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  1. LIMS
  2. LIMS-3185

Processing bulk Dairy Samples 2. Batch Sample Import


    • Type: Story
    • Status: Resolved
    • Priority: Major
    • Resolution: Could be better
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
    • Labels:


      Using a first configuration for Bika LIMS being implemented at http://greenhilllabs.co.za/ analysing Raw Milk for Mastitis

      Continued from Processing bulk Dairy Samples 1. Configuration

      Import spreadsheet

      NB See using an improved spreadsheet, LIMS-3199 Batch Sample Import made simpler

      I updated the GreenHill Master Sample Import Template v1.0 with the new Profile and all GreenHills Clients and other config items, and removed everybody’s editing authorisation to protect its integrity.

      Please please make own copy when needed

      Batch header data

      On the first tab, Batch, atv the top, complete the Client information and other Batch header data from the lookups populated earlier

      Sample information

      1 Sample per row

      Please ensure all rows beyond the last, in this case 50th, Sample are empty, else it could cause an import error

      Should you need more rows, add more Samples sequentially, by selecting as series of the existing ones, than drag the selection by its bottom right handle down in standard spreadsheet fashion


      We assume the containers were pre-labelled and can either be scanned in, or are available in simple sequential order, say 001 to 999. These will be recorded in the LIMS as the CSID, Client Sample ID. Furthermore, in the best case scenario, cow IDs can be scanned in to and they became Patient IDs in the LIMS

      Date Sampled

      Capture the Sampling Date in the format YYYY-MMM-DD, and Time if required YYYY-MMM-DD hh:mm. The column is formatted to accept only valid dates and ind invalid input will be rejected. A date picker is available, but Googles does not capture the time

      Cow ID

      Capture the rest of the Sample information via the lookups provided and configured earlier. We assume the the Sample Container was labelled earlier and can be scanned, ditto for the Cow ID, scanned by RFID from the animals chip implant

      Test Panels / Analysis Profiles

      Select the Analysis Profiles to be used for requesting Analyses per Sample , more than one vcan be used. They are listed by their unique keywords which the system uses to identify them correctly

      Enter a 1 in the corresponding Sample and Profile intersect to select the Profiles to be used per Sample, we'll be using DU_MID_SCC (Dairy, Udder Health, Microbial ID and SCC) only, a combination of bacterial identification and SCC analyses. Leaving the field empty or entering 0 will see a Profile excluded


      Complete for all the Samples - in essence only the CSID, Sampling datetime and PatientID differ per Sample in this case, which means the sheets can be simplified further

      In a separate Story, we'll be investigating that, one could use a page like this, referenced by the true sheet to be imported:

      Download the sheet as CSV

      Import the CSV

      Also see the manual, Bulk Sample Import. The video Bika Batched Sample registration explains how this process would be completed manually, sans importing the Samples

      1. Load

      Navigate to the Client's Imports page, and pres Add, select the CSV and submit

      2. Validate

      The LIMS scans the file for its DB references to ensure all configuration entries, Client, Contacts, Sample Types etc do exist, and returns the Import with state Valid if all went OK, and the data can be imported


      If Invalid, the errors encountered will be listed at the bottom of the page and can either be fixed in the UI right there, or in the spreadsheets and re-imported

      To fix errors in the UI, navigate back to the Client's Imports list, and open the Import - it opens in and editable form where valid data entries can be looked up from the DB via drop downs

      Press Save when done, and if all errors were fixed, the import will be listed as Valid, and can then be imported

      3. Import

      If Valid, click import on the state drop-down (shown in previous screen shot). The import takes longer than the validation process as the new information is being written to the DB

      The new Batch

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        Issue Links


          lemoene lemoene added a comment -

          Note Batch issue, date not captured. Please enter in the UI

          logged at https://jira.bikalabs.com/browse/LIMS-3187

          lemoene lemoene added a comment - Note Batch issue, date not captured. Please enter in the UI logged at https://jira.bikalabs.com/browse/LIMS-3187


            • Assignee:
              lemoene lemoene
              lemoene lemoene
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