Inventoried At
- Reviewed By
- Reviewed At
- Created By
- Created At
- Updated By
- Updated At


![SE Search Results](../../assets/screenshots/specimens/seSearch.gif)

On this page you can filter how many results are shown per page, as well as search the results.
To view the details of a skeletal elements, click on the key in the search results. You can also export the search results in Excel and PDF format.

### Search Options
Two search options are available to the user inside the User Profile Project tab.

![Search Option View](../../assets/screenshots/specimens/searchOption.png)

*Client-Side Pagination - **Ideal for small projects***

**Max Search Limit 500**

![Old Search View](../../assets/screenshots/specimens/oldSearch.png)

The server renders all results queried from the project search bar request, allowing the user to paginate and search through the entire response. Limitations with this search options, include longer response times or application overload for projects with large sets of data.

*Server-Side Pagination (Default) - **Ideal for large projects***

**Max Search Limit 250**

![New Search View](../../assets/screenshots/specimens/newSearch.gif)

The server will render only the selected quantity of data provided by show rows options at the top left corner of the page.

![Show Row View](../../assets/screenshots/specimens/showRows.png)

Each tab will generate a new call to the server and retrieve the next set of data. This search option is ideal for project with larger sets of data. Search result filter is not available with this option.

![Search Tabs View](../../assets/screenshots/specimens/searchPagination.png)

---------------

## DNA Search

Expand Down

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