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  1. LIMS
  2. LIMS-1805

Instrument Interface. Horiba JY ICP

    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Critical
    • Resolution: Duplicate
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
    • Labels:
    • Epic Link:
    • Sprint:
      May 2015, Aug 2015

      Description

      I asked for the instruments full name and update the issue title then. Please ignore the XLS and use a CSV version of it

      1. ICP limstest bog envas.csv
        32 kB
        Pau Soliva
      2. lemoene 150806.txt
        2 kB
        lemoene
      3. RAW ICP 2013-12.pdf
        79 kB
        lemoene
      4. RAW ICP 2013-12.xls
        96 kB
        lemoene
      1. icpxmpl.png
        22 kB
      2. jira-capture-screenshot-20150922-131433-673.png
        171 kB
      3. jira-capture-screenshot-20150922-131551-859.png
        297 kB
      4. jira-capture-screenshot-20150922-134239-819.png
        174 kB

        Issue Links

          Activity

          Hide
          lemoene lemoene added a comment -

          I am splitting this issue into 2. Title is misleading by now too. Both small

          1. Error message resolution
          1. Line name as keyword
          Show
          lemoene lemoene added a comment - I am splitting this issue into 2. Title is misleading by now too. Both small Error message resolution Line name as keyword
          Hide
          lemoene lemoene added a comment - - edited

          So this is the only bit that remains. needs a quote, cannot be too difficult. Lower priority for now

          • Resolve ${analysis_keyword) in error message
          • Use full linename (quote) as keyword

          See LIMS-1988 re dealing with multiple instruments using the same keywords.

          To get pass it at Metron, we can use the full LineName from the file, e.g. Ca 315.887 but strip the space and . out of it as keywords do not allowed that in the LIMS. 315.887 refers to the wavelength in nm of the Ca's spectral analysis.

          e.g. read Ca 315.887 in the file and look up Ca315887 in the system, Mg 279.806 for Mg279806 etc. The element abbreviation and wavelength combination is pretty unique the lab ensures me.

          Please quote for this customisation. No doubt we'll run into this eslewhere too where the line name cannot be used and then we can reconsider the deluxe solution at LIMS-1988.

          Show
          lemoene lemoene added a comment - - edited So this is the only bit that remains. needs a quote, cannot be too difficult. Lower priority for now Resolve ${analysis_keyword) in error message Use full linename (quote) as keyword See LIMS-1988 re dealing with multiple instruments using the same keywords. To get pass it at Metron, we can use the full LineName from the file, e.g. Ca 315.887 but strip the space and . out of it as keywords do not allowed that in the LIMS. 315.887 refers to the wavelength in nm of the Ca's spectral analysis. e.g. read Ca 315.887 in the file and look up Ca315887 in the system, Mg 279.806 for Mg279806 etc. The element abbreviation and wavelength combination is pretty unique the lab ensures me. Please quote for this customisation. No doubt we'll run into this eslewhere too where the line name cannot be used and then we can reconsider the deluxe solution at LIMS-1988 .
          Hide
          lemoene lemoene added a comment -

          Confirmed. Imports correctly. It is only the Error message ${analysis_keyword) that needs to be resolved. The 'error message'itself is correct - the file includes AS Keywords for Analyses not requested

          Show
          lemoene lemoene added a comment - Confirmed. Imports correctly. It is only the Error message ${analysis_keyword) that needs to be resolved. The 'error message'itself is correct - the file includes AS Keywords for Analyses not requested
          Hide
          lemoene lemoene added a comment - - edited

          Some imported. Will investigate the others.

          I think the only bug could be the error message that does not rseolve

          And implementing the fix to use the full Linename as keyword.

          Investigatig. Uploading file ICPTest20160922.csv i ran this test with. Worksheet metrontest.bikalabs.com/worksheets/WS15-002

          Show
          lemoene lemoene added a comment - - edited Some imported. Will investigate the others. I think the only bug could be the error message that does not rseolve And implementing the fix to use the full Linename as keyword. Investigatig. Uploading file ICPTest20160922.csv i ran this test with. Worksheet metrontest.bikalabs.com/worksheets/WS15-002
          Hide
          lemoene lemoene added a comment -

          See https://jira.bikalabs.com/browse/LIMS-1988 re dealing with multiple instruments using the same keywords.

          To get pass it at Metron, we can use the full LineName from the file, e.g. Ca 315.887 but strip the space and . out of it as keywords do not allowed that in the LIMS. 315.887 refers to the wavelength in nm of the Ca's spectral analysis.

          e.g. read Ca 315.887 in the file and look up Ca315887 in the system, Mg 279.806 for Mg279806 etc. The element abbreviation and wavelength combination is pretty unique the lab ensures me.

          Please quote for this customisation. No doubt we'll run into this eslewhere too where the line name cannot be used and then we can reconsider the deluxe solution at https://jira.bikalabs.com/browse/LIMS-1988.

          More from IRC:

          <lemoene> rockfruit, do you know whether AS keywords will handle spaces and full stops, e.g 'Ca 315.887' ?
          <rockfruit> spaces? I really want to say no to spaces. let me check.
          <lemoene> maybe we could just strip them out. NP
          <lemoene> full stops?
          <lemoene> Ca 315.887 is the wavelength the ICP test for and appears like that in the results file
          <rockfruit> accepts [A-Za-z\w\d\-\_] - that's a-z, A-Z, word-characters, numbers, dashes and underscores. anything else fails validation
          <lemoene> just strip them out before loading and keep a keyword Ca315887 in the LIMS?
          <rockfruit> I'm not sure why the validator is so restrictive. offhand, can't think of a reason we couldn't allow keywords to be anything they want to be. BUT I'm sure we had a reason.... so needs some exploratory digging.
          <lemoene> if stripping them out works, fine
          <rockfruit> We use it for the ID of analyses in the AR... there are some restrictions there..
          <lemoene> ok. not lose time
          <rockfruit> yeah stripping sounds good, and is also a good plan. stripped, then the same no-duplications check applied. cannot clash with another service keyword, and cannot clash with a calculation interim field's ID.

          Show
          lemoene lemoene added a comment - See https://jira.bikalabs.com/browse/LIMS-1988 re dealing with multiple instruments using the same keywords. To get pass it at Metron, we can use the full LineName from the file, e.g. Ca 315.887 but strip the space and . out of it as keywords do not allowed that in the LIMS. 315.887 refers to the wavelength in nm of the Ca's spectral analysis. e.g. read Ca 315.887 in the file and look up Ca315887 in the system, Mg 279.806 for Mg279806 etc. The element abbreviation and wavelength combination is pretty unique the lab ensures me. Please quote for this customisation. No doubt we'll run into this eslewhere too where the line name cannot be used and then we can reconsider the deluxe solution at https://jira.bikalabs.com/browse/LIMS-1988 . More from IRC: <lemoene> rockfruit, do you know whether AS keywords will handle spaces and full stops, e.g 'Ca 315.887' ? <rockfruit> spaces? I really want to say no to spaces. let me check. <lemoene> maybe we could just strip them out. NP <lemoene> full stops? <lemoene> Ca 315.887 is the wavelength the ICP test for and appears like that in the results file <rockfruit> accepts [A-Za-z\w\d\-\_] - that's a-z, A-Z, word-characters, numbers, dashes and underscores. anything else fails validation <lemoene> just strip them out before loading and keep a keyword Ca315887 in the LIMS? <rockfruit> I'm not sure why the validator is so restrictive. offhand, can't think of a reason we couldn't allow keywords to be anything they want to be. BUT I'm sure we had a reason.... so needs some exploratory digging. <lemoene> if stripping them out works, fine <rockfruit> We use it for the ID of analyses in the AR... there are some restrictions there.. <lemoene> ok. not lose time <rockfruit> yeah stripping sounds good, and is also a good plan. stripped, then the same no-duplications check applied. cannot clash with another service keyword, and cannot clash with a calculation interim field's ID.

            People

            • Assignee:
              Espurna Pau Soliva (Inactive)
              Reporter:
              lemoene lemoene
            • Votes:
              0 Vote for this issue
              Watchers:
              4 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved:

                Agile