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Converts iLab service requests to Illumina Clarity Projects.

Project description

UA-Project-Transfer

Transfers service requests from Agilent's iLab software to Illumina's Clarity LIMS software.

Motivation

To transfer service requests from iLab to Clarity LIMS programmatically.

Features

  • Creates projects in Clarity LIMS based on corresponding iLab service requests.
  • Route samples to the correct workflow in Clarity LIMS.
  • Validates service request prices.
  • If the transfer fails at any point in sample creation, there will not be side effects of project transfer.

Installation

git clone https://github.com/UACoreFacilitiesIT/UA-Project-Transfer.git

Code Example

cd UA-Project-Transfer/ua_project_transfer
python project_transfer.py --ilab {iLab environment} --lims {LIMS environment}

Tests

cd UA-Project-Transfer/ua_project_transfer/tests
nosetests test_project_lims_tools.py

How to Use

To use project_transfer with default settings in your environment, you will need to make a few changes:

Environment changes

  • Add a file named "lims_token.json" in the form of:

    • { "host": "{api_endpoint(https://.*v2/)}", "username" : "{api_creds_username)", "password" : "{api_creds_password}" }
  • Add a file named "ilab_token.json" in the form of:

    • { "token": "{ilab_api_token}", "core_id": "{ilab_core_id}" }

- If you want to customize logging, run monitoring, or credential harvesting, create a "core_specifics.py" file with that code. Otherwise, save the "core_specifics_template.py" file as "core_specifics.py".
  • To customize logging: Either save the "log_config_template.py" as "log_config.py" OR create a custom log_config file, including at least what is in the template file.

  • To customize run monitoring: Add the setup for whichever software monitoring you decide to use. Can be left blank if no monitoring is desired.

  • To customize credential harvesting: Either use what is written in the template, utilizing the two token files you just created. OR delete those two token files and implement your own credential harvesting method.

  • The wf_locations dictionary must also be updated to map the iLab Form names to their respective next_steps functions.

  • The unroutable_forms list must be updated to contain any iLab Form names you want to skip.

Clarity changes

  • The UDF's in either the custom form's grid or fields with _each_sample in their identifiers must be exactly the name of the target Clarity UDF.

  • A sample's container type's name must map exactly to a container type's name in Clarity.

  • Workflows can only have samples routed to them if they are active.

  • WF_STEPS in wf_steps.py must hold the mappings of conditions to a tuple containing (the workflow, the step name).

iLab changes

  • The code that interprets service requests (ua_ilab_tools) has a few requirements with you iLab setup:

  • Sample specific changes (sample grid):

    • The information for samples must be stored in a "grid" custom form data type.

    • The first column of that grid will be interpreted as the sample names.

    • Any text added to this grid will have it's input scrubbed so that it matches r"[^a-zA-Z0-9:,.+]", where '+' is replaced with "plus", and is encoded as ascii -- special characters are converted using unicodedata.normalize("NFKD", text).encode("ascii", "ignore").decode("ascii")

    • If a form is set up with 96-well plate(s) as the form's container type (see below how to set a form's container type), the it must have the column name of "Well Location".

      • The formats that are allowed in the "Well Location" column are A:1, H12, B09, or C:09 (of course including A-H and 1-12).
    • If a UDF is of the "numeric" type in Clarity, add that UDF identifier (the column name in the grid or the .*_each_sample form field identifier) to extract_custom_forms.py's ONLY_INT_FIELDS.

    • Similarly, anything that is set as a "Toggle Switch" UDF in CLarity should be added to extract_custom_forms.py's BOOL_FIELDS.


  • Price Check specific changes:

    • You will need to define the quantity of each unit of a charge in price_check.py's unit_definitions (e.g. {"each": 1, "prep":11}).

  • Form specific changes:

    • Custom forms with names that match the pattern in ua_ilab_tools' SKIP_FORM_PATTERNS will not be evaluated.

      • You can have a service request with a skipped form and a not skipped form, and the request will transfer.

      • Each service request can only have one form that has sample information.

      • Any custom form fields that end with "_each_sample" will be applied to every sample in the form.

        • For example, if your Clarity environment had the UDF "Concentration", and you wanted a single concentration value to be added to every sample within a form's sample grid, the identifier for that field in the custom form's iLab setup should say "Concentration_each_sample".
        • These identifiers must be exactly the name of the UDF in Clarity, before the "_each_sample" portion.
    • The container type of the form is determined by whether:

      • There's a grid column named "Container Name" (multiple 96-well plates)
      • There's a custom form field with the identifier of container_name (single 96-well plate)
      • Else, the container type is a Tube
    • If you need to add more container types or change these rules, you can do so by editing the .*_bind functions, and updating the con_strategy dict() in bind_container_info() in extract_custom_forms.py.

    • Each form must have only 1 container type.

    • Duplicate location values are handled based on the container type of the form. The rules for what is allowed are:

Container Type Duplicate Names Allowed Duplicate Wells Allowed
Tube :x: Always 1:1
96 Well Plate :heavy_check_mark: :x:

Credits

sterns1 raflopjr RyanJohannesBland EtienneThompson

License

MIT

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