Validation

By default, parameters for tracks are validated to catch errors at creation time rather than upload time.

In this example, we set fake_param. Note that track object is created with no errors…

import os
import trackhub

hub, genomes_file, genome, trackdb = trackhub.default_hub(
    hub_name="quickstart",
    genome="hg38",
    email="you@email.com")

track1 = trackhub.Track(
    name="signal1",
    source=os.path.join(trackhub.helpers.data_dir(), 'sine-hg38-0.bedgraph.bw'),
    fake_param='asdf',
    tracktype='bigWig -2 2',
)
trackdb.add_tracks(track1)

…but when we render the track either by printing it directly, or indirectly by rendering any of its parents, we get validation errors:

print(trackdb)

Traceback (most recent call last):
trackhub.track.ParameterError: The following parameters are unknown for track type bigWig -2 2: {'fake_param': 'asdf'}

If we specify a correct parameter name, but the value is incorrect, we get a ValidationError (maxHeightPixels should be a colon-separated values, not an integer):

track2 = trackhub.Track(
    name="signal1",
    source=os.path.join(trackhub.helpers.data_dir(), 'sine-hg38-0.bedgraph.bw'),
    maxHeightPixels=15,
    tracktype='bigWig -2 2',
)
trackdb.add_tracks(track2)
print(track2)

Traceback (most recent call last):
trackhub.validate.ValidationError: Value 15 failed ColSV3 validation; Example value(s): 'a:b:c' or '0:10:100'

Sometimes the validation is too picky, or perhaps you’re using a beta version of the Genome Browser with additional features that trackhub does not yet know about. In that case, we can disable the validation by setting settings.VALIDATE to False:

trackhub.settings.VALIDATE = False
print(trackdb)

track signal1
bigDataUrl signal1.bigWig
shortLabel signal1
longLabel signal1
type bigWig -2 2
fake_param asdf

track signal1
bigDataUrl signal1.bigWig
shortLabel signal1
longLabel signal1
type bigWig -2 2
maxHeightPixels 15

Updating parameters

The track hub specification changes. In order to stay up-to-date with these changes, the trackhub.parse module can be used to parse the HTML of the Track Database Definition page and create the corresponding Param objects.

The general workflow is to run:

python trackhub/parse.py > parsed_results.py

And then use a diff tool (meld, vim -d, etc) to manually evaluate the difference between the existing parsed_params.py module and the output generated by trackhub/parse.py. In general, mostly only the validators will be different, although there are some params that are not defined in the database documnet and had to be added manually.

After making the necessary changes, please either open an issue or create a pull request on the GitHub repository.