Configure an Import Template

In AssayNet LIMS, the import template setup is used to manage the flow of data between the system and instruments. This includes configuring the export of sample information, such as sample ID, weight, or any other details required by the instrument to perform the analysis. Labels and data can be exported from AssayNet LIMS in various file formats compatible with the instruments. Similarly, results from the instruments can be imported back into LIMS using different file extensions, with CSV being the most commonly used format.

This activity presumes that you have created an instrument and an import template. For more information, see Add an Instrument and Add an Import Template.

Activity Steps

To configure the import template for managing data import and export between the instrument and AssayNet LIMS:
1. Select the import template and click Setup » Options.
  
  The Setup Import Template screen displays in the File Layout category field.
2. Select the file layout format that matches the data structure of the instrument's output. Tabular is the most common format. For questions or clarification, consult AssayNet support.
3. In the Category field group, click File Format.
  1. Select from the following options based on the file structure:
    - Fixed Width—Data fields in the file are of fixed length, with no delimiters used and fields are separated by specific character counts. If checked, an additional window is enabled below to enter the Column Separator and the Line to Check.
    - Delimited—Fields in the file are separated by a delimiter. Enter the delimiter in the field to the right and complete the following delimiter options as required:
      - Tab
      - Comma—For example, CSV files.
      - Space
      - Semicolon
      - Other—Allows you to specify a custom delimiter by entering the desired character in the adjacent field.
      - Field Delimiter—Defines the specific character that acts as the field separator, when none of the predefined options apply.
      - Consecutive Delimiters as One—Treats multiple consecutive delimiters as a single separator. Useful for cleaning up poorly formatted files.
    - Excel—The file format is an Excel spreadsheet, which must include the necessary headers and structure for accurate data mapping.
    - Database—The file is part of a database connection, requiring configuration of database parameters such as the path and connection details.
    - WinLab 32 Database (Jet/Paradox)—The file originates from WinLab 32's Jet or Paradox database formats. For example, AA instruments.
  2. Select from the following based on the instrument output type:
    - Single File—Select if the data will be imported from a single file.
    - Multiple Files—Select if the data is spread across multiple files.
    - Folder—Select if the files are located in a single folder. The system will process all files in the folder.
    - Folder - by single file—Select if each file in the folder represents a separate data set for import.
    Note: Instrument Parameters, Conversion Factor and Database Path can generally be left blank. For any specific requirements or questions, consult AssayNet support.
4. In the Category field group, click Identifiers to identify the data from the output file.
  
  Note: It is important to correctly identify the sample, analyte and results columns for the output file from the instrument. The remaining fields and options can generally be left blank unless otherwise needed. For specific configurations or additional questions, consult AssayNet support.
  1. In the Data Column field group, enter the column number for the following:
    - Sample—The column for sample ID.
    - Analyte—The column for the element analyzed.
    - Result
5. In the Category field group, click Options.
  1. Complete the following fields as required:
    - No blank lines—Skips any blank lines in the data file during import.
    - Count only non-blank lines—Processes only lines with data.
    - Leave leading spaces—Preserves spaces at the beginning of fields.
    - Leave trailing spaces—Preserves spaces at the end of fields.
    - Non-numeric results as zero—Converts non-numeric results to zero.
    - Eliminate non-alpha characters—Removes any characters that are not letters.
    - Strip Quoted Identifiers—Removes quotes around identifiers for cleaner processing.
    - Missing Analytes as Zero—Assigns zero to any missing analytes.
    - Over-Range Flag—Specifies a flag for over-range results. Enter the value in the adjacent field.
    - Over-Range Value—Specifies a flag for over-range results. Enter the value in the adjacent field.
    - Text Value—Processes specified text values in results.
    - Missing Samples as Zero—Assigns zero to any missing samples.
    - First Row Column Heads—Indicates the first row contains column headings.
    - Re-Calculate Results—Allows recalculating results after import.
    - Ignore Duplicate Samples—Skips duplicate sample entries during import.
    - Auto Add Control Samples—Automatically adds control samples if missing.
    - Find and Match Samples—Specifies how samples in the import file are matched to those in LIMS. Enter the column number or position to locate the sample identifiers.
    - Find and Match Analytes—Indicates the column number or position for matching analytes in the import file with those in Assay Net LIMS.
    - Group Lines—Defines how many lines should be grouped together when processing multi-line data for a single sample or analyte.
    - Result Offset—Adjusts the position from which result values are read. Typically used to skip unwanted columns or lines.
    - Curves—Sets the column or position containing curve-related data, if applicable to the analysis.
    - Cut Sample Length At—Truncates sample ID to the specified length (0 means no truncation).
  2. In the Auto Match Analyte and Auto Match Samples category field group, select from the following options:
    - None—No automatic matching of analytes are performed. Analytes must be matched manually.
    - By Text Value—Analytes in the import file will be matched to those in AssayNet LIMS based on their text values: for example, analyte names or identifiers.
    - By Position—Analytes will be matched to those in AssayNet LIMS based on their column position in the import file. This option poses a risk, as the sample positions in the file and the system may not align. For this reason, using this option is discouraged.
6. In the Category field group, click Display.
  
  Note: In both the Sample Display and Analyte Display categories, select the option that matches how the data is presented in the instrument's result file. If none of the Analyte Display options align with how the analytes are named in AssayNet LIMS, you can assign specific labels to each analyte to ensure they match the result file output format. For more information, see Add Specific Labels for Analyte Schemes.
  1. In the Sample Display category field group, select from the following options:
    - Client ID—The sample identifier using the client-specific sample ID. This is the most commonly used method for matching samples.
    - Lab Code—Displays the sample identifier as assigned by the batch code.
    - Custom Field—Allows you to define and display a custom identifier for the sample. The custom field is configured in a separate screen within the Setup options.
  2. In the Analyte Display category field group, select from the following options:
    - Scheme Code—Displays the analyte using its scheme-specific code.
    - Scheme Name—Displays the analyte using its scheme-specific name.
    - Analyte Symbol—Displays the analyte using its commonly recognized symbol.
    - Analyte Name—Displays the analyte using its full descriptive name.
    - CAS Number—Displays the analyte using its Chemical Abstracts Service (CAS) number.
7. In the Category field group, click File Import.
  
  Note: The options in the File Import category provide advanced configuration settings for AssayNet LIMS to efficiently manage the flow of data from the instrument's result files back into the application. In most cases, these settings are left as default.
  1. Complete the following fields as required:
    - Auto Archive—Defines the time interval (in days, hours, or minutes) after which imported files are archived. A value of 0 disables archiving.
    - Poll for Results—Specifies the interval (in milliseconds) for checking new result files. A value of 0 disables polling.
    - Instrument Application Name—Specifies the name of the instrument's software application used for managing imports.
    - Instrument Application Class Name—Indicates the class name of the instrument application. Use the show running class names option to identify the correct name.
    - Instrument Start Send Keys—Defines the keys or commands required to start the instrument's operation.
    - Instrument End Send Keys—Defines the keys or commands required to stop the instrument's operation.
    - File Name Replacement Characters—Allows replacement of invalid or unsupported characters in file names with specified characters.
    - Instrument Application Character Delay (ms)—Specifies the delay (in milliseconds) between sending characters to the instrument's application.
    - Delete After Import—Deletes the file from its source location after it has been successfully imported.
    - Continue On Error—Allows the import process to proceed even if errors occur.
    - Delete Before Reading—Deletes the file from its source location before it is read by the system.
    - Labels File from Lab Job—Uses the labels associated with the lab job to identify or process the imported file.
    - Read First Line Only—Processes only the first line of the file.
    - Read Last Line Only—Processes only the last line of the file.
    - Auto Upload (requires Upload Service)—Automatically uploads files for import.
    - Results File Date > Run Date—Ensures that the date of the results file is after the run date, to prevent older files from being imported.
8. In the Category field group, click File Export.
  
  Note: The options in the File Export category are used to configure the labels that AssayNet LIMS generates for importing into the instrument for analysis. The File Format provides a comprehensive list of commonly used instruments along with their standard label configuration requirements. If the predefined configurations do not meet the specific label file format requirements of the instrument, the labels can be customized for specific needs in the Export Data Options screen within the Setup. For more information, see Add Export Data Options.
  1. In the Sample Label Export category field group, complete the following fields as required:
    - Init. Meas. Conversion—Applies a conversion factor to the initial measurement values before generating the label file.
    - Final Meas. Conversion—Applies a conversion factor to the final measurement values before generating the label file.
    - Init. Meas. Text—Adds specific text or labels to represent the initial measurement values in the label file.
    - Final Meas. Text—Adds specific text or labels to represent the final measurement values in the label file.
    - File Format—Provides predefined configurations for commonly used instruments, ensuring the generated label file matches the instrument’s required format.
  2. In the Replicate Indication category field group, complete the following fields as required:
    - LIMS Default—Uses the replicate numbering as configured in AssayNet LIMS for the label file.
    - Without Replicate Numbers—Excludes replicate numbers from the generated label file.
    - Add Character—Appends a specified character to replicate identifiers in the label file for differentiation.
    - Make Duplicates Unique—Ensures unique identifiers for duplicate entries in the label file.
    - Unix-style Carriage Return—Generates the label file with Unix-style line endings for compatibility with certain instruments.
    - Use Custom File Dialog—Allows customization of the file dialog for managing label file exports.
    - Export Lab Job Data—Includes lab job-related information in the generated label file.
    - Export Unique Sample IDs—Ensures each sample has a unique identifier in the label file.
    - Use Short File Names—Shortens file names for compatibility with instruments that have file name length restrictions.
  3. In the Concentration category field group, select from the following options:
    - Calibration Units—Exports concentration values using calibration units for compatibility with the instrument.
    - Sample Units—Exports concentration values using sample units as specified in the configuration.
  4. Complete the rest of the options as required:
    - Initial Measurement Unit Symbol—Specifies the unit symbol for the initial measurement in the label file.
    - Final Measurement Unit Symbol—Specifies the unit symbol for the final measurement in the label file.
    - Default Initial Measurement—Defines a default value for the initial measurement if it is not provided.
    - Default Final Measurement—Defines a default value for the final measurement if it is not provided.
9. In the Category field group, click File Location.
  
  Note: The fields allow you to specify the locations where AssayNet LIMS will generate or access files, along with the file extension associated with each file. Most instruments require specifying locations for the label and result files. However, some instruments. However, some instrument manufacturers, such as Perkin Elmer, whose instruments store data in an Access database, also require the database location to be entered in the Workspace field.
  1. Enter the location for the required fields. Use the Folder icon to browse for the location of the file.
  2. Enter the file extension in the field next to the location.
10. The Header/Footer and Excel categories can be left as default.
Click OK.
To configure the rest of the options for the import template, see: