Files can be classified as SOP files, instrument files, specifications files, and so on. Before starting to work with SDMS, it is important to identify the nature of files that will be stored and processed by SDMS so that when adding a file type, you can define whether advanced parsing should be enabled or disabled. Ask the following questions: Will a document be stored or exported? If the latter, will the data be extracted (parsed) to update individual database fields or exported intact? Depending on the answers, select one of the following:
| • | Disable advanced parsing - Typically this is for unstructured documents such as books or image files. In such cases, UXML templates, workflows, and their entry points are defined directly because a DRP for parsing is not involved. Then documents with this file type automatically use the UXML template and workflow defined in this tab for an export step. Alternatively, to just store documents in SDMS, you can omit the UXML and workflow steps. |
| • | Enable advanced parsing - In this case you allow a DRP that parses keywords for updating LIMS database fields to be attached to this file type. The actual template is created elsewhere. The UXML and workflow are also defined in that template and not in this application window. |
NOTE Also, using this option, different workflows and UXMLs can be associated with different documents of the same file type. For example, documents with a STARLIMS_Instrument file type can be assigned to different workflows based on the instrument that generated the document. Thus, Gas Chromatography instruments can generate an analysis report that can be attached to a workflow including review, approve, and export stages, while HPLC instruments can generate analysis reports that will be attached to a workflow including an export stage only.
The following procedure can help you add a file type.
>> To add or edit a file type
| 1. | Log on as a user with access to Utilities > SDMS Admin and open that branch in the console. |
| 2. | Click on the File Types tab to view available file type records. |
| 3. | To add a file type, click Add. In the Add File Type dialog box, enter the following values: |
| • | File Type - Descriptive file type name, such as STARLIMS_Instrument. |
| • | Description - File type description, such as Instrument report files. |
| 4. | Also in the Add File Type dialog box, either mark Disable Advanced Parsing then configure Non Parsed Files Routing Properties or clear the check box so you that can attach this file type to an FRP/DRP template. For more details about data extraction alternatives, see the bullets prior to this procedure. |
TIP When you add a new file type into SDMS, decide how that document will be used. If it is exported, will the data be extracted to update database fields? If you answered "Yes" to this question, you should clear Disable Advanced Parsing.
| • | Enable advanced parsing - Clear Disable Advanced Parsing to allow parsing (data extraction). Now you can use a Data Recognition Pattern (DRP) template to extract document content and, optionally, you can assign alternate workflows for this file type. |
| o | Typically you configure a template for data extraction using a File Recognition Pattern (FRP), Data Recognition Pattern (DRP), and Output XML utilities. For more information about how to configure and then associate these templates with a file type, see the section Designing Document Templates. |
| o | Optionally the template referred to in the prior bullet is also associated with a workflow. For more information about configuring a workflow to attach to the template, see the section Workflows. |
| • | Disable advanced parsing - Mark Disable Advanced Parsing, if you want to use a document, such as an SOP, without parsing (data extraction). |
| o | Attach an Output XML template. Use the Unified XML drop-down box to select from those configured in the Unified XML tab. |
| o | Optionally attach a workflow. Use the Attach to Workflow drop-down box to select from those configured in the Workflows tab. |
| o | Depending on the workflow selected, you can select a Workflow Entry Point using the drop-down box by that name. Typically the entry point for a document is labeled Creator step. |
| 5. | To trigger a prompt to appear when users upload this type of file, mark the Define Input Prompts check box. When this check box is marked, you can select the prompt you want to appear from those displayed in the Trigger User Prompts on Upload pane. |
| 6. | Click OK to add the new File Type. The file type is added with a unique ID. |
| 7. | To modify a highlighted file type, click Edit. The Edit File Type dialog box is configured exactly as described in the prior steps. |
>> To associate an importing script with a file type
| 1. | The importing script is used to read the unified XML structure carrying the parsed data and update STARLIMS database tables with the data. To associate an importing script with a highlighted file type, click the ... link inside the Importing Script field. In the resulting dialog box, choose a server script and click Select. |
| • | SDMSImportScripts._ImportTemplate passes the required input parameters file ID and the associated UXML structure containing the extracted data. All importing scripts should use the parameters provided by this script. |
| • | SDMSImportScripts._HelperFunctions includes the SSL functions GetNumberOfRuns, FindKeywordByName, FindKeyWordByCName1, FindKeywordByCName2, FindKeywordByAttribute, and similar functions such as those for finding and getting tables or images. All importing scripts should be configured to call the appropriate functions from this list. _HelperFunctions also includes information in comments to help you write an importing script. |
IMPORTANT Importing scripts are stored in the STARLIMS Designer at path Server Scripts > SDMSImportScripts. You can add an SSL script to update tables using the data contained in the unified XML structure associated with a File Type. Use existing scripts for guidance.
| 2. | To clear a server script associated with a highlighted file type, click Clear Script Info and accept the prompt. |
>> To set permissions for a file type
When creating a file type, you can specify the access permissions that are given to users according to the file type. More information about permissions is provided in the Permissions section.
| 1. | Log on as a user with access to Utilities > SDMS Admin and open that branch in the console. |
| 2. | Select a file type and click on Permissions. Permissions per file type are displayed. |
>> To delete a file type
| 1. | Log on as a user with access to Utilities > SDMS Admin and open that branch in the console. |
| 2. | Select a file type and click Delete. Select between the options Delete or Shred and complete the electronic signature to execute the action. Shredded records cannot be restored. Note that deleting a file type will also delete the documents related to it. |
TIP Deleted records can be restored using the Undelete button within the Advanced tab. If you restore the documents relating to the file type without restoring the file type itself, they will be assigned a Default file type.