Barcodes.md

Barcodes for the study are generated as CualIDs using ID3C's id3c identifier mint command.

A good overview of the study's barcodes exists elsewhere.

Creating new collections

Before creating a new collection (typically for a new study arm), the following questions should be answered:

• What is the new collection name?
• What do you want the collection barcode label to say?
• How many replicates do you want? (e.g. singlet, duplicate, triplicate)

Once these concerns are addressed, use the id3c identifier set command to create a new collection. Then, create a new label layout for the labelmaker. Now, you're ready to mint barcodes!

Note: One-off requests for new collections do not necessarily need to have their label settings merged to master or be tracked in the following barcode settings table. For example, if an identifier set's layout normally prints two copies of each barcode, you can locally edit the appropriate class in the labelmaker.py for the run.

Once the labelmaker is ready with the new layout, announce in the slack #barcodes channel that the barcodes for the new identifier set can be requested, and add the identifer set to the table below on this docs page.

Note: If your new layout uses tiny barcodes (LCRY-2380), or if your new collection will need to have its sample identifiers backfilled for another reason, then you will also need to add the new collection sets' name to the query in the backfill sample ids job in addition to creating the new layout in labelmaker.py.

Making new barcodes

Each type of barcode used by the study is printed on different labels:

Different study arms use different colors and different numbers of copies of each barcode, described by this spreadsheet and summarized below:

Note: The Barcodes/sheet reflects the number of unique barcodes per sheet according to the default copies per barcode of each collection set. This number will change if you specify a different number of copies per barcode using the --copies-per-barcode option when minting or creating labels for barcodes.

Identifier set (type)	SKU of labels	Barcodes/box	Barcodes/sheet	Notes
samples	LCRY-2380	1,020	51	in duplicate, with the last column blank
collections-seattleflu.org	LCRY-1100-Y	1,040	52	These are used for retrospective SCH samples
collections-kiosks	LCRY-1100-Y	520	26	in duplicate, one-off mint of singlets for shelters
collections-kiosks-asymptomatic	LCRY-1100	1,040	52
collections-swab&send	LCRY-1100-G	260	13	in triplicate, with the last column blank
collections-swab&send-asymptomatic	LCRY-1100	520	26	in duplicate
collections-self-test	LCRY-1100-G	260	13	in triplicate, with the last column blank
collections-household-observation	LCRY-1100-O	260	13	in triplicate, with the last column blank, one-off mint of singlets for baseline swabs
collections-household-observation-asymptomatic	LCRY-1100-O	1,040	52
collections-household-intervention	LCRY-1100-B	260	13	in triplicate, with the last column blank, one-off mint of singlets for baseline swabs
collections-household-intervention-asymptomatic	LCRY-1100-B	1,040	52
collections-environmental	LCRY-1100-R	1,040	52
collections-fluathome.org	LCRY-2380-Y	2,380	119
collections-scan	LCRY-1100	520	26	in duplicate for now, might be triplicate if we start ROR
collections-scan-kiosks	LCRY-1100	1,040	52	SCAN STAVE-surge testing around vulnerable/exposures
collections-scan-tiny-swabs	LCRY-2380	2,380	119	singlets, TINY SCAN
collections-clia-compliance	LCRY-1100	1,040	52	CLIA barcodes (default layout)
collections-clia-compliance	LCRY-2380	2,380	119	CLIA barcodes ('small' layout)
kits-fluathome.org	LCRY-1100-B	1,040	52
test-strips-fluathome.org	LCRY-2380-G	2,380	119
samples-haarvi	LCRY-2380	2,380	119	small aliquoting barcodes for HAARVI
collections-haarvi	LCRY-1100	1,040	52
collections-household-general	LCRY-1100-O	1,040	52	Season 3 household collection
collections-uw-home	LCRY-1100-B	520	26	in duplicate, Husky Coronavirus Testing mail (at-home)
collections-uw-observed	LCRY-1100-B	1,040	52	Husky Coronavirus Testing kiosk (in-person)
collections-uw-tiny-swabs	LCRY-2380	2,380	119	singles, UW Tiny Swabs (pilot project)
collections-uw-tiny-swabs-home	LCRY-2380	2,380	119	singles, UW Tiny Swabs at home (unobserved)
collections-uw-tiny-swabs-observed	LCRY-2380	2,380	119	singles, UW Tiny Swabs in-person (observed)
collections-childcare	LCRY-1100	1,040	52	INACTIVE, singles, Childcare Study
collections-school-testing-home	LCRY-1100	520	26	INACTIVE, duplicates, Snohomish Schools at home
collections-school-testing-observed	LCRY-1100	1040	52	INACTIVE, singles, Snohomish Schools observed/in-person
collections-apple-respiratory	LCRY-1100	520	26	duplicates, Apple Study
collections-apple-respiratory-serial	LCRY-1100	520	26	duplicates, the "serial" barcodes for Apple Study
collections-adult-family-home-outbreak	LCRY-1100	1,040	52	singlets, Adult Family Home (AFH) Outbreaks (not for Workplace Outbreaks)
collections-adult-family-home-outbreak-tiny-swabs	LCRY-2380	2,380	119	singlets, TINY Adult Family Home (AFH) Outbreaks (not for Workplace Outbreaks)
collections-workplace-outbreak	LCRY-1100	1,040	52	singlets, Workplace Outbreaks (not for Adult Family Home AFH Outbreaks)
collections-workplace-outbreak-tiny-swabs	LCRY-2380	2,380	119	singlets, TINY Workplace Outbreaks (not for Adult Family Home AFH Outbreaks)
collections-radxup-yakima-schools-home	LCRY-1100	520	26	INACTIVE, duplicates, Yakima Schools (Radxup) at home
collections-radxup-yakima-schools-observed	LCRY-1100	1,040	52	INACTIVE, singlets, Yakima Schools (Radxup) observed/in-person
collections-airs	LCRY-1100-W	520	26	duplicates, FH Prospective Sero Study AIM 3B (AIRS)
collections-cascadia-tiny-swabs-home	LCRY-2380	1,020	51	duplicates, tiny swabs, final column blank

The filepaths in the following examples may need to be modified according to the location of the backoffice on your local system. It also requires a connection to an ID3C database.

These types exist as identifier sets within ID3C, which you can verify by running:

PGSERVICE=seattleflu-production \
  pipenv run id3c identifier set ls

To generate, for example, one box of new Seattle Flu collection barcodes for printing, run:

cd ~/id3c

PGSERVICE=seattleflu-production \
  pipenv run id3c identifier mint collections-seattleflu.org 1040 --labels barcode-labels.pdf

An example value for 'labels': Melissa_collections-seattleflu.org_default_20_sheets_2021-08-04_1.pdf, where we find it useful to include requester's name, identifier set, layout, number of sheets, and date generated for file naming purposes.

Assuming you're on a Linux machine, you can stream the barcode minting process with tail -f /var/log/syslog.

The new identifiers and their associated barcodes will be stored in the ID3C database for future reference. A PDF of formatted barcode labels will be made and saved to your computer.

Open up the new barcode-labels.pdf file. It should have 20 pages (of 52 barcodes each) formatted to print on a box of LCRY-1100-Y sheets.

Note: If you need to recreate labels for a previously generated set of barcodes, use the id3c identifier labels command.
For example:

PGSERVICE=seattleflu-production pipenv run id3c identifier labels _barcode-labels.pdf

Modify the _barcode-labels filename at the end depending on what you want the output file to be called.

It will open up an interactive dialog and ask you which batch you want to reprint, and you’ll enter the index number of the batch you want to reprint.

Be mindful in what you select - do not want to reprint the same labels twice — duplicate barcode labels is no fun for us, the lab or participants.

Minting batches

We have a script on the backoffice server that is useful for generating batches of barcodes when the requester wants a maximum number of sheets in each PDF file.

The filepaths in the following examples may need to be modified according to the location of the backoffice and directories on your local system.

For example, if the requester asked for 40 sheets of CLIA barcodes in the small layout in files of no more than 20 sheets each, the command would be:

cd ~/id3c

PGSERVICE=seattleflu-production pipenv run /opt/backoffice/bin/mint-barcodes-in-batch \
  --identifier-set=collections-clia-compliance \ 
  --per-sheet=26 \
  --layout=small \
  --max-sheets=20 \
  --sheets=40 \
  --prefix="/home/ubuntu/temp/"

• --identifier-set: specifies which collection barcode to mint
• --per-sheet: specifies how many barcodes fit on a sheet of labels (refer to table above)
• --layout: specifies which label layout to print with. The default is 'default'.
• --max-sheets: specifies the maximum number of sheets per PDF file
• --sheets: specifies the number of sheets total to be minted
• --prefix: specifics the text to pre-pend to the filename; this sets the path. We've found it useful to include the requester's name, e.g., --prefix="/home/ubuntu/temp/Evan_"

Files will be named with this pattern: prefix_identifier_set_(the layout)(number of sheets in the file)sheets(current date)(the iteration number).pdf

For example: Peter_collections-uw-observed_default_15_sheets_2020-10-26_1.pdf

Uploading files to Google Drive

The Google Drive location where to put label PDFs is in the #barcodes channel topic in Slack. Name the PDF file clearly and put it into the appropriate folder in the Google Drive. The lab team will delete the PDF files from Google Drive when they have finished printing them. We don't delete the PDFs.

Printing files

When printing there a couple tips for higher-quality output:

1. Change the paper type to labels in your computer's print dialog.

2. Make sure the sheets are oriented correctly in the paper tray. The pre-printed number on each sheet marks the intended bottom left corner of the page.

3. Use the secondary or auxiliary paper tray on your printer if possible to avoid other people's print jobs interrupting yours.

Labels include a reference (e.g. seattleflu.org) so that there is a point-of-contact to gain more context about what's in a tube. Otherwise, the only information would be an opaque id. This is important for the future longevity of samples when someone unrelated to the current project may be responsible for their care.