--- title: "v3.0.3 Assay Manager" canonical: "https://servicedesk.maxgeo.com/space/DS/1412105550/v3.0.3%20Assay%20Manager" format: markdown --- > Macro (toc) DataShed5 provides an Assay Manager option to users only if Assay Management module is assigned to them in DataShed5Admin. Upon clicking on Assay Manager option, it enables user to see Assay Manager module as per below. ![image](media://71a68649-0d11-40f3-9a0c-7db0d62b99f1) The Assay Manager module will provide the ability for a user to query assay batches loaded, process, analyse, approve and report on assay batches. On clicking Assay Manager sub menu, Assay Manager page will appear with the assay manager filters, a multiview option and the Admin menu button. Admin menu button is available for the users with SysAdmin security level only. ![image-20240517-035015.png](media://893d99ef-5d4a-4916-9adc-8ea5b4733c60) ## > Macro (anchor) Assay Manager Filters Assay Manager Filtering will appear allowing the users to select filters to apply on assays based on the following options. Currently always displaying ‘Assay’. Schemes filter: It is single select drop down list with list of imported schemes. Assays is the default scheme set in the import post processing schemes. Date Range filter: It is single select drop down list as below allows to user to select date periods. Last week is selected by default. This filter allows user to filter assays based on the load date from Assay Batch table. ![image](media://ab0dd3c7-381a-48ff-8318-7d66cc6d77ac) Date From & Date To: This filter allows user to filter assays based on the load date from Assay Batch table. BatchStatus: It is a multiple select drop down list with list of items from AssayBatchStatus. AllBatchStatus is selected by default. Users: It is a multiple select drop down with list of items including loaded by users from Assay Batch for the selected scheme and selected Batch Status. All Users are selected by default. Labs: It is a multiple select drop down with list of lab codes from Assay Batch for the selected Scheme, Date Range, users, BatchStatus. All Labs are selected by default. Batches: It is a multiple select drop down with list of batch numbers available for selected Scheme, Date Range, users, BatchStatus. All Batches are selected by default. After selecting the filters, click on Apply button to see the list of components for the selected schemes, DateRange, BatchStatus, Users, labs and batches as below. ![image](media://7b2c30c8-93c9-4af5-a056-9f66c53dce9d) ## > Macro (anchor) Assay Manager Components The Assay Manager module consists of the standard components i.e., Batch List, Unmerged Assay Results, Assay batch header, Assay batch Details, Unmerged Assay results, QC Results and Batch approval. ### > 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. - 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 REJECTED. - 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 Filter List has a **Process Batch **and **Delete** option available in the first column for a SysAdmin only. Process Batch: When SysAdmin clicks on (**Process Batch**) a confirmation prompt will appear enabling 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 and 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 user has the ability to cancel the process anytime. ![image](media://700619df-39fd-43b6-aced-48690702a209) On completion of running the stored procedures, when clicked on close button the Filter data grid and all component data grids displayed will be refreshed. Delete Batch:** Delete** option gives SysAdmin 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 the SysAdmin for the reasons for quarantining the data and once the user has rectified the errors the user can Process Batch to merge the data to the assay tables. Column filter is available for the Exception Type column to the user to filter data based on unique exception Type. ### > Macro (anchor) Assay Batch Header This component will display grid data of from Assay Batch table filtered by Assay Manager labcodes and batch numbers. ### > Macro (anchor) Assay Batch Detail This component will display grid data of from 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 ![image-20240517-035128.png](media://478d4d04-58d3-46be-967e-23d0a1bc809b) 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. ![image-20240517-035200.png](media://c60043c8-f28f-47ec-a5aa-852f0243d961) 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. ![image-20240517-035232.png](media://dd57376d-5b81-499c-a3a0-3fadade831cf) This standard rule has been configured for “Standards within 2STD of expected value” **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. ![image-20240517-035300.png](media://7e151d68-7412-4a67-a634-f3fd69ad1104) 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, thee 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 ![image-20240517-035332.png](media://cf70b117-274d-4ca9-8287-5c0c105f8893) This repeats rule has been configured for “Lab Repeat 1 within 10% difference of original value” **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) ![image-20240517-035523.png](media://de218918-922b-441b-8ba1-a919461bea1c) #### QCType: Screen A screen test rule will display details similar to the following in the QC Result section ![image](media://ba326ad1-23a5-4784-8206-f1a961c5180f) ![image](media://1a5b8f39-de84-474d-be32-b2eb63c7264f) This screen test rule has been configured for “Screen Test check for p75pum” **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. ![image](media://9c3b2f75-3d31-4409-b469-f0a1eaad4ce6) ![image](media://2da39897-f92c-4963-b029-e60d6ff86326) 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 and User Plus the ability to accept/reject batches and automatically email a notification with batch summary details and QC Results. ![image](media://7dfc94e7-f5bb-4379-932c-f26bc9b3f1cd) 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. User is allowed to select only accepted or rejected. ![image](media://a87ce7e8-940b-4e6e-95b6-c99ec80465e3) When approving a batch and changing the status to rejected or accepted a notification will displayed if reranking will run. For example if the Batch status is changed from Accepted to rejected the reranking will run on saving. ![image](media://53bdf8ac-5bab-4c6f-85c7-998fc904d603) Emails are configured for the approval from QC Emails in QC Rules Configuration. Once email is configured in QC Emails it will appear in Batch Approval grid. So, when saving the batch status and emails are configured, email is sent to with Batch Summary and QC Results. If there is any issue with the email not being sent message will be shown to the user as below. ![image](media://859cc02b-90ee-4f1e-92b6-f92adf2a811a) ## > Macro (anchor) Admin Menu The admin menu allows the administrator to configure QC rules, maintain assay management library table codes and details and setup assay configurations required for importing assay data. ![image-20240517-035606.png](media://69d11e42-f7fe-48d3-a959-28f37eb0a2d4) ### > Macro (anchor) Library Tables Maintenance Library Tables menu displays a list of library tables as below and allows the SysAdmin the ability to add, edit, delete and copy assay library table codes. ![image](media://6c2eb07d-7ce7-4372-bed7-57142141a13e) 1. Element Groups: This grid displays the list of element groups from 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. ![image](media://aebbc115-1fa1-4961-ab18-63ee6dd02b06) 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 ### > Macro (anchor) Configuring QC Rules QC Rules in Assay Manager can only be configured by Sys Admin only. SysAdmin 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. ![image](media://72ee32d6-bff2-4905-b5eb-7ec3f14376b9) #### 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. ![image](media://ff471e1b-6367-424e-b198-c095a320d737) A popup window as above will appear upon clicking on edit option. QC Rule Standards will allow user to enter below fields - Code: a user defined name for the rule, is a unique name. - Description: a user defined description of the QX 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. ![image](media://dc2232da-f31b-4fdb-94df-610fc9c687b2) - 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. ![image](media://70da1faa-adfe-4b3e-9a40-05b35ba7797a) - 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. ![image](media://0c62f90c-51ec-4e0d-811e-c382cf20085b) - 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. #### QC Policy Rule Allows SysAdmin to assign existing QC Rules to an existing QC Policy. #### 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. The Batch List will display the *Active QC Policy* for the Import layout. ** ** ![image](media://e934f82b-70c0-4d1b-88b7-5785ca550423) #### 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. ### > 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. ![image](media://2604bb35-daf1-46f6-bdfe-e5b3f61e0f89) #### 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. ![image](media://43fa1c4b-cc48-48a4-8347-2734226ebd34) 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’. ![image](media://4f3921eb-b105-40d1-a5af-7dfe4ed4e51a) #### Assay Structure Configures the normalised assay table (tblAssay). ![image](media://2dda6499-b4a4-4e46-bb88-e46851d6ed17) A popup window as above will appear on clicking on create new 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). ![image](media://131bc8ee-967b-4d92-8765-5dd84ec310ed) #### 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. ![image](media://db0edefe-0cff-4d3e-bc96-02715b3249b7) A popup window as above will appear on clicking on create new RH Norm Structure. Creating new RH Norm 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_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 the ability 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. ![image](media://39cfe5ef-d051-437c-a31c-83853b1c0e76) 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. ![image](media://c55d0766-ef8c-460b-a377-9273df7758fd) Creating new Attributes will allow user to enter below fields. - Element: Select the name of the Element in the dropdown list (tblSYSAssElement). - Attribute Name: Type in a suitable name. - Mode: User 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 in SQL Management Studio. - Static: Populates a field in the flat assay table based on criteria defined in the database. This may is not always populated in the flat assay table. This field MUST be added to the table tblAssayFlat in SQL 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. In DataShed. **Add Definition Type for Element** ![image](media://75bf59a0-cf11-4909-a109-d1a4b58128e7) Clicking on arrow and it will show sub details of Element definition type. A popup window will appear on clicking on create new Definition for selected Element. Creating new Definition will allow user to enter below fields. ![image](media://a9faf39a-a983-47a4-bd81-05ba36fb7cdb) - Definition Type: lists of the type will be depends on 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: lists 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. #### LH Norm: Left Hand Normalisation Configures the sample metadata tables (tblDHSamp, tblDHSampQC etc.) and links this to the assay table. ![image](media://c8e0ad2c-0e98-4e10-8b90-83be0363ca40) A popup window as above will appear on clicking on create new Attributes for selected RH Norm Structure. Creating new Attributes will allow user to enter below fields. - Sample Table: Select the name of the table in the dropdown list which is register 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, user 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. Assign LH Attributes ![image](media://39c86eed-a52b-4654-b866-6bcbbfe823cb) To Assign Attributes to LH table, check the element available in RH table lists and click on Assign button. #### 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. ![image](media://c17c005f-1b95-42d3-a516-7b0a95203a31) 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 in library (and that it is defined with single quotes in the attribute definition.) - Check that the conversion factor specified is a non-zero numeric. ![image](media://fff900bd-201d-4be0-94f8-f73cb3ef765b) 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. ![image](media://90004229-ed1f-4ae0-b606-4c908d3ae48d) ## > Macro (anchor) Security Levels: User, UserPlus, and SysAdmin The following details all the functions that will be available to a user that has a security Level assigned to them of User, User Plus and Sys Admin. **User**: will be given access to view data in the Assay manager. **User Plus:** will be given access to the following in Assay Manager. - Process Batch: allows user to run the stored procedures required for assay management data: Incoming Data driver, merging , Qc Checker, and Reranking. - Can view and edit Unmerged Assay Results, Assay Batch Header, Assay Batch Detail grids. - Cannot delete data from Unmerged Assay Results, Assay Batch Header, Assay Batch Detail grids. - Approve Batches: Accept or reject batches. **SysAdmin:** will be given access to the following in the Assay Manager. - Maintain Assay Schemes and Normalisations database structures required for the importing of assay data to a specified assay files, i.e. standard assay, assay water, pXRF Assay data. - Maintain assay management configuration data for Library Tables, Qc Configuration and Assay Structures, LH Nominations, RH normalisations and Post Processing schemes. - Process Batches: running the Process Batch option will run the stored procedures required for assay management importing of data: Incoming Data driver, merging, Qc Checker and Re-ranking. - Approve batches by Accepting or rejecting batches. - Delete batches. ## > Macro (anchor) Grid Modifications Assay Manager allows user with security Level Sys Admin will allows to create, edit, copy and delete the records. Clicking the ‘[+]’ button next to Assay Manager tables opens the popup, which allows the SysAdmin to create new record. ![image](media://ba0168a9-fb53-4b7f-b037-97d433f84314) **Copy: **A SysAdmin can copy a records by selecting the copy option. A popup window will appear helping the user with the fields copied to create new record. ![image](media://a98f1ec5-6a3f-4f6e-8038-87a457bf308c) **Delete:** A SysAdmin can delete a record by selecting the delete option. A confirmation prompt will display to confirm the deletion of the record. ![image](media://485a121f-3121-4d97-87c2-d81375a1aee2) **Edit: **A SysAdmin can edit a record by selecing the Edit option. ![image](media://e8365e7f-7139-4f6b-832d-25d415433730) **Save: **Once the record is saved in the grid user will be notified with a message showing the save successful along with the title of grid as below. ![image](media://22099963-3277-487e-89a1-242569617658) User will be prompted an error message if the record already exists in the database with the same unique key as below. ![image](media://5f8814d5-c0da-4ca6-913d-69614872b828) ### > Macro (anchor) Searching & Filtering Assay Manager allows users to search and filter the columns in the grid. User can search values in the filter row column as shown below. It will filter the grid with the searched value. ![image](media://789d2a99-6566-4941-afe0-f4f2ad89bf6f) Users can reset the filter by clicking on reset option as shown below. ![image](media://bb411d81-7419-4d66-b067-9813e0f68296) The foreign key columns will have dropdown 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 record by selecting the paging options at bottom of grids. ![image-20240517-035744.png](media://cffde4b4-9a83-4f1d-9cc7-4fc07993efb1) Users can sort the grid ascending or descending by clicking on the column heading as shown below. In order to refresh the grid user can close and open on the title. ![image-20240517-035805.png](media://2c5896cf-56c6-44b8-9873-b3eab93adb87) **Refresh** In order to refresh the grid manually user have to click on grid title to close the grid and open again to get the refreshed data in the grid. ![image](media://14f63a32-c179-45c3-bc69-8137ca90151d) ## > Macro (anchor) Download Batch List Download Batch List button is available for the user once clicked on Apply after selecting the filters. It will download the filtered data from the Batch List in the excel format. ![image-20240517-035857.png](media://3cb58057-a86c-4dfb-b01a-aa9206d1f3e8) ## > Macro (anchor) Process Batches Process batches button is available for the users once clicked on Apply after selecting the filters. When clicked on process batches button it will open a popup with list of procedures enabling the user to know which procedures will run for the batches available in the Batch List grid. The procedures will after the other. When running the stored procedures display a status, and allow the process to be cancelled by the user. The process batches will run 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 as below. ![image](media://3225268a-d910-4045-97a0-d43724e8cfdc)