DPL-240 - The sequencing team would like a web page within the LIMS where they can either add annotations or upload associated documents to a sequencing batch (C=M, V=4)

[stevieing]

Description

Current process:

• you print batch sheets from Sequencescape
• You annotate them with various pieces of information e.g. volume, amount of elution buffer, loading concentrations, instrument number
• Once you have finished you need to keep a copy of annotations (which should not be seen by the customer) for future reference
• Each batch sheet is scanned and placed in an archive directory
• Once a week someone runs a python script which takes each archived batch sheet and renames it with the unique batch id to identify it later on
• The files are then checked manually to ensure all of the files have been renamed
• You currently produce 50-100 batch sheets a week

Limitations of current solution:

• The script is only 95% effective as if it can’t rename the file it drops it
• The script requires the use of a third party library Tesseract OCR to read from the pdf
• You have contacted IT and they have indicated that the script needs to be secure and maintained
• The script is run on the command line so note everyone has the skills to be able to set it up and use it
• The script is not maintainable as it was created by a former colleague and no-one has the ability to amend or improve it

Ideal solution:

• a web page within our current LIMS where you can either add annotations to a current batch or upload associated documents which would then be associated with that batch
• ability to upload several documents to a single batch

Who the primary contacts are for this work Robert / Tristram

Knowledge or Stake holders Other people that may have specific knowledge about this work or have a stake in how it is implemented. e.g. John Smith is an expert on x

Additional context or information Relates to RT740861 The current script: Python-batch-script.txt

[stevieing]

20/01 - Emma to discuss with Rich about whether there needs to be a bigger process change. A lot of this seems to be unnecessary. Also the SSRs spend at least half a day a week preparing batch sheets. The question is can we remove the need for them but still allow the sequencing team to add annotations to the batch.

[stevieing]

RT740861

[harrietc52]

James thinks uploads docs used to be possible in back end code, but was no longer being used (and out of date code).

[harrietc52]

Outputs:

• show them how to use current annotation feature, and if this is enough
• or figure out what extra fields are needed
• or if they just want to attach document
• or if they do need a new page, why and what for