Page History

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Overview: Detailed Workflow Spec (slides)

Functionality: Staff authentication and authorization- 10/25/12- no interaction possible

• Can authentication be accomplished via the CLC lims and then a token be passed to minilims as a form of SSO? no
• It isn't clear from the minilims docs whether built-in roles can be extended or if roles can be given permissions on a per-page or per data object basis.
  • IGD will be preparing a list of roles and map them the list of pages and we will compare how they map to minilims built-in versus cu$tom dev

Functionality: Customer Authentication and Authorization- 10/25/12- this has been eliminated

• customers will log into the CLC lims (as they do for other cores)
• CLC lims will collect and store payment information (including PCI-DSS scope)
• customers will be handed off to the sample submission interface in minilims where they will provide GBS specific ordering information
  • implies that no additional authentication is needed for minilims explicitely, pass a token from CLC lims
• Data distribution: see data distribution section

Functionality: Project management- 10/25/12- still not started

• What we like about redmine-  A really nice way to see the history of a particular plate of DNA or project:
  • Project summary: enzyme to use, contact information, expected sample number, comments for data analysis
  • Project workflow where we can check off status and note if something did not go as expected
  • Links that cross-reference.  I link all costs to plates so I know what has been paid for.  We also can link redo plates with the original preps.
  • Upload submission sheet, quantification, experion files (.pdf)
  • Note payment status
  • Track optimization results and R&D
• Would be great if we could check in samples are received when we print the barcode and automatically notify sender that they have arrived.

Data Structure: GBS Database Schema- 10/25/12- trying to replicate

• May not need full implementation, especially most of "passport" info.
• should be extended for Stat and QC management. right now the tables for "stat" and "qc" are really just placeholders.

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• re-implement
• sample submission change requests
• suggest implementing as part of LSCLC Cores LIMS
  • Single Sign-in with other cores. consistent customer interface for all services.
• could populate information in Minilims module, or customer development within LSCLC LIMS
• Can probably use the order forms in minilims- no
  • integrate with LSCLC LIMS authentication
  • consider possible dual-path authentication that supports cuwebauth as an option
• concept slides
  **Step 1 and 2 are literally true. customer will authenticate using CLC lims - customer will select GBS as the service and will provide payment information - customer session will be passed to Minilims
  • #7 we should consider querying minilims from our core lims and displaying the status information along with other core services on that dashboard.

• Sample submissions are required to be in a plate format with 95 samples and 1 random blank. - need coding 
• We ask for concentration, but we re-quantify and it would be great to be able to enter those new numbers into the database.- done
• I would love a system which would notify sender when I check in the DNA so I don't have to manually send them an email.

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• no changes required at this time ???
• possibly change SOP to record that data was released
• Our current scope does not include any changes to data distribution, which is currently done manually via dropbox or hard drive.
• detailed specification for the information/format of data and metadata distribution:
  • Rob Elshire will be producing a standard for information (In my mind I think of it like MIAME or MIAPE standards).
    there may be different definitions for different classes of customers
    • customers that receive only sequence data and metadata about panel in the form of a "Key File".
    • customers for whom the facility has produced genotypes. they may or may not also want will also receive the sequence data.
• build a distribution mechanism that defines the contents of an archive file that can be accessed via web link, including programmatically (curl or wget) and suitable notification
  • could be modelled on the distribution that our sequencing facility produces
    • note use of "cntrl" parameter which is a keycode so that anyone with that link that includes that parameter can download the file without explicit authentication. Since it could be brute forced it nags at me a little bit, but it does make programmatic downloads easier and security by obscurity should be sufficient enough for this purpose.
  • CLC will provide storage available to minilims from which files can be served. whoever runs the pipeline analysis will assemble archive and place in filesystem

    data distribution spec:- don't worry about specific files, just need a system to distribute zipped file.

Functionality/Page(s): Billing

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• Configure new adapter plate configurations - done
  • self service interface/upload?

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• Make more editable.  Need to be able to edit web submission fields after they are entered into database. - done
  • Sometimes we find mistakes after data has been analyzed, these revisions must be tracked somehow.
  • Other things we may want to change
    • Allow edits to submission before approval?  Keeps from having to reject over small issue, can just edit and approve.
    • Other mistakes (i.e. taxa names, standardizing project names) only a special person can enter these and it isn't easy- keep it that way?
  • Batch edits?