CGI Testing

Before testing your CGIs, check the version notes for recent changes particular to your CGIs. Pay extra attention to the changes when testing.

hgTracks, hgc

1. The TrackCheck robot checks this pretty thoroughly
2. manually check anything that has been an issue during the past 2-week release cycle
3. hgTracks:
   1. set position to 20bp & turn on all the tracks in hg18 to dense (using configure page); make sure all tracks load
   2. check that drag/reorder of tracks works
4. hgc: check the hgc details of one track per group on hg18, try a few links on the details page for a few, and try at least one composite to try composite specific things like metadata link.

hgTrackUi

There are a couple of tracks to always check since they are very popular.

• ENCODE
  • test the correspondence between the matrix and the list of tracks when you turn on or off different tracks, including the graying out of boxes in the matrix
  • test different views for multiple tracks while testing correspondence between matrix and list of tracks
  • test one track that has 3 dimensional matrix
  • try sorting list of tracks by different columns
  • test links at the top of the page to downloads, subtracks and description
  • test that the buttons allowing users to go to super-tracks from child-tracks at the top of the page work
• Conservation (a "full" track like the one found on hg19)
  • test all aspects and buttons of the multiz track, including codon frames and the mini-wiggles visible when both the subtrack and parent track are on "full"
  • use this as an opportunity to test all aspects of a wiggle track
  • try filtering by score
• SNPs
  • test that adding different gene prediction tracks do change the details page for individual SNPs
  • test either the Minimum Average Heterozygosity or Maximum Weight filtering
  • test the filtering by attribute
  • test color specification, including changing the default color for a specification
• mRNAs
  • test filtering by one and more than one search term, as well as different filtering options
  • test that the coloring by codons/alignment function as expected

Finally, test a few random tracks from a few different assemblies (good candidates with non-standard trackUis include Chain/Nets, TransMap, Human Proteins, Restriction Enzymes). A fun one to test is HapMap LD Phased on hg18 since it has a radically different hgTrackUi.

Also test the "configure" button for one assembly.

hgGene

1. Heather has a robot to check this CGI
2. test one known gene - click off-site, check entire page
3. test all possible paths among KG, PB, GS, VG (not that you wind up in mouse VG and need to use "Other Species" to get back to human.)

hgNear

1. To test on this click on "Gene Sorter" from the blue navigation bar.
2. Type a gene into the search text box
3. Pick a gene that has a long list of results.
4. Test sort by.
5. Test configure (make sure new columns show up and test the order feature)
   • Expression colors (change them to see if they are displaying)
6. Click the column headers to make sure that the descriptions show up
7. Click on a couple of entires to make sure they display in the browser.
8. Click on "sequence" from the sorter
9. Click on "filter" and try filtering from a specific column. Don't for get to put a "*" next to the search term or it most likely won't return any results.

hgCustom

1. Test all three methods of entering a CT: typed in, uploaded by file, URL.
2. Test editing, deleting, adding, updating, HTML docs, etc.
3. Test adding mutiple tracks at once (multiple tracks in one file, multiple URLs, and pasting in mutiple tracks)
4. Test CTs in relation to the Table Browser.

• See also examples page here: Custom Track Examples

hgVisiGene

1. test the search box by entering a gene name
2. check the zoom buttons
3. check that the "Gene" link opens the correct gene details page, and that that "visiGene" link in that gene details page retrieves the correct images in visiGene
4. pick an image and check all of the links for that page
5. for images composed of several smaller images, check that the pane descriptions are displaying correctly (not all panes will have an associated pane description)
6. (Note: the images from Mahoney are a subset of the MGI/Jax images. The Mahoney images should list two sources and should show two sets of acknowledgements.)

hgTables

1. check all drop-downs
2. press on summary/stats button
3. do an intersection with a couple of different output formats
4. make sure filtering is functioning
5. create a custom track in the browser
6. check all output formats
7. try sending output to Galaxy and GREAT; make sure checkboxes stay checked when applying filters, etc.
8. do a subtrack merge (select a table from a composite track to get the option)
9. do a correlation
10. try defining regions

hgPal

1. check a "Protein FASTA" click-through from a UCSC Gene details page
2. check a "CDS FASTA" click-through from a RefSeq Genes details page
3. using the Table Browser, choose "CDS FASTA" as the output format (this should work for any genePred track)
4. check that different settings give expected results

hgBlat

1. perform both a nucleotide and a protein search with default settings
2. make sure colors listed in description section are right
3. zoom in on an alignment and test "View details of parts of alignment within browser window"
4. try different sorts and output types
5. make sure all the buttons work, including uploading a file
6. try uploading a file with too many bases or too many queries and verify error message

hgPcr

1. test some perfectly matching primers, including a pair on the negative strand
2. find a pair of primers that shouldn't match UCSC Genes and test that they don't
3. vary settings and input primers for several assemblies and see if results make sense
4. for human and mouse browsers, test the "UCSC Genes" target. Check that UI functions as expected
5. check that the UI functions as expected for regular primers as well

hgLiftOver, hgConvert

1. Choose an assembly and go to hgTracks
2. Hit "Convert" in the blue bar at the top of the page
3. Compare the output to the same conversion using liftOver:
4. LiftOver is at Home -> Utilities -> Batch Coordinate Conversion (liftOver)
5. Test both position and BED format
6. Test a variety of settings
7. Try converting multiple positions at once
8. Try uploading a file

pbGateway, pbGlobal, pbTracks

1. general testing; click around
2. enter a protein symbol
3. review results page
4. click into pbGlobal and check display

hgSession

1. check that a new session can be saved
2. check that old sessions are still there
3. delete a session
4. check browser & email button; click the title of session & make sure you can save changes to the description
5. try loading a session via a file and via a URL
6. logout and try to load a session that can be shared and one that can't be shared

hgGenome

1. find it by going Home -> Genome Graphs
2. upload a dataset from a file
3. upload a data set from a URL
4. import data from a track
5. change some configurations
6. check that "browse regions" & "sort genes" work
7. check the correlate button

Some good genome graph data for testing: http://hgwdev.cse.ucsc.edu/~rhead/genomeGraphsWithColumns

cartDump, cartReset

1. check cart
2. reset cart
3. check cart again

See also: cart test protocol

hgApi

This CGI is responsible for the metadata "..." links on the hgTrackUi page and the "metadata" links on the hgc details pages of composite tracks with metadata.

1. click on a "..." link and check that it opens up - no need to check the content. You only need to test one "..." link - if hgApi is broken, it will break all "..." links.
2. This CGI can also be tested by clicking on a "meatadata" link in hgc details and check that it opens up - no need to check the content.

Probably doing 1 or 2 is sufficient, but it is a good habit to have the testers of hgTrackUi and hgc check 1 and 2 respectively, that way we are double covered in case one person forgets.

hgEncodeVocab

1. Go to an ENCODE track, most matrix headers should be links. Click on them, should take you to a page with a row of info about the term.
2. Go to a couple of these pages and check that the sections are displaying (these pages use hgEncodeVocab to display the info on them):
   • Registered Variables
   • Antibodies
   • Human Cell Types
   • Mouse Cell Types
3. Check a few links in the metadata from hgc details (click "metadata" link to view other links) or hgTrackUi (click "..." link to view other links)