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  1. LIMS
  2. LIMS-3234

Maldi Biotyper2 bi-directional interface revisited

    Details

    • Type: Improvement
    • Status: Open
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
    • Labels:
      None

      Description

      The Interface we developed form the tech manual, proved nonexistent, in classic vendor operation.

      Lesson for Bika - don't get complacent wrt critical documentation...

      However, it might be possible to use the XLS produced by the instrument, herewith to follow

      The summary of the results at the top of the CSV

      can easily be massaged into Bika's generic import format, by simply looking cell values up

      Online Converter

      It only features 2 organisms though.

      • Is their any possibility the vendor will add the extra columns for GreenHill? They should. We followed their manual up the garden path
      • How were the XLS and XLSX obtained? I understand the original out put of the instrument is HTML

      I think you answered some of these before...

        Issue Links

          Activity

          Hide
          lemoene lemoene added a comment -

          With the 3rd organism critical, we can import the first 2, and make Worksheet Templates for the 3rd for easy manual capturing from look-ups

          Show
          lemoene lemoene added a comment - With the 3rd organism critical, we can import the first 2, and make Worksheet Templates for the 3rd for easy manual capturing from look-ups
          Hide
          lemoene lemoene added a comment -
          Show
          lemoene lemoene added a comment - Attached Results CSV online
          Hide
          shaun Shaun Groenink added a comment -

          Ok, so those two organisma you see are first and second best match per sample. But we only ever refer to the first best match. However, there can be multple isolates per sample (eg. 075 in example has two isolates, but we would only report both first matches).

          Show
          shaun Shaun Groenink added a comment - Ok, so those two organisma you see are first and second best match per sample. But we only ever refer to the first best match. However, there can be multple isolates per sample (eg. 075 in example has two isolates, but we would only report both first matches).
          Hide
          lemoene lemoene added a comment - - edited

          Example COA 200727A uploaded

          Importing the first two IDs requires a small customisation to be used in the generic Bika importer, from where only the first ID be published, and all counts and secondary IDs kept online for the lab only. 3rd and further IDs, scores, will have to be captured manually

          Please confirm assumptions Shaun Groenink, Cara

          The above assumes that the header data, Results Overview will consistently be the same in the XLSXs you reap from the instruments.

          View online

          NB this remains a workaround

          Until full automation is achieved through reading the Instrument XLSX directly, this procedure will speed things up by a lot but a caveat remains in the conversion process, to be eliminated later

          SOP top level

          Please confirm first 2 steps Shaun Groenink , Cara

          1. Instrument exports HTML
          2. User convert it to XLSX
          3. Copy Results Overview rows, to Tab 1 of conversion spreadsheet
          4. NB Edit Manually remove secondary Isolates per Sample. Only one can ever be loaded
          5. The spreadsheet reads the data into Bika generic format on Tab 2 of the Conversion sheets
          6. The user reviews Tab 2 to be correct for all the samples, and then captures end in the first cell next row after the last sample

            View Online
          7. Export Tab 2 as CSV
          8. Import the CSV into Bika
          9. Bika automatically uploads the imported file as attachment to the worksheet containing the imported Analyses
          10. The user manually uploads the original instrument xlsx to the worksheet too
          11. The Analyses and Worksheets continue with standard Bika workflow towards Verification and Publication
          Show
          lemoene lemoene added a comment - - edited Example COA 200727A uploaded Importing the first two IDs requires a small customisation to be used in the generic Bika importer, from where only the first ID be published, and all counts and secondary IDs kept online for the lab only. 3rd and further IDs, scores, will have to be captured manually Please confirm assumptions Shaun Groenink , Cara The above assumes that the header data, Results Overview will consistently be the same in the XLSXs you reap from the instruments. View online NB this remains a workaround Until full automation is achieved through reading the Instrument XLSX directly, this procedure will speed things up by a lot but a caveat remains in the conversion process, to be eliminated later SOP top level Please confirm first 2 steps Shaun Groenink , Cara Instrument exports HTML User convert it to XLSX Copy Results Overview rows, to Tab 1 of conversion spreadsheet NB Edit Manually remove secondary Isolates per Sample . Only one can ever be loaded The spreadsheet reads the data into Bika generic format on Tab 2 of the Conversion sheets The user reviews Tab 2 to be correct for all the samples, and then captures end in the first cell next row after the last sample View Online Export Tab 2 as CSV Import the CSV into Bika Bika automatically uploads the imported file as attachment to the worksheet containing the imported Analyses The user manually uploads the original instrument xlsx to the worksheet too The Analyses and Worksheets continue with standard Bika workflow towards Verification and Publication
          Hide
          shaun Shaun Groenink added a comment -

          Yes, look sgood for workaround.
          Except, the "Analyte ID" will contain the sample name. "Analyte Name" is just the position on the plate, so is not linked to actual sample.

          Show
          shaun Shaun Groenink added a comment - Yes, look sgood for workaround. Except, the "Analyte ID" will contain the sample name. "Analyte Name" is just the position on the plate, so is not linked to actual sample.

            People

            • Assignee:
              shaun Shaun Groenink
              Reporter:
              lemoene lemoene
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              Watchers:
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              Dates

              • Created:
                Updated: