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Core Informatics Utilities

Freezer configuration

A utility for generating configuration data in the form of Excel files is available as a Python (2.7+) script:

freezer-configuration-generator.py

The script makes no assumptions about the freezer layout. Any of the following are possible:

FREEZER > SHELF > RACK > DRAWER > BOX

FREEZER > SHELF > BIN > BOX

In the first example, one might want to configure 1 freezer, which contains 3 shelves. Each shelf would contain 5 racks, each rack 7 drawers and each drawer 4 boxes.

Freezer Shelf Rack Drawer Box
# of containers per parent 1 3 5 7 4
Expected container totals 1 3 15 105 420

The script abstracts out each level into a "container", creating a tree described as c1 > c2 > c3 > c4 where c1 is the parent of c2, etc...

Input

The configuration parameters are to be loaded via a YAML-based configuration file, which is easier for humans to edit. See configuration/sample_configuration.yaml for an example that matches the example above.

Pick a delimiter - when creating the location names, include a delimiter if desired. For example, F2S3R1D1B4 vs F2-S3-R1-D1-B4:

name_delimiter: "-"

Set what containers to parse through:

containers_to_use:
  - c1
  - c2
  - c3
  - c4

Set up the freezer:

freezer: F1
barcode_freezer: FRZ1

Lastly, populate the following dictionary in a way that best reflects your environment. Here are definitions of the configuration options:

  • name_prefix - the human-readable prefix for this level. Example: 'S' for Shelf
  • name_starting_index - the human-readable container-integer for this level. Example: '1' would be added to 'S' to create 'S1' (Shelf #1).
  • barcode_prefix - the LIMS-specific barcode for the container type. Example 'SHF' for Shelf.
  • barcode_starting_index - the LIMS-specific and next-available barcode integer for the container in question. Example: '374' should be added to 'SHF' to create 'SHF374' (LIMS unique barcode identifier for that shelf container)
c1:
  name_prefix: S
  name_starting_index: 1
  barcode_prefix: SHF
  barcode_starting_index: 1
  number_to_create: 3
c2:
  name_prefix: R
  name_starting_index: 1
  barcode_prefix: RCK
  barcode_starting_index: 1
  number_to_create: 5
c3:
  name_prefix: D
  name_starting_index: 1
  barcode_prefix: DRW
  barcode_starting_index: 1
  number_to_create: 7
c4:
  name_prefix: FB
  name_starting_index: 1
  barcode_prefix: FB
  barcode_starting_index: 1
  number_to_create: 4

Output

Output (for each level) will need to be 3 columns. Headers are

  • BARCODE
  • NAME
  • LOCATION BARCODE

The values for BARCODE should remain blank, but are there as placeholders for LIMS-generated barcodes. The LOCATION BARCODE is the parent entity's barcode. For example, if entering a SHELF, then the LOCATION BARCODE would be the parent FREEZER barcode.

Example Excel output:

BARCODE NAME LOCATION BARCODE
F2S1 FRZ2
F2S2 FRZ2
F2S3 FRZ2

The script will output an individual spreadsheet for each level processed. The example above (C1 > C2 > C3 > C4) would generate c1_exceldata.xlsx, c2_exceldata.xlsx, c3_exceldata.xlsx, and c4_exceldata.xlsx. Files are written to the output/ folder, within a subfolder named after the configuration filename (without path or file extension). In the case of the input file 'configuration/sample_configuration.yaml', the output folder/subfolder would be 'output/sample_configuration/'.

Dependencies

The xlsxwriter module is required and can easily be installed with pip install xlsxwriter.

The PyYAML module is required and can easily be installed with pip install pyyaml.