---
title: "Assay Manager v3.2.1.2"
canonical: "https://servicedesk.maxgeo.com/space/DS/2185168080/Assay%20Manager%20v3.2.1.2"
format: markdown
---
*This guide provides an overview of the Assay Manager module, covering how to query, manage and review assay batches. It includes step-by-step instructions for using filters, updating batch statuses, and setting QC rules. User roles and permissions are also outlined to help users understand their access and responsibilities. Ideal for anyone managing assay data in DataShed5.*
Table of Contents
> Macro (toc)
## Assay Loading Workflow
The Assay Manager module provides the ability to query batches loaded, process, analyse, approve and report on assay batches.
Click on Assay Manager to open this module. This module is available for all users, but user role restrictions do apply depending on your database user security level.
The Assay Manager page displays the Assay Manager Filters, a Multi View option and the Admin menu button.
> ℹ️ **Note:** The Admin menu is only available for users with **SysAdmin** or **User Plus** security levels. SysAdmin users can access ALL Admin Menu options. User Plus users can access Library Tables only.
## Security Levels:
### SysAdmin, UserPlus and User
The following details all the functions that will be available to a user that has a security level assigned to them of Sys Admin, User Plus or User
---
## > Macro (anchor)
Assay Manager Filters
Assay Manager Filtering will appear allowing users to select filters to apply on assays based on the following options.
- **Scheme Filter:** This is a single select drop down list of imported schemes. Assays is the default scheme set, with options for **Assay**,** Historical, Hyperspectral**, **Water** and **XRF**.
- **Date Range Filter:** Is a single select drop down list which allows users to select date periods. "**Current Week**" is selected by default. This filter allows users to filter assays based on the Load Date from the Assay Batch table.
- **Date From & Date To:** Allows users to filter assays based on the Load Date from the Assay Batch table.
- **Batch Status:** Is a multiple select drop down list of items from AssayBatchStatus. "**All Batch Status**" is selected by default.
- **Users: **A multiple select drop down list of users that have loaded data, selected from Assay Batch table for the selected Scheme and Batch Status. All Users is selected by default.
- **Labs:** A multiple select drop down list with Lab Codes from Assay Batch for the selected Scheme, Date Range, Users and Batch Status. All Labs are selected by default.
- **Batches:** A multiple selection drop down list of batch numbers available for selected Scheme, Data Range, Users and Batch Status. All Batches are selected by default.
- After selecting the filters, click the "**Apply**" button to see the list of components for the selected filter criteria.
## > Macro (anchor)
Assay Manager Components
The Assay Manager module consists of the standard components - Batch List, Unmerged Assay Results, Assay Batch Header, Assay Batch Details, Unmerged Assay Results, QC Results, Batch Approval and Assay Stored Procedures.
### > Macro (anchor)
Batch List
The Batch List will display filtered data from the Assay Batch table. The Batch List has a Batch status field, the batch status is assigned to a batch on importing to the system. The following details the batch status values that can be assigned.
- **Accepted:** when all QC Rules pass the batch will be set to **ACCEPTED**.
- **New:** when a file has been imported but is **UNMERGED.**
- **Rejected:** when all QCRules fail the batch will be set to **REJECTED**.
- **Queried:** when one or more rules but not all rules fail, the batch will be set to **QUERIED**.
- **QC not applied:** when no QC Policy is assigned to a batch, the batch will be set to **QC_NA**.
- **Unmerged:** If a batch has unmerged data, the batch will be set to **UNMERGED.**
This Batch List has a **Process Batch** and **Delete** option available in the first column for SysAdmin & User Plus users only.
**Process Batch:** When SysAdmin or User Plus users click on “**Process Batch**” a confirmation prompt will appear enabling the user to confirm to start the process for that batch number. When clicked on ‘**Yes**’, the process batch will run the incoming data driver, retry merge procedures to process any records existing in the Unmerged Assay Results, then runs the QC Checker procedure if the batch status is not Unmerged, then runs the re-ranking procedure if the batch status is Accepted.
The list of processes running is shown as below with the checkbox associated to it. Once the process is completed the status of each is updated as below in green colour if succeeded, else the error message will be shown in red colour. When running the stored procedures users have the ability to cancel the process at anytime.
On completion of running the stored procedures, when the ‘**Close**’ button is clicked, the Filter data grid and all component data grids displayed will be refreshed.
**Delete Batch: Delete** option gives SysAdmin & User Plus users a confirmation prompt to delete the data from Admin Batch Delete procedure.
### > Macro (anchor)
Unmerged Assay Results:
The Unmerged Assay Results option allows users to display the assay data that is quarantined due to data validation issues. This option also provides details to users for the reasons for quarantining the data and once the user has rectified the errors, they can then click ‘**Process Batch’** to merge the data to the assay tables.
A column filter is available for the Exception Type column allowing the user to filter data based on unique Exception Types.
**Dataset Selection for Assay Merging:**
A drop down list is available on the Assay Manager tab within the Unmerged Assay Results section to streamline the assay merging process.
The “**Target DataSets**” drop down allows users to open a new interface and choose a DataSet to set as *current* for assay merging.
This simplifies the workflow by removing the need to navigate away from the Assay Manager and makes multi-dataset merging faster and more intuitive.
> ℹ️ **Note:** Only one batch at a time can be processed when using the **Target DataSet** option.
### > Macro (anchor)
Assay Batch Header
This component will display grid data from the Assay Batch table filtered by Assay Manager labcodes and batch numbers.
Clicking the "**Edit**" icon will display a modal popup where the Assay Batch Header can be edited.
Click "**Save**" or "**Cancel**" to close this window.
### > Macro (anchor)
Assay Batch Detail
This component will display grid data from the Assay Batch Detail filtered by Assay Manager labcodes and batch numbers.
### > Macro (anchor)
QC Results
The QC Results component will display the QC results details associated with the selected batches. The QC Results will display a non-editable data grid with QC Results and QC Result details, allowing the user to drill into a QC result to display the QC result details associated.
An example of data that will display in the QC Results, QC Result details for each QC type (Blank, Standard, Repeat, Screen Test) is given below.
#### QC Type: Blank
A blank rule will display details similar to the following in the QC Result section
This blank rule has been configured for “**Blanks are within expected min and max value**”
**QC Status: **will equal Pass/Fail/NoData**.** “QC Rule Pass %” determines if the blank rule will pass or fail.
- **Pass: ** “Results Pass%” > “QC Rule Pass%”. The “QC Rule Pass%” is set by the user in the QC Rule, Pass% field. The “Result Pass%” is calculated when processing the rule. The “Result Pass %” = Total number of blank samples for the batch that failed the rule / total number of blanks samples for the batch.
- **NoData: **There are no blank sample existing for the batch.
A user can drill into the QC result to display all the blank sample results with a QC status Pass/Fail status, as shown in below screenshot.
A blank sample will be assigned a status of Pass/Fail with the following conditions:
- **FAIL:** if no reference values exists, i.e. Expected Min and Expected Max values.
The Expected Min and Expected Max values are selected from the QC Reference Value Library Table where
- If a record exists for the combination of standard, generic method and element where the Expected Min and Expected Max values exist, these values will be used for the comparison above.
- If no record exists for the above combination, a search for the standard and element where preferred = 0 and Expected Min and Expected Max values exist, the values will be used.
- **FAIL:** if reference values exist AND the blank sysResult is outside of the ExpectedMin and ExpectedMax
- **PASS:** if reference values exist AND the blank sysResult is between the ExpectedMin and ExpectedMax. For example, the sysResult value 0.02 is within the Expected Min value 0.01 and Expected Max value 100, so the status is passed.
#### QC Type: Standards
A standard rule will display details similar to the following in the QC Result section. This record will be highlighted red when it has a failed QC Status.
This standard rule has been configured for “**STD RULE 2STD AU**”
**QC Status:** will equal Pass/Fail/NoData.** The “QC Rule Pass %” determines if the standard rule will pass or fail.
- **Pass:** “Results Pass%” > “QC Rule Pass%”. The “QC Rule Pass%” is set by the user in the QC Rule, Pass% field. The “Result Pass%” is calculated when processing the rule. The “Result Pass %” = Total number of standard samples for the batch that failed the rule / total number of standard samples for the batch.
- **NoData:** There are no standard samples existing for the batch.
A user can drill into the QC result to display all the standard sample results with a QC status Pass/Fail status, as shown in below screenshot.
A standard sample will be assigned a status of Pass/Fail with the following conditions
**Fail:** if no reference values exists, i.e. Expected Value and Expected StdDev values.
The Expected Value and Expected StdDev values are selected from the *QC Reference Value *Library Table where
- If a record exists for the combination of standard, generic method and element and where the Expected Value and Expected StdDev values exist, these values will be used for the comparison above.
- If no record exists for the above combination, a search for the standard and element where preferred = 0 and Expected Value and Expected StdDev values exist, these values will be used.
- For example sysResult value 2.16 is not in between LowerLimitStDev -1.9 and UpperLimitStDev 2.1. So, the status is failed.
- **Pass**: Standard Sample Result is between LowerLimitStDev and UpperLimitStDev.
- **Fail**: Standard Sample Result is **not between** LowerLimitStDev and UpperLimitStDev.
#### QCType: Repeats
A repeat rule will display details similar to the following in the QC Result section.
This repeats rule has been configured for “**LAB CHECK AU**”
**QC Status:** will equal Pass/Fail/NoData.** The “QC Rule Pass %” determines if the repeat rule will pass or fail.
- **Pass:** “Results Pass%” > “QC Rule Pass%”. The “QC Rule Pass%” is set by the user in the QC Rule, Pass% field. The “Result Pass%” is calculated when processing the rule. The “Result Pass %” = Total number of Lab Repeat1 samples for the batch that failed the rule / total number of Lab Repeat 1 samples for the batch.
- **NoData:** There are no LabRepeat1 samples existing for the batch.
A user can drill into the QC result to display all the repeat sample results with a QC status Pass/Fail status, as shown in below screenshot.
A repeat sample will be assigned a status of Pass/Fail with the following conditions
- **Pass**: (repeat result – original Result)/ original Result < 10% ((i.e. “% difference From original Value”) AND Repeat Result < (10% * original Result Limit lower)
- **Fail**: (repeat result – original Result)/ original Result >= 10% ((i.e. “% difference From original Value”) AND Repeat Result > (10% * original Result Limit lower)
#### QCType: Screen
A screen test rule will display details similar to the following in the QC Result section.
This screen test rule has been configured for “**Screen Test check for p75um**”.
**QC Status:** will equal Pass/Fail/NoData.** The “QC Rule Pass %” determines if the screen test rule will pass or fail.
- **Pass:** “Results Pass%” > “QC Rule Pass%”. The “QC Rule Pass%” is set by the user in the QC Rule, Pass% field. The “Result Pass%” is calculated when processing the rule. The “Result Pass %” = Total number of results for element: p75um for the batch that failed the rule / total number of results for element: p75um for the batch.
- **NoData:** There are no results for element: p75um samples existing for the batch.
A user can drill into the QC result to display all the results for element: p75um sample results with a QC status Pass/Fail status, as shown in below screenshot.
A screen test sample will be assigned a status of Pass/Fail with the following conditions:
- **Pass**: when the sysResult is outside of the Lower and Upper limit. The Lower and Upper limits are set by the user in the QC rule.
- **Fail**: when the sysResult is inside the Lower and Upper limit.
### > Macro (anchor)
Batch Approval
The Batch Approval component will allow a SysAdmin or User Plus the ability to accept/reject batches and automatically email a notification with batch summary details and QC Results.
On selecting the **Approve** button, a pop window will appear allowing user to change the batch status and send the email to the email address configured and **Save**. Users are allowed to select only accepted or rejected.
When approving a batch and changing the status to rejected or accepted, a notification will be displayed if reranking will run. For example, if the Batch status is changed from **Accepted** to **Rejected** the reranking will run on saving.
Emails are configured for the approval from QC Emails in QC Rules Configuration. Once the email is configured in QC Emails it will appear in the Batch Approval grid. So, when saving the batch status and emails are configured, an email is sent with Batch Summary and QC Results.
## Assay Stored Procedures
The **Assay Manager** section allows SysAdmin or User Plus users to execute specific stored procedures related to Assay Management directly from the **DataShed5**. This functionality is available under a dedicated tab in the concertina menu called **Assay Stored Procedures**.
From this tab, authorised users can:
- Select and run any of the available stored procedures.
- Provide required input parameters when prompted.
- Receive feedback messages upon completion of the process.
- Check the "**Use Filtered Batches"** checkbox to apply the top-panel filter.
> ℹ️ **Note:** When merging assays using the unfiltered option, only one batch can be merged at a time.
**Available Stored Procedures**
The following stored procedures can be executed:
**Notes:**
- For **Incoming** and **Merge** processes, separate procedures exist for XRF data.
- Ranking does **not** apply to XRF.
- Each stored procedure requires different parameters. After selecting a procedure, the system will prompt you to enter the appropriate values.
> ℹ️ Hover over the label to see the actual stored procedure name.
The below flowchart illustrates the process:
**Steps:**
1. **Select Procedure** – Choose the stored procedure from the Assay Stored Procedures tab.
2. **Enter Parameters** – Provide required input values as prompted.
3. **Execute** – Run the selected procedure.
4. **View Feedback** – Review the success or error message returned by the system.
**Parameter Validation Logic**
Before running any stored procedure, the system validates the input parameters to ensure correctness and completeness. Below is the logic applied:
**General Rules**
1. **Mandatory Parameters**
- All required fields must be provided before execution.
- Drop-down selections must have a valid value from the source query.
2. **System-Supplied Parameters**
- Parameters such as @Loaded_By, @UserName, and @ReportOnly are auto-populated and hidden from the user.
3. **Data Type Checks**
- Text fields (e.g., BatchSize, ColumnLimit) must contain numeric values within acceptable ranges.
- Boolean fields (e.g., BatchStatusNewOnly) must be TRUE or FALSE.
**Validation by Parameter**
**@AssayTable -** Must match a BaseName from tblSYSDSConfig where obclass='ASSAY' and Type='TABLE' and BaseName <> 'tblXRFResults'.
**@LabCodeBatchNo -** User must select at least one valid LabCode/Batch combination. Multiple selections allowed.
**@BatchSize -** Must be an integer > 0. Default = 100,000.
**@ColumnLimit -** Must be an integer > 0. Default = 90.
**@DataSetFilter -** If provided, must match valid Cascade filter values for DH, LS, or FS tables.
**@AssayFlatTable**
Must match a BaseName from tblSYSDSConfig where BaseName LIKE '%flat%'.
**@BatchStatusNewOnly -** Checkbox defaulted to TRUE; user can toggle.
**Execution Block**
- If any validation fails:
- Display an error message specifying the missing or invalid parameter.
- If all validations pass:
- Proceed to execute the stored procedure and return feedback.
**Receiving Feedback**
- Success/Failure Notification: Sent via email.
- Error Handling:
- Missing parameters → Failure email.
- Common errors: Invalid object name, Arithmetic overflow.
- Test Assay Flat:
- If results exist, an Excel file with multiple sheets is attached to the email.
---
## > Macro (anchor)
## Admin Menu
The admin menu allows a **SysAdmin** user to configure QC rules, maintain assay management library table codes and details and setup assay configurations required for importing assay data. **User Plus** users will be able to maintain library tables only.
### > Macro (anchor)
Library Tables Maintenance
Library Tables menu displays a list of library tables as below and allows the **SysAdmin** and **User Plus** users the ability to add, edit, delete and copy assay library table codes.
1. **Element Groups:** This grid displays the list of element groups.
2. **Elements:** This grid displays the list of elements.
3. **Method Priorities:** This grid displays data from method priorities. The method priorities will automatically sort the order of the priority on save. After saving it will run the re-rank procedure as below.
1. **Generic Methods:** This grid displays the list of generic methods.
2. **Labs:** This grid displays the list of labs with their information from Assay Labs table.
3. **Lab Method:** This grid displays the list of lab methods from Assay Lab Method table.
4. **Lab Element Alias:** This grid displays the list of alias names for the labs from Assay Lab Alias table.
5. **Units:** This grid displays the list of units from Units table.
6. **Conversion Factor:** This grid displays the list of conversion factors from conversion factors.
7. **Import Substitutions:** This grid displays data from import substitutions table.
8. **Import File Type:** This grid displays the list of files imported into the system from import file type table.
9. **Incoming Data Mask:** This grid displays data from incoming data mask table.
10. **QC Category:** This grid displays data from QC Category table.
11. **QC Reference:** This grid displays data from QC Reference table.
12. **QC Reference Type:** This grid displays data from QC Reference Type table.
13. **QC Reference Values:** This grid displays data from QC Reference Value table.
### QC Rules Configuration
### > Macro (anchor)
Configuring QC Rules
QC Rules in Assay Manager can only be configured by SysAdmin users only.
SysAdmin users will have the ability to assign and maintain QC rules to one or more layouts. Below are the list of options available in the QC Rules Configuration.
#### QC Rule Standards
Three Action icons are available Copy, Edit and Delete.
### Edit QC Rule Standards
Allows the user to maintain QC Rules for standard samples. Clicking on the Add option in QC Rule Standards grid will enable user to add new QC Rule Standard.
A popup window as above will appear upon clicking on edit option. QC Rule Standards will allow SysAdmin users to enter the below fields:
- **Code:** a user defined name for the rule, is a unique name.
- **Description:** a user defined description of the QC Rule standard and will be displayed in the email notifications.
- **QCType:** is the QC type, always STD.
- **StandardTypes:** is a list of types from the Reference Type library table, will not display reference types containing Blank or BLK.
- **Element:** is a list of elements from the Ass Element Library table, one Element can be selected.
- **Pass%:** is a percentage that determines if the rule will pass or fail. For example, this rule will fail if 75% or more of the standard samples for the batch are not within 2std deviations.
- **Exclude BDL:** true/false. If true, standard samples that have a Below detection limit (tblAssay.sysAssayStatus=BDL) will be excluded from the rule.
- **Exclude UP:** true/false. If true, standard samples that require updating (eg I/S, X, NS) (tblAssay.sysAssayStatus=UP) will not be included in the rule.
- **Exclude OR:** true/false. If true, standard samples that are Over Range (tblAssay.sysAssayStatus=OR) will be excluded from the rule.
- **Reference Values:** is a dropdown selection with UseExpectedValue/UseHighLow.\
- **UseExpectedValue:** the standard sample rule will be computed using the QC Reference values: Expected Value and Expected StdDev. For example, a sample will fail if the sysResult is not within 2std deviations of the expected value.
- **UseHighLow:** the standard sample rule will be computed using the QC Reference values: Expected Min and Expected Max. For example, a sample will fail if the sysResult is not within Expected Min and Expected max.
- **Std Deviation:** is a dropdown selection with 1/2/3, this option is required if you are using ReferenceValues=UseExpectedValues.
#### QC Rule Blanks
Allows the user to maintain QC Rules for blank samples. A popup window as below will appear upon clicking on edit new option. QC Rule Blanks will allow user to enter below fields.
Action icons available - **Copy**, **Edit** and **Delete**.
- **QCType:** is the QC type, always BLANK.
- **StandardTypes:** is a list of the types from the Reference Type library table and will only display Reference Types containing Blank or BLK.
- **Element:** is a list of elements from the Ass Element Library table, one Element can be selected.
- **Pass%:** is a percentage that determines if the rule will pass or fail. For example, this rule will fail if 75% or more of the blank samples for the batch are not within the expected min and expected Max for the batch.
- **Exclude BDL:** true/false. If true, blank samples that have a Below detection limit (tblAssay.sysAssayStatus=BDL) will not be included in the rule.
- **Exclude UP:** true/false. If true, blank samples that require updating (eg I/S, X, NS) (tblAssay.sysAssayStatus=UP) will not be included in the rule.
- **Exclude OR:** true/false. If true, blank samples that are Over Range (tblAssay.sysAssayStatus=OR) will not be included in the rule.
- **Reference Values:** is a dropdown selection with UseExpectedValue/UseHighLow.
- **UseExpectedValue:** the blank sample rule will be computed using the QC Reference values: Expected Value and Expected StdDev. For example, a sample will fail if the sysResult is not within 2std deviations of the expected value.
- **UseHighLow:** the blank sample rule will be computed using the QC Reference values: Expected Min and Expected Max. For example, a sample will fail if the sysResult is not within Expected Min and Expected max.
- **Std Deviation:** is a dropdown selection with 1/2/3, this option is required if you are using ReferenceValues= UseExpectedValues.
#### QC Rule Repeat
Allows the user to maintain QC Rules for repeat samples. A popup window as below will appear upon clicking on edit new option. QC Rule Repeats will allow user to enter below fields.
Action icons available - **Copy**, **Edit** and** Delete**.
- **QCType:** is the QC type, always REPEAT.
- **RepeatType:** a list of values from the QC Category Library Table, one repeat type can be selected.
- **Element:** is a list of elements from the Ass Element Library table, one Element can be selected.
- **Pass%:** is a percentage that determines if the rule will pass or fail. For example, this rule will fail if 75% or more of Lab repeat1 samples for the batch if
- the difference percentage of the repeat result from the original result is less than 10% (i.e. “% difference from original Value”) AND
- the repeat result is less than 10% of the detection limit (i.e. “Value *Detection Limit (lower limit)”).*
- **%Difference from original value:** is a percentage that will determine if the repeat result fails or passes. Therefore, if the difference percentage is less than 10% from the original value the repeat sample will pass.
- **Exclude BDL:** true/false. If true, repeat samples that have a Below detection limit (tblAssay.sysAssayStatus=BDL) will be excluded from the rule.
- **Exclude UP:** true/false. If true, repeat samples that require updating (eg I/S, X, NS) (tblAssay.sysAssayStatus=UP) will not be included in the rule.
- **Exclude OR:** true/false. If true, repeat samples that are Over Range (tblAssay.sysAssayStatus=OR) will be excluded from the rule.
- **Value** *** Detection Limit (lower limit):** is a percentage that will determine if the repeat result fails or passes.
#### QC Rule Screen Test
Allows the user to maintain QC Rules for screen tests. A popup window as below will appear upon clicking on edit option. QC Rule Standards will allow user to enter below fields.
Action icons available - **Copy**, **Edit** and **Delete**.
- **QC Type:** the QC type, always equal Screen.
- **Element:** is a list of elements from the Ass Element Library table, one Element can be selected.
- **Lower Limit Value:** defines the minimum value required for the rule to pass/fail.
- **Upper Limit Value:** defines the maximum value required for the rule to pass/fail
- **Exclude UP:** true/false. If true, screen samples that require updating (eg I/S, X, NS) (tblAssay.sysAssayStatus=UP) will not be included in the rule.
- **Pass%:** is a percentage that determines if the rule will pass or fail.
#### QC Policy
Allows SysAdmin to create new policy with a unique policy name. Edit a Policy name form.
Action icons available - **Edit** and **Delete**.
Edit a Policy name form.
#### QC Policy Rule
Allows SysAdmin to assign existing QC Rules to an existing QC Policy.
Action icons available - **Delete**.
#### QC Policy Layout
Allows SysAdmin to assign one QCPolicy to one or more layouts. The QC Policy has to be active for the policy to be applied to a batch on importing a batch or processing a Batch.
Action icons available - **Edit** and **Delete**.
** **
The Batch List will display the Active QC Policy for the Import layout.
#### QC Emails
A QC Email can be configured for the Batch Approval notifications here. One or more emails can be added. When approving a batch, the user emails configured in the QC emails will be emailed.
Action icons available - **Delete**.
### Assay Configuration
### > Macro (anchor)
Assay Configuration
Assay Configuration allows Sys Admin to setup Import Post Processing Scheme, Assay Structure, RH Norm, LH Norm and Below Detection Treatment.
#### Import Post Processing Scheme
An Import Post-Processing Scheme is a logical listing of tables that the incoming assays will be merged to. The Default Post Processing scheme is configured in the standard MDS. Additional Import Post Processing schemes may need to be configured if multiple normalised assay tables are utilised.
Action icons available - **Edit** and** Delete**.
A popup window as above will appear on clicking on create new import post processing scheme option. Creating new import post processing scheme will allow user to enter below fields.
- **Name:** Type in a suitable name.
- **Assay Structures: **Is the list of tables default standard assay merge tables.
- **Description:** Field allows to enter the description of the Assay Structures merge table.
- **Unmerged Assay Results Table: **Is the list of tables.
For example: tblSYSAssIncomingData (Most of the users are defined the name with Incoming Data at the end of the naming).
- Data Driver Store Procedure: Is default as ‘usp_ProcessInComingDataDriver’.
- Merge Stored Procedure: Is default as ‘usp_DataAssayMergingProcess’.
- ReRanking Stored Procedure: Is default as ‘usp_DataAssayRankingProcess’.
#### Assay Structure
Configures the normalised assay table (tblAssay).
Action icons available - **Edit** and **Delete**.
A popup window as below will appear on clicking on create new or edit Assay Structure. Creating new Assay Structure will allow user to enter below fields.
- **Assay Table:** Select the name of the normalised Assay Results table in the dropdown list (tblAssay).
- **Name:** Type in a suitable name. It is Maxgeo’s nomenclature to start all structures with AM (Assay Management) followed by the abbreviated structure type and table name. (AM_ASS_Assay).
- **Sample Register:** Select the name of the Sample Register in the dropdown list (tblSampleRegister).
#### RH Norm: Right Hand Normalisation
Links the flat assay table (tblAssayFlat) to the normalised assay table.
These structures are all preconfigured as part of the Maxgeo Data Model.
Action icons available - **Details**, **Edit** and **Delete**.
A popup window as above will appear on clicking on create new RH Norm Structure. Creating new RH Norm Structure will allow users to enter the below fields.
- **Assay Table:** Select the name of the normalised Assay Results table in the dropdown list (tblAssay).
- **Name:** Type in a suitable name. It is Maxgeo’s nomenclature to start all structures with AM (Assay Management) followed by the abbreviated structure type and table name (AM_RH_Assay).
- **Assay Flat Table:** Select the name of the Assay Flat table in the dropdown list (naming is followed by abbreviated table name and “Flat” word).
**RH Attributes:** allows a SysAdmin to configure elements for the tblAssay Flat table. The element field is assumed to be existing in the tblAssay flat table before configuring in the RH attributes.
Attributes of assay table section details will appear on clicking on detail RH Norm Structure. Lists of attributes assay table will show as above. A popup window as below, will appear on clicking on create new Attributes for selected RH Norm Structure.
Creating new Attributes will allow users to enter the below fields.
- **Element**: Select the name of the Element in the dropdown list (tblSYSAssElement).
- **Attribute Name:** Type in a suitable name.
- **Mode:** Users can select three modes such as **Dynamic**, **Preferred Value Calculation** and **Static**.
- **Field Name:** Select the field name from the dropdown list of selected Assay table.
- **Field Type:** Select suitable field type according to selected field name.
- **Field Length:** Type suitable field length for selected field type (Double, Integer, Long, Single, Text).
The Attributes tab configures how the assay results are to be ranked.
There are 3 ways to rank the assay values
- **Preferred Value Calculations:** Populates a field in the flat assay table based the generic methods priority for the element group the result’s element has been assigned to. This means the field defined will always be populated if there is a result for this element. This field MUST be added to the table tblAssayFlat using SQL Server Management Studio.
- **Static:** Populates a field in the flat assay table based on criteria defined in the database. This may not always be populated in the flat assay table. This field MUST be added to the table tblAssayFlat using SQL Server Management Studio.
- **Dynamic:** Can create a virtual field based on criteria specified, if the attribute is selected. Will attach the virtual field to the select LH sample table.
Click on the arrow and it will show sub details of Element definition type. A popup window will appear on clicking create new Definition for selected Element. Creating a new Definition will allow users to enter the below fields.
- **Definition Type:** list of the type will depend on the Element’s mode. If element defined as Preferred Value Calculation, definition dropdown will populate only Conversion. For Dynamic and Static mode, Conversion and Field type will populate in dropdown.
- **Field Type:** list of field type populate as selected definition type. (For example: Select Conversion definition type, conversion value will populate in dropdown.)
- **Value:** Input only required for Field Definition Type. Keep it blank for Conversion Definition Type
### RH Norm Check Config
Select the ‘**Check Config**’ button to check the configuration of the assay table that has just been configured.
**RH Norm**
- Check that the attributes are defined in the corresponding RH table.
- Check for static table existence and that all parameters are filled in (non-fatal) (Only check if there are static/prefer attributes).
- Check the relationship between RH and Static.
- Check for static and dynamic attributes, check that the restriction fields exist and that the restrictions placed on these fields are consistent with the field data types.
- Check for prefer attributes, check that the element exists in the element library (and that it is defined with single quotes in the attribute definition).
- Check that the conversion factor specified is a non-zero numeric.
#### LH Norm: Left Hand Normalisation
Configures the sample metadata tables (**tblDHSamp**, **tblDHSampQC** etc.) and links this to the assay table.
Action icons available - **Edit** and **Delete**.
A popup window as below will appear on clicking on create new Attributes for selected RH Norm Structure. Creating new Attributes will allow users to enter below fields.
- **Sample Table:** Select the name of the table in the dropdown list which is registered in DataShed configuration.
- **Name:** Name will be automatically assign with ‘AM_LH’ and selected Sample Table name.
- **RH Table:** Select the name of the assay structure table in dropdown list.
- **Related Sample QC:** Select the sample QC table that stores the QC sample relating to the sample table specified.
- **Is Standard Table:** Check if table type is Standard Table type.
- **Depth From:** If Depth_From field does not exists in the LH Sample Table Name, dropdown function will disable. The Depth_From will display a list of fields that exist for the LH table name specified. Only save the details if a user has selected a different field name than Depth_From.
- **Parent Table:** display a list of registered tables, users can only select Parent Table when Sample Table has no Dataset column. This field is used for the production sample table currently, when a Dataset is not the Parent key you need to specify the parent table here. For example when selecting **tblProdSamp** as LHNormalisation a Parent Table has to be specified as **tblProdLocation**.
#### Check Config
Select the ‘**Check Config**’ button to check the configuration of the assay table that has just been configured. Following actions are performed
**LH Norm**
- Check that the attributes are defined in the corresponding LH table
- Check the Field name clash with Assay table.
- Check relationships exist for attributes and are defined.
**RH Norm**
- Check that the attributes are defined in the corresponding RH table.
- Check for static table existence and that all parameters are filled in (non-fatal) (Only check if there are static/prefer attributes).
- Check the relationship between RH and Static.
- Check for static and dynamic attributes, check that the restriction fields exist and that the restrictions placed on these fields are consistent with the field data types.
- Check for prefer attributes, check that the element exists in the element library (and that it is defined with single quotes in the attribute definition).
- Check that the conversion factor specified is a non-zero numeric.
The message returned will indicate if the configuration has all the required fields populated correctly.
#### Below Detection Treatment
The detection limit can be set to either –1 times the lower detection limit or to half the lower detection limit. The sysresult will be calculated as 0.5*LLD or -1*LLD.
BDL substitutions ensure that the lower limit is populated and that the substitution for the import layout has been populated correctly. The sysAssayStatus will be populated with BDL if the substitutions table has been populated correctly. For example, a “<” before the results indicates that it is Below Detection Level for that method and “BDL” is inserted in the sysAssayStatus field.
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Grid Modifications
**New Records**
Assay Manager allows users with the correct security level to create, edit, copy and delete the records.
Clicking the [**+**] button next to Assay Manager tables opens the popup, which allows the creation of new records.
**Copy: **A user with the correct security level can copy a record by selecting the copy option. A popup window will appear helping the user with the fields copied to create new record.
**Delete:** A user with the correct security level can delete a record by selecting the delete option. A confirmation prompt will display to confirm the deletion of the record.
**Edit: **A user with the correct security level can edit records by selecting the Edit option.
**Save: **Once the record is saved in the grid user will be notified with a message showing the save success along with the title of grid as below.
User will be prompted with an error message if the record already exists in the database with the same unique key as below.
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Searching & Filtering
Assay Manager allows users to search and filter the columns in the grid. Users can search values in the filter row column as shown below. It will filter the grid with the search value.
**Reset Filters**
Users can reset the filter by selecting the **Reset** option as shown below.
The foreign key columns will have dropdowns in the filter allowing the users to filter amongst the list. By default All is selected. Users can clear the filter by clicking on the cross icon. The Users can navigate through the grid pages by selecting the paging options at bottom of grids.
**Sort**
Users can sort the grid ascending or descending by clicking on the column heading as shown below. In order to refresh the grid, users can close and open on the title.
**Refresh**
In order to refresh the grid manually users have to click on grid title to close the grid and open again to get the refreshed data in the grid.
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Download Batch List
Download Batch List button is available for the user after selecting the filters and clicking ‘**Apply’**. It will download the filtered data from the Batch List in an excel format.
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Process Batches
The ‘**Process Batches**’ button is available for the users after selecting the filters and clicking on ‘**Apply**’.
When clicked, the ‘**Process Batches**’ button opens a popup with a list of procedures enabling the user to know which procedures will run for the batches available in the Batch List grid. A status bar displays, when running the stored procedures and allows the process to be cancelled by the user. The Process Batches runs the incoming data driver and retry merge procedures to process any records existing in the unmerged Assay Results, runs the QC Checker procedure if the batch status is not Unmerged and runs the re-ranking procedure if the batch status is Accepted. The status will be updated as below:
- Processing incoming data driver
- Processing retry merge
- Processing QC Rules
- Processing Re-Rank
- Completed
On close it will refresh all the components.
If there is any error while running the procedures it will display the error message in red colour and will continue running the other procedures.
