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| Before testing your CGIs, check the [http://genecats.cse.ucsc.edu/builds/versions.html version notes] for recent changes particular to your CGIs. Pay extra attention to the changes when testing.
| | This page is no longer maintained. |
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| ==hgTracks==
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| * The TrackCheck robot checks the first 4 links at the default position for every track in every assembly (except for UCSC Genes). If zoomcount is set to something higher than 1, it also zooms out and checks the first 4 links there, and repeats this until zoomcount is reached. Check the TrackCheck output (located in hgwdev:/cluster/bin/build/scripts/logs/) for errors. TrackCheck is run automatically on hgwbeta as part of the build process, but it also needs to be run by the hgTracks tester on hgw0 ([[CGI_Build_Process#Push_to_hgwN_only|instructions]]).
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| * Manually check anything that has been an issue during the past release cycle.
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| * Set position to a region of about 20bp and turn on all of the tracks in hg18 to dense (using configure page). You may need to do this in several chunks (as of the v244 CGIs, if you get too many tracks on at once, you will see an error that says "Image is over 32,000 pixels high (32013 pix) at the following track which is now hidden:"). Make sure all tracks load okay.
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| * Check that drag/reorder of tracks works
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| * Check that reverse works
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| * Check the various options on the configure page
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| * Try a few of the right click functions
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| ===track search===
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| * Try a search that will bring up the 3 different kinds of tracks, which are are shaded with different colors:
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| ** tan: super-track (has a folder/wrench icon)
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| ** light orange: composite (has a folder/wrench icon)
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| ** light yellow: an actual data track (not a container)
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| (note that ENCODE Regulation track on hg18 is a special kind of super-track)
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| * Make sure you can configure tracks via the folder/wrench icons as well as by adjusting the "view" drop-downs (after hitting submit on a configure page, you should be returned to the track search page)
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| * Try the different sort types ("Alphabetically" sorts on the longLabel)
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| * Check that the track description pops up when you click a blue track name
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| * Check that metadata appears when you click the "..." after a track name
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| ** Check that the links within the metadata work
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| * Try a couple of advanced searches
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| ** Make sure searching with "ENCODE terms" is working
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| ==hgc==
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| 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.
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| ==hgTrackUi==
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| There are a couple of tracks to always check since they are very popular.
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| * ENCODE
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| ** 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
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| ** test different views for multiple tracks while testing correspondence between matrix and list of tracks
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| ** test one track that has 3 dimensional matrix
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| ** try sorting list of tracks by different columns
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| ** test links at the top of the page to downloads, subtracks and description
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| ** test that the buttons allowing users to go to super-tracks from child-tracks at the top of the page work
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| * Conservation (a "full" track like the one found on hg19)
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| ** 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"
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| ** use this as an opportunity to test all aspects of a wiggle track
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| ** try filtering by score
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| * SNPs
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| ** test that adding different gene prediction tracks do change the details page for individual SNPs
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| ** test either the Minimum Average Heterozygosity or Maximum Weight filtering
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| ** test the filtering by attribute
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| ** test color specification, including changing the default color for a specification
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| * mRNAs
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| ** test filtering by one and more than one search term, as well as different filtering options
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| ** test that the coloring by codons/alignment function as expected
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| 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.
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| Also test the "configure" button for one assembly.
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| ==hgGene==
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| Pick a UCSC Gene / Known Gene on one of the organisms with a knownGene track (Human, Mouse, Rat, D. melanogaster, C. elegans, or S. cerevisiae). Then check:
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| * Under "Sequence and Links to Tools and Databases"
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| ** the internal links (in green boxes)
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| ** the external links (in blue boxes). Make an effort to see that these link to gene-specific pages. There should be a "User Annotations" link (to the wiki track) should be available for the later human and mouse assemblies.
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| * Check a representative link from each section.
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| * Make sure you can change the expression ratio to blue/yellow.
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| * In the "Orthologous Genes in Other Species" section, make sure that if there is a link in any particular column, all entries of that column have links (except for Zebrafish -- it doesn't have an hgGene page to link back to).
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| * Make sure the documentation links at the bottom of the page work.
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| * Check LS-SNP and Chimera links
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| ==hgNear==
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| # To test on this click on "Gene Sorter" from the blue navigation bar.
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| # Type a gene into the search text box
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| # Pick a gene that has a long list of results.
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| # Test sort by.
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| # Test configure (make sure new columns show up and test the order feature)
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| #* Expression colors (change them to see if they are displaying)
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| # Click the column headers to make sure that the descriptions show up
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| # Click on a couple of entires to make sure they display in the browser.
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| # Click on "sequence" from the sorter
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| # 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.
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| ==hgCustom==
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| # Test all three methods of entering a Custom Track (CT): typed in, uploaded by file, URL.
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| # Test editing, deleting, adding, updating, HTML docs, etc.
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| # Test adding mutiple tracks at once (multiple tracks in one file, multiple URLs, and pasting in mutiple tracks)
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| # Test CTs in relation to the Table Browser.
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| *See also examples page here: [[Custom_Track_Examples|Custom Track Examples]]
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| * Can also see Hiram's page of nearly all custom track types: http://genome-test.cse.ucsc.edu/~hiram/ctDb/hg19.chr21.ct.txt
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| ==hgVisiGene==
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| # test the search box by entering a gene name
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| # check the zoom buttons
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| # 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
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| # pick an image and check all of the links for that page
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| # for images composed of several smaller images, check that the pane descriptions are displaying correctly (not all panes will have an associated pane description)
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| (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.)
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| ==hgTables==
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| # check all drop-downs
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| # press on summary/stats button
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| # do an intersection with a couple of different output formats
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| # make sure filtering is functioning
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| # create a custom track in the browser
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| # check all output formats
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| # try sending output to Galaxy and GREAT; make sure checkboxes stay checked when applying filters, etc.
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| # do a subtrack merge (select a table from a composite track to get the option)
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| # do a correlation
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| # try defining regions
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| ==hgPal==
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| There are 3 ways to get to the hgPal CGI:
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| # check a "Protein FASTA" click-through from a UCSC Gene details page
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| # check a "CDS FASTA" click-through from a RefSeq Genes details page
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| # using the Table Browser, choose "CDS FASTA" as the output format (this should work for any [http://genome.ucsc.edu/FAQ/FAQformat.html#format9 genePred] track)
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| Check that different settings give the expected results.
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| ==hgBlat==
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| # perform both a nucleotide and a protein search with default settings
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| # make sure colors listed in description section are right
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| # zoom in on an alignment and test "View details of parts of alignment within browser window"
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| # try different sorts and output types
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| # make sure all the buttons work, including uploading a file
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| # try uploading a file with too many bases or too many queries and verify error message
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| ==hgPcr==
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| # test some perfectly matching primers, including a pair on the negative strand
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| # find a pair of primers that shouldn't match UCSC Genes and test that they don't
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| # vary settings and input primers for several assemblies and see if results make sense
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| # for human and mouse browsers, test the "UCSC Genes" target. Check that UI functions as expected
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| # check that the UI functions as expected for regular primers as well
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| ==hgLiftOver, hgConvert==
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| # Choose an assembly and go to hgTracks
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| # Hit "Convert" in the blue bar at the top of the page
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| # Compare the output to the same conversion using liftOver:
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| # LiftOver is at Home -> Utilities -> Batch Coordinate Conversion (liftOver)
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| # Test both position and BED format
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| # Test a variety of settings
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| # Try converting multiple positions at once
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| # Try uploading a file
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| ==pbGateway, pbGlobal, pbTracks==
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| # general testing; click around
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| # enter a protein symbol
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| # review results page
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| # click into pbGlobal and check display
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| ==hgSession==
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| #check that a new session can be saved
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| #check that old sessions are still there
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| #delete a session
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| #check browser & email button; click the title of session & make sure you can save changes to the description
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| #try loading a session via a file and via a URL
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| #logout and try to load a session that can be shared and one that can't be shared
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| ==hgGenome==
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| #find it by going Home -> Genome Graphs
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| #upload a dataset from a file
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| #upload a data set from a URL
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| #import data from a track
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| #change some configurations
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| #check that "browse regions" & "sort genes" work
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| #check the correlate button
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| Some good genome graph data for testing: http://hgwdev.cse.ucsc.edu/~rhead/genomeGraphsWithColumns
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| ==cartDump, cartReset==
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| # check cart
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| # reset cart
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| # check cart again
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| See also: cart test protocol
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| ==hgApi==
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| 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. | |
| # 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.
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| # 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.
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| 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.
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| ==hgEncodeVocab==
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| # 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.
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| # Go to a couple of these pages and check that the sections are displaying (these pages use hgEncodeVocab to display the info on them):
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| #* [http://hgw2.cse.ucsc.edu/ENCODE/otherTerms.html Registered Variables]
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| #* [http://hgw2.cse.ucsc.edu/ENCODE/antibodies.html Antibodies]
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| #* [http://hgw2.cse.ucsc.edu/ENCODE/cellTypes.html Human Cell Types]
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| #* [http://hgw2.cse.ucsc.edu/ENCODE/cellTypesMouse.html Mouse Cell Types]
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| # 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)
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| ==hgFileUi==
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| # Check that the Downloads links on hgTrackUi page of a track that is known to have fileSortOrder goes to hgFileUi, e.g. Broad Histone hg19 ([http://hgwbeta.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone beta] | [http://hgw0.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone hgw0])
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| # Manipulate the URL to see a composite without fileSortOrder in hgFileUi ([http://hgwbeta.cse.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeGisRnaSeq beta] | [http://hgw0.cse.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeGisRnaSeq hgw0])
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| # Make sure download button prompts a download (and doesn't take you to an error page)
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| # Check the sorting of columns
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| # Check the "Track Settings" link takes you back to the track's hgTrackUi page
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| '''More info about this CGI:'''
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| Only tracks with a '''fileSortOrder''' line in their trackDb blocks will have links to the hgFileUi page, however, all composites with downloads and metadata should have a functioning hgFileUi page. If a track has a fileSortOrder line, then the "Downloads" links in the top-most light blue bar and under the subtrack list will link to the appropriate hgFileUi page. If not, then the same Download links will go to the index.html on hgdownload (or hgdownload-test), but you can still get to the hgFileUi page for a track of this kind by manipulating the URL: <machine>.ucsc.edu/cgi-bin/hgFileUi?g=<trackname> (for example: genome.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeCaltechRnaSeq). The first track with the fileSortOrder and therefore links that go to hgFileUi is [http://genome.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeBroadHistone ENCODE Broad Histone on hg19]
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| [[Category:Browser QA]]
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