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- Can authentication be accomplished via the CLC lims and then a token be passed to minilims as a form of SSO?
- 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
- 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
- not clear if redmine is the right solution, but it has its place now. would need similar functionality, probably with better integration with other components.
- 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
- 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
- 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.
I uploaded this info to confluence.
- Sample submissions are required to be in a plate format with 95 samples and 1 random blank.
- We ask for concentration, but we re-quantify and it would be great to be able to enter those new numbers into the database.
- 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.
Functionality/Page(s): Integration with Submitting DNA Sequencing requests to service providers
- Currently I have to enter sample information onto the Core Facility website by hand. Automation of this would be complicated by my need to assign billing to different accounts. In addition, after Tom has made the flowcell I go onto Wikilims to get the flowcell name and lane assignments for the samples I submitted.
- If it is a 384-plex I make a new name for the sample submitted that is not recorded anywhere (could be written in redmine, but I don't always remember). The database lane_id is also appended to the name so there is a numerical way to check back, but people like a human readable name that correlates to the project.
- If samples are going to be sequenced off site then, in addition to the above steps I need to create additional emails and packing slips.
Functionality: QC Scripts
- QC Scripts
- Comments and request changes for QC output
- Besides the changes I listed above, but the biggest bug is that the scripts look for the cut site overhang and then the barcode. Barcodes containing the cut-site overhang are not recognized and we see it as 0 reads. The data pipeline does barcode and cut-site recognition simultaneously and so you still get data for these barcodes.
- Am excited by the possibility of pulling reports off the Illumina machines to further our QC. I was also introduced to a Java based program, FastQC, which may be helpful for us.
- Assuming qc reports are pulled into minilims and parsed, how flexible can we do queries to find statistics over time and although each report is by lane, it contains plate information. slice and dice
Functionality/Page(s): Data Distribution
- 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 the sequence data.
- Rob Elshire will be producing a standard for information (In my mind I think of it like MIAME or MIAPE standards).
- 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:
- could be modelled on the distribution that our sequencing facility produces
Functionality/Page(s): Billing
- minilims will provide a "dashboard" page
- dashboard info from Theresa Theresa will define the information on this page. I'm not sure what "level" of view she needs. per project, per sample, per order?
- minilims can make a RESTful query to CLC LIMS/Billing System and return existing invoice information per project (or sample or order)
- minilims page will provide functionality to open an existing invoice (in new window?)
- minilims page will provide functionality to submit an HTTP GET or POST to RESTful interface in the CLC LIMS/Billing System that will
- provide an order or invoice number (available to minilims at time order is placed), a line item(s) description, price, quantity
- service will create an invoice and return a reference to the invoice so that it can be opened from minilims
Functionality:Page(s): Misc operations
- Configure new adapter plate configurations
- self service interface/upload?
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