QANCODE is a Python object for running browser automation tasks that are part of ENCODE quality assurance testing but may require manual review/interpretation. This notebook gives an overview of its functionality. Full documentation at https://docs.google.com/document/d/1G1-TofLknZKq4FUVUjhqMKqjkH5sRhRS03tUXi-NKZU/.

Notebook formatting



In [1]:

    
%config InlineBackend.figure_format = 'retina'
from IPython.core.display import display, HTML
display(HTML("<style>.container { width:80% !important; }</style>"))
# Change to parent directory
import os
os.chdir("..")

Load QANCODE



In [2]:

    
import qancode

Instantiate QANCODE object with release candidate URL



In [3]:

    
qa = qancode.QANCODE(rc_url='https://test.encodedcc.org')

QANCODE methods



In [4]:

    
qa.list_methods()









    



check_downloads
check_permissions
check_requests
check_response_time
check_tools
check_trackhubs
compare_facets
find_differences
list_methods
show_differences

Three main areas of functionality

1. Crawl website and scrape/download data

- compare_facets
- check_downloads

2. Compare screenshots between production and RC

- find_differences
- check_permissions
- check_trackhubs

3. Submit RC to external (non-browser) requests

- check_requests
- check_tools
- check_response_time

Use compare_facets

Allows you to specify:

List of browsers
List of users
List of facets to check (item_types)
Browser comparison (True/False)

Outputs comparison for each facet category:

Blue - match
Red - same facet term, different value
Yellow - facet term found on one list but not other



In [5]:

    
qa.compare_facets(browsers=['Safari'],
                  users=['Public'],
                  item_types=['/search/?type=Experiment'],
                  browser_comparison=False)









    



Opening https://www.encodeproject.org in Safari
Getting type: /search/?type=Experiment
Search page detected
Opening https://test.encodedcc.org in Safari
Getting type: /search/?type=Experiment
Search page detected

---------------------------------- Experiment ----------------------------------
Comparing data between URLs.
As user: Public
Browser: Safari
First URL: https://www.encodeproject.org
Second URL: https://test.encodedcc.org
Item type: /search/?type=Experiment
ASSAY
     ChIP-seq: 7812 (prod), 7783 (rc)
ASSAY CATEGORY
     DNA binding: 7812 (prod), 7783 (rc)
AUDIT CATEGORY
     rc: [('inconsistent replicate', '1')]
AUDIT CATEGORY2
     insufficient read depth: 1475 (prod), 1474 (rc)
     missing controlled_by: 628 (prod), 627 (rc)
     partially characterized antibody: 101 (prod), 99 (rc)
     uncharacterized antibody: 24 (prod), 26 (rc)
AUDIT CATEGORY3
     borderline replicate concordance: 360 (prod), 358 (rc)
     control low read depth: 740 (prod), 737 (rc)
     inconsistent platforms: 973 (prod), 967 (rc)
     low read depth: 1824 (prod), 1822 (rc)
     mild to moderate bottlenecking: 2444 (prod), 2443 (rc)
     missing external identifiers: 252 (prod), 273 (rc)
     moderate library complexity: 1096 (prod), 1095 (rc)
AVAILABLE DATA
     bam: 10421 (prod), 10397 (rc)
     bed broadPeak: 2242 (prod), 2246 (rc)
     bed narrowPeak: 5918 (prod), 5893 (rc)
     bigBed broadPeak: 1772 (prod), 1776 (rc)
     bigBed narrowPeak: 5576 (prod), 5551 (rc)
     bigWig: 9229 (prod), 9210 (rc)
     fastq: 11469 (prod), 11440 (rc)
Biosample treatment
     MATCH
BIOSAMPLE TYPE
     immortalized cell line: 5090 (prod), 5086 (rc)
     tissue: 4112 (prod), 4087 (rc)
DATE SUBMITTED
     2016-04-27: 72 (prod), 71 (rc)
DATE RELEASED
     August, 2017: 71 (prod), 45 (rc)
     July, 2011: 263 (prod), 260 (rc)
EXPERIMENT STATUS
     archived: 355 (prod), 352 (rc)
     released: 13394 (prod), 13368 (rc)
GENOME ASSEMBLY (VISUALIZATION)
     GRCh38: 5056 (prod), 5026 (rc)
     hg19: 5462 (prod), 5432 (rc)
LAB
     Bradley Bernstein, Broad: 1978 (prod), 1953 (rc)
     Michael Snyder, Stanford: 1955 (prod), 1954 (rc)
     Sherman Weissman, Yale: 65 (prod), 62 (rc)
Library depleted in
     MATCH
LIBRARY INSERT SIZE (NT)
     150-350: 476 (prod), 474 (rc)
     200-600: 692 (prod), 667 (rc)
     450-650: 939 (prod), 938 (rc)
LIBRARY MADE FROM
     DNA: 10119 (prod), 10091 (rc)
Library treatment
     MATCH
LIFE STAGE
     adult: 6121 (prod), 6095 (rc)
     unknown: 1463 (prod), 1461 (rc)
MAPPED READ LENGTH (NT)
     100: 714 (prod), 713 (rc)
     30: 56 (prod), 55 (rc)
     36: 2622 (prod), 2614 (rc)
     76: 608 (prod), 583 (rc)
ORGAN
     blood: 1992 (prod), 1991 (rc)
     embryo: 902 (prod), 900 (rc)
     epithelium: 642 (prod), 643 (rc)
     esophagus: 110 (prod), 109 (rc)
     gonad: 103 (prod), 98 (rc)
     intestine: 465 (prod), 455 (rc)
     large intestine: 346 (prod), 336 (rc)
     ovary: 52 (prod), 51 (rc)
     pancreas: 142 (prod), 141 (rc)
     prostate gland: 108 (prod), 103 (rc)
     spleen: 188 (prod), 185 (rc)
     testis: 66 (prod), 62 (rc)
     thyroid gland: 57 (prod), 54 (rc)
ORGANISM
     Homo sapiens: 10255 (prod), 10229 (rc)
     Mus musculus: 1783 (prod), 1781 (rc)
PROJECT
     ENCODE: 9046 (prod), 9017 (rc)
RFA
     ENCODE2-Mouse: 564 (prod), 561 (rc)
     ENCODE3: 5654 (prod), 5653 (rc)
     prod: [('ENCODE4', '25')]
READ LENGTH (NT)
     100: 1878 (prod), 1877 (rc)
     36: 4149 (prod), 4146 (rc)
     76: 1267 (prod), 1242 (rc)
REPLICATION TYPE
     isogenic: 7773 (prod), 7770 (rc)
     unreplicated: 5796 (prod), 5770 (rc)
RUN TYPE
     paired-ended: 3703 (prod), 3702 (rc)
     single-ended: 8412 (prod), 8384 (rc)
TARGET OF ASSAY
     RNA binding protein: 1346 (prod), 1341 (rc)
     broad histone mark: 1716 (prod), 1706 (rc)
     control: 2192 (prod), 2186 (rc)
     histone: 3063 (prod), 3046 (rc)
     histone modification: 3063 (prod), 3046 (rc)
     narrow histone mark: 1236 (prod), 1229 (rc)
     transcription factor: 3234 (prod), 3228 (rc)

Default list of item_types for compare_facets:



In [6]:

    
qa.compare_facets_default_actions









    Out[6]:





['/search/?type=Experiment',
 '/search/?type=File',
 '/search/?type=AntibodyLot',
 '/search/?type=Biosample',
 '/search/?type=Dataset',
 '/search/?type=FileSet',
 '/search/?type=Annotation',
 '/search/?type=Series',
 '/search/?type=OrganismDevelopmentSeries',
 '/search/?type=UcscBrowserComposite',
 '/search/?type=ReferenceEpigenome',
 '/search/?type=Project',
 '/search/?type=ReplicationTimingSeries',
 '/search/?type=PublicationData',
 '/search/?type=MatchedSet',
 '/search/?type=TreatmentConcentrationSeries',
 '/search/?type=TreatmentTimeSeries',
 '/search/?type=Target',
 '/search/?type=Pipeline',
 '/search/?type=Publication',
 '/search/?type=Software',
 '/matrix/?type=Experiment',
 '/matrix/?type=Annotation']

Want to check that downloads work?

Use check_downloads

Allows you to specify:

List of browsers
List of users
List of action_tuples specifying page and download-specific task
URL (if only want to run on RC)

Clicks download link on page and checks for downloaded file:

Waits for download to complete
Deletes file afterward by default (use delete=False to keep)

Download BED file from page (single file)



In [7]:

    
qa.check_downloads(browsers=['Chrome'],
                   users=['Public'],
                   action_tuples=[('/files/ENCFF931OLL/', qancode.DownloadFileFromFilePage)])









    



Running check downloads
Opening https://www.encodeproject.org in Chrome
Getting type: /files/ENCFF931OLL/
Loading complete
Performing click path: DownloadFileFromFilePage
Waiting for download to finish
Checking for downloaded file ENCFF931OLL.bed.gz
DOWNLOAD SUCCESS: ENCFF931OLL.bed.gz
Opening https://v60rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /files/ENCFF931OLL/
Loading complete
Performing click path: DownloadFileFromFilePage
Waiting for download to finish
Checking for downloaded file ENCFF931OLL.bed.gz
DOWNLOAD SUCCESS: ENCFF931OLL.bed.gz

Download documents from antibody page (multiple files)



In [8]:

    
qa.check_downloads(browsers=['Chrome'],
                   users=['Public'],
                   action_tuples=[('/antibodies/ENCAB749XQY/', qancode.DownloadDocumentsFromAntibodyPage)])









    



Running check downloads
Opening https://www.encodeproject.org in Chrome
Getting type: /antibodies/ENCAB749XQY/
Loading complete
Performing click path: DownloadDocumentsFromAntibodyPage
Downloading #1143 A549 SMC3 ab9263.jpg from https://www.encodeproject.org/antibody-characterizations/c521bab2-2603-4474-bf1b-e09b3f597534/@@download/attachment/%231143%20A549%20SMC3%20ab9263.jpg
Downloading IP Protocol (Light Chain Specific Secondary) 092313.pdf from https://www.encodeproject.org/documents/3394b2a7-a796-4097-b53a-b45611907c81/@@download/attachment/IP%20Protocol%20%28Light%20Chain%20Specific%20Secondary%29%20092313.pdf
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://www.encodeproject.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Downloading #1143 IMR90 SMC3(ab9263).jpg from https://www.encodeproject.org/antibody-characterizations/10c4b28a-dac1-496f-ab3b-ae01f246dab0/@@download/attachment/%231143%20IMR90%20SMC3%28ab9263%29.jpg
Downloading IP Protocol (Light Chain Specific Secondary) 092313.pdf from https://www.encodeproject.org/documents/3394b2a7-a796-4097-b53a-b45611907c81/@@download/attachment/IP%20Protocol%20%28Light%20Chain%20Specific%20Secondary%29%20092313.pdf
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://www.encodeproject.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Downloading #1143 HepG2 SMC3(ab9263).jpg from https://www.encodeproject.org/antibody-characterizations/a8ff6fa7-7588-4417-b7d4-869333e1d381/@@download/attachment/%231143%20HepG2%20SMC3%28ab9263%29.jpg
Downloading IP Protocol (Light Chain Specific Secondary) 092313.pdf from https://www.encodeproject.org/documents/3394b2a7-a796-4097-b53a-b45611907c81/@@download/attachment/IP%20Protocol%20%28Light%20Chain%20Specific%20Secondary%29%20092313.pdf
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://www.encodeproject.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Downloading SMC3_ab9263_final.pdf from https://www.encodeproject.org/antibody-characterizations/7be7df17-2171-4714-90bc-c6cb023b8b5d/@@download/attachment/SMC3_ab9263_final.pdf
Downloading Mass Spec protocol.pdf from https://www.encodeproject.org/documents/971a91d7-5a1f-4c86-93c8-3d576c5560ed/@@download/attachment/Mass%20Spec%20protocol.pdf
Downloading SMC3_ab9263_proteingroups.txt from https://www.encodeproject.org/documents/0a9c5903-2399-4dde-a834-aecd281a677d/@@download/attachment/SMC3_ab9263_proteingroups.txt
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://www.encodeproject.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Downloading SMC3_ab9263.jpg from https://www.encodeproject.org/antibody-characterizations/b1ccde77-1ec6-4eb3-8930-2dd9fe002bcd/@@download/attachment/SMC3_ab9263.jpg
Downloading IP Protocol (Light Chain Specific Secondary) 092313.pdf from https://www.encodeproject.org/documents/3394b2a7-a796-4097-b53a-b45611907c81/@@download/attachment/IP%20Protocol%20%28Light%20Chain%20Specific%20Secondary%29%20092313.pdf
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://www.encodeproject.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Waiting for download to finish
Checking for downloaded file #1143 A549 SMC3 ab9263.jpg
DOWNLOAD SUCCESS: #1143 A549 SMC3 ab9263.jpg
Checking for downloaded file IP Protocol (Light Chain Specific Secondary) 092313.pdf
DOWNLOAD SUCCESS: IP Protocol (Light Chain Specific Secondary) 092313.pdf
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Checking for downloaded file #1143 IMR90 SMC3(ab9263).jpg
DOWNLOAD SUCCESS: #1143 IMR90 SMC3(ab9263).jpg
Checking for downloaded file IP Protocol (Light Chain Specific Secondary) 092313.pdf
DOWNLOAD SUCCESS: IP Protocol (Light Chain Specific Secondary) 092313.pdf
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Checking for downloaded file #1143 HepG2 SMC3(ab9263).jpg
DOWNLOAD SUCCESS: #1143 HepG2 SMC3(ab9263).jpg
Checking for downloaded file IP Protocol (Light Chain Specific Secondary) 092313.pdf
DOWNLOAD SUCCESS: IP Protocol (Light Chain Specific Secondary) 092313.pdf
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Checking for downloaded file SMC3_ab9263_final.pdf
DOWNLOAD SUCCESS: SMC3_ab9263_final.pdf
Checking for downloaded file Mass Spec protocol.pdf
DOWNLOAD SUCCESS: Mass Spec protocol.pdf
Checking for downloaded file SMC3_ab9263_proteingroups.txt
DOWNLOAD SUCCESS: SMC3_ab9263_proteingroups.txt
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Checking for downloaded file SMC3_ab9263.jpg
DOWNLOAD SUCCESS: SMC3_ab9263.jpg
Checking for downloaded file IP Protocol (Light Chain Specific Secondary) 092313.pdf
DOWNLOAD SUCCESS: IP Protocol (Light Chain Specific Secondary) 092313.pdf
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Opening https://v60rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /antibodies/ENCAB749XQY/
Loading complete
Performing click path: DownloadDocumentsFromAntibodyPage
Downloading #1143 A549 SMC3 ab9263.jpg from https://v60rc1-master.demo.encodedcc.org/antibody-characterizations/c521bab2-2603-4474-bf1b-e09b3f597534/@@download/attachment/%231143%20A549%20SMC3%20ab9263.jpg
Downloading IP Protocol (Light Chain Specific Secondary) 092313.pdf from https://v60rc1-master.demo.encodedcc.org/documents/3394b2a7-a796-4097-b53a-b45611907c81/@@download/attachment/IP%20Protocol%20%28Light%20Chain%20Specific%20Secondary%29%20092313.pdf
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://v60rc1-master.demo.encodedcc.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Downloading #1143 IMR90 SMC3(ab9263).jpg from https://v60rc1-master.demo.encodedcc.org/antibody-characterizations/10c4b28a-dac1-496f-ab3b-ae01f246dab0/@@download/attachment/%231143%20IMR90%20SMC3%28ab9263%29.jpg
Downloading IP Protocol (Light Chain Specific Secondary) 092313.pdf from https://v60rc1-master.demo.encodedcc.org/documents/3394b2a7-a796-4097-b53a-b45611907c81/@@download/attachment/IP%20Protocol%20%28Light%20Chain%20Specific%20Secondary%29%20092313.pdf
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://v60rc1-master.demo.encodedcc.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Downloading #1143 HepG2 SMC3(ab9263).jpg from https://v60rc1-master.demo.encodedcc.org/antibody-characterizations/a8ff6fa7-7588-4417-b7d4-869333e1d381/@@download/attachment/%231143%20HepG2%20SMC3%28ab9263%29.jpg
Downloading IP Protocol (Light Chain Specific Secondary) 092313.pdf from https://v60rc1-master.demo.encodedcc.org/documents/3394b2a7-a796-4097-b53a-b45611907c81/@@download/attachment/IP%20Protocol%20%28Light%20Chain%20Specific%20Secondary%29%20092313.pdf
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://v60rc1-master.demo.encodedcc.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Downloading SMC3_ab9263_final.pdf from https://v60rc1-master.demo.encodedcc.org/antibody-characterizations/7be7df17-2171-4714-90bc-c6cb023b8b5d/@@download/attachment/SMC3_ab9263_final.pdf
Downloading Mass Spec protocol.pdf from https://v60rc1-master.demo.encodedcc.org/documents/971a91d7-5a1f-4c86-93c8-3d576c5560ed/@@download/attachment/Mass%20Spec%20protocol.pdf
Downloading SMC3_ab9263_proteingroups.txt from https://v60rc1-master.demo.encodedcc.org/documents/0a9c5903-2399-4dde-a834-aecd281a677d/@@download/attachment/SMC3_ab9263_proteingroups.txt
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://v60rc1-master.demo.encodedcc.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Downloading SMC3_ab9263.jpg from https://v60rc1-master.demo.encodedcc.org/antibody-characterizations/b1ccde77-1ec6-4eb3-8930-2dd9fe002bcd/@@download/attachment/SMC3_ab9263.jpg
Downloading IP Protocol (Light Chain Specific Secondary) 092313.pdf from https://v60rc1-master.demo.encodedcc.org/documents/3394b2a7-a796-4097-b53a-b45611907c81/@@download/attachment/IP%20Protocol%20%28Light%20Chain%20Specific%20Secondary%29%20092313.pdf
Downloading ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf from https://v60rc1-master.demo.encodedcc.org/documents/c7cb0632-7e5f-455e-9119-46a54f160711/@@download/attachment/ENCODE_Approved_May_2016_TF_Antibody%20Characterization_Guidelines.pdf
Waiting for download to finish
Checking for downloaded file #1143 A549 SMC3 ab9263.jpg
DOWNLOAD SUCCESS: #1143 A549 SMC3 ab9263.jpg
Checking for downloaded file IP Protocol (Light Chain Specific Secondary) 092313.pdf
DOWNLOAD SUCCESS: IP Protocol (Light Chain Specific Secondary) 092313.pdf
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Checking for downloaded file #1143 IMR90 SMC3(ab9263).jpg
DOWNLOAD SUCCESS: #1143 IMR90 SMC3(ab9263).jpg
Checking for downloaded file IP Protocol (Light Chain Specific Secondary) 092313.pdf
DOWNLOAD SUCCESS: IP Protocol (Light Chain Specific Secondary) 092313.pdf
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Checking for downloaded file #1143 HepG2 SMC3(ab9263).jpg
DOWNLOAD SUCCESS: #1143 HepG2 SMC3(ab9263).jpg
Checking for downloaded file IP Protocol (Light Chain Specific Secondary) 092313.pdf
DOWNLOAD SUCCESS: IP Protocol (Light Chain Specific Secondary) 092313.pdf
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Checking for downloaded file SMC3_ab9263_final.pdf
DOWNLOAD SUCCESS: SMC3_ab9263_final.pdf
Checking for downloaded file Mass Spec protocol.pdf
DOWNLOAD SUCCESS: Mass Spec protocol.pdf
Checking for downloaded file SMC3_ab9263_proteingroups.txt
DOWNLOAD SUCCESS: SMC3_ab9263_proteingroups.txt
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
Checking for downloaded file SMC3_ab9263.jpg
DOWNLOAD SUCCESS: SMC3_ab9263.jpg
Checking for downloaded file IP Protocol (Light Chain Specific Secondary) 092313.pdf
DOWNLOAD SUCCESS: IP Protocol (Light Chain Specific Secondary) 092313.pdf
Checking for downloaded file ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf
DOWNLOAD SUCCESS: ENCODE_Approved_May_2016_TF_Antibody Characterization_Guidelines.pdf

Default action list for check_downloads:



In [9]:

    
qa.check_downloads_default_actions









    Out[9]:





[('/experiments/ENCSR810WXH/', qancode.clickpaths.DownloadBEDFileFromTable),
 ('/experiments/ENCSR966YYJ/', qancode.clickpaths.DownloadBEDFileFromModal),
 ('/experiments/ENCSR810WXH/',
  qancode.clickpaths.DownloadGraphFromExperimentPage),
 ('/experiments/ENCSR810WXH/', qancode.clickpaths.DownloadDocuments),
 ('/ucsc-browser-composites/ENCSR707NXZ/',
  qancode.clickpaths.DownloadDocuments),
 ('/antibodies/ENCAB749XQY/',
  qancode.clickpaths.DownloadDocumentsFromAntibodyPage),
 ('/report/?searchTerm=nose&type=Biosample',
  qancode.clickpaths.DownloadTSVFromReportPage),
 ('/search/?type=Experiment&searchTerm=nose',
  qancode.clickpaths.DownloadMetaDataFromSearchPage),
 ('/files/ENCFF931OLL/', qancode.clickpaths.DownloadFileFromFilePage),
 ('/files/ENCFF291ELS/', qancode.clickpaths.DownloadFileFromFilePage)]

Want to highlight differences between pages?

Use find_differences

Allows you to specify:

List of browsers
List of users
List of pages to check (item_types) and actions to perform before taking screenshot (click_paths). Alternatively can specify action_tuples, which is a list of item_type, click_path tuples, e.g. [(item_type1, click_path1), (item_type2, click_path2)]

Outputs distance metric (pixel difference) and image showing difference (find in image_diff folder on Desktop):

Production screenshot on left
RC screenshot on right
Difference overlaid on production background in middle

Tips:

Use item_types='random' to check three random items from the default action list
Use qa.show_differences() to display image difference in Jupyter notebook

Compare front page of production with front page of release candidate:



In [10]:

    
qa.find_differences(browsers=['Safari'],
                    users=['Public'],
                    item_types=['/'])









    



Opening https://www.encodeproject.org in Safari
Loading complete
Taking picture of https://www.encodeproject.org/
/var/folders/v8/vsjvg3vn5mz0nrhvkpp7f0_40000gp/T/tmp_hh0f863/prod74344761720580028494082090765232247950.png
Opening https://v60rc1-master.demo.encodedcc.org/ in Safari
Loading complete
Taking picture of https://v60rc1-master.demo.encodedcc.org/
/var/folders/v8/vsjvg3vn5mz0nrhvkpp7f0_40000gp/T/tmp_hh0f863/RC276551871122272408996421566754189334384.png

Comparing screenshots between URLs.
As user: Public
Browser: Safari
First URL: https://www.encodeproject.org
Second URL: https://v60rc1-master.demo.encodedcc.org/
Item type: /
Click path: None
Difference detected
Outputting file safari_FRONT_PAGE_public_None_prod_rc_diff.png
Distance metric: 41645745






    Out[10]:





[(True, 'safari_FRONT_PAGE_public_None_prod_rc_diff.png')]

Show differences between screenshots:



In [11]:

    
qa.show_differences()









    



safari_FRONT_PAGE_public_None_prod_rc_diff.png:

Compare three random pages from default list:



In [16]:

    
qa.find_differences(browsers=['Safari'],
                    users=['Public'],
                    item_types='random')









    



Opening https://encodeproject.org in Safari
Getting type: /biosamples/ENCBS030ENC/
Loading complete
Taking picture of https://www.encodeproject.org/biosamples/ENCBS030ENC/
/var/folders/v8/vsjvg3vn5mz0nrhvkpp7f0_40000gp/T/tmplpnxl3vv/prod121526589078956467618635144079635019545.png
Opening https://encodeproject.org in Safari
Getting type: /pipelines/ENCPL985BLO/
Loading complete
Taking picture of https://www.encodeproject.org/pipelines/ENCPL985BLO/
/var/folders/v8/vsjvg3vn5mz0nrhvkpp7f0_40000gp/T/tmplpnxl3vv/prod142123383960303874345408967632625553483.png
Opening https://encodeproject.org in Safari
Getting type: /search/?searchTerm=ENCBS619ENC&type=Biosample
Loading complete
Taking picture of https://www.encodeproject.org/search/?searchTerm=ENCBS619ENC&type=Biosample
/var/folders/v8/vsjvg3vn5mz0nrhvkpp7f0_40000gp/T/tmplpnxl3vv/prod223132608811852558900790788544127291303.png
Opening https://test.encodedcc.org/ in Safari
Getting type: /biosamples/ENCBS030ENC/
Loading complete
Taking picture of https://test.encodedcc.org/biosamples/ENCBS030ENC/
/var/folders/v8/vsjvg3vn5mz0nrhvkpp7f0_40000gp/T/tmplpnxl3vv/RC251063279171038367479212355786038245658.png
Opening https://test.encodedcc.org/ in Safari
Getting type: /pipelines/ENCPL985BLO/
Loading complete
Taking picture of https://test.encodedcc.org/pipelines/ENCPL985BLO/
/var/folders/v8/vsjvg3vn5mz0nrhvkpp7f0_40000gp/T/tmplpnxl3vv/RC260092492631451948546420191690072186144.png
Opening https://test.encodedcc.org/ in Safari
Getting type: /search/?searchTerm=ENCBS619ENC&type=Biosample
Loading complete
Taking picture of https://test.encodedcc.org/search/?searchTerm=ENCBS619ENC&type=Biosample
/var/folders/v8/vsjvg3vn5mz0nrhvkpp7f0_40000gp/T/tmplpnxl3vv/RC62930233993979457582099864964247000141.png

Comparing screenshots between URLs.
As user: Public
Browser: Safari
First URL: https://encodeproject.org
Second URL: https://test.encodedcc.org/
Item type: /biosamples/ENCBS030ENC/
Click path: None
Difference detected
Outputting file safari_BIOSAMPLES_ENCBS030ENC_public_None_prod_rc_diff.png
Distance metric: 107456957

Comparing screenshots between URLs.
As user: Public
Browser: Safari
First URL: https://encodeproject.org
Second URL: https://test.encodedcc.org/
Item type: /pipelines/ENCPL985BLO/
Click path: None
MATCH
Distance metric: 0

Comparing screenshots between URLs.
As user: Public
Browser: Safari
First URL: https://encodeproject.org
Second URL: https://test.encodedcc.org/
Item type: /search/?searchTerm=ENCBS619ENC&type=Biosample
Click path: None
MATCH
Distance metric: 0






    Out[16]:





[(True, 'safari_BIOSAMPLES_ENCBS030ENC_public_None_prod_rc_diff.png'),
 (False, 'safari_PIPELINES_ENCPL985BLO_public_None_prod_rc_diff.png'),
 (False,
  'safari_SEARCH_SEARCHTERM_ENCBS619ENC_TYPE_BIOSAMPLE_public_None_prod_rc_diff.png')]

Show difference if any:



In [17]:

    
qa.show_differences()









    



safari_BIOSAMPLES_ENCBS030ENC_public_None_prod_rc_diff.png:

Default list of action_tuples for find_differences:



In [12]:

    
qa.find_differences_default_actions









    Out[12]:





[('/', None),
 ('/targets/?status=deleted', None),
 ('/antibodies/?status=deleted', None),
 ('/search/?type=Biosample&status=deleted', None),
 ('/experiments/ENCSR000CWD/', None),
 ('/biosamples/ENCBS574ZRE/', None),
 ('/biosamples/ENCBS883DWI/', None),
 ('/experiments/ENCSR985KAT/', None),
 ('/biosamples/ENCBS298YPF/', None),
 ('/biosamples/ENCBS142DVU/', None),
 ('/biosamples/ENCBS562NPI/', None),
 ('/human-donors/ENCDO999JZG/', None),
 ('/biosamples/ENCBS615YKY/', None),
 ('/search/?searchTerm=puf60&type=Target', None),
 ('/experiments/ENCSR502NRF/', None),
 ('/experiments/ENCSR000AEH/', None),
 ('/search/?searchTerm=ENCSR000AEH&type=Experiment', None),
 ('/experiments/ENCSR000CPG/', None),
 ('/search/?searchTerm=ENCSR000CPG&type=Experiment', None),
 ('/experiments/ENCSR000BPF/', None),
 ('/search/?searchTerm=ENCSR000BPF&type=Experiment', None),
 ('/experiments/ENCSR178NTX/', None),
 ('/experiments/ENCSR651NGR/', None),
 ('/search/?searchTerm=ENCSR651NGR&type=Experiment', None),
 ('/antibodies/ENCAB000AEH/', None),
 ('/search/?searchTerm=ENCAB000AEH&type=AntibodyLot', None),
 ('/antibodies/ENCAB000AIW/', None),
 ('/search/?searchTerm=ENCAB000AIW&type=AntibodyLot', None),
 ('/biosamples/ENCBS000AAA/', None),
 ('/search/?searchTerm=ENCBS000AAA&type=Biosample', None),
 ('/biosamples/ENCBS030ENC/', None),
 ('/search/?searchTerm=ENCBS030ENC', None),
 ('/biosamples/ENCBS098ENC/', None),
 ('/search/?searchTerm=ENCBS098ENC&type=Biosample', None),
 ('/biosamples/ENCBS619ENC/', None),
 ('/search/?searchTerm=ENCBS619ENC&type=Biosample', None),
 ('/biosamples/ENCBS286AAA/', None),
 ('/search/?searchTerm=ENCBS286AAA&type=Biosample', None),
 ('/biosamples/ENCBS314VPT/', None),
 ('/search/?searchTerm=ENCBS314VPT&type=Biosample', None),
 ('/biosamples/ENCBS808BUA/', None),
 ('/search/?searchTerm=ENCBS808BUA&type=Biosample', None),
 ('/targets/AARS-human/', None),
 ('/targets/FLAG-GABP-human/', None),
 ('/search/?type=Target&name=AARS-human', None),
 ('/ucsc-browser-composites/ENCSR707NXZ/', None),
 ('/treatment-time-series/ENCSR210PYP/', None),
 ('/search/?searchTerm=WASP&type=Software', None),
 ('/publications/67e606ae-abe7-4510-8ebb-cfa1fefe5cfa/', None),
 ('/search/?searchTerm=PMID%3A25164756', None),
 ('/biosamples/ENCBS632MTU/', None),
 ('/biosamples/ENCBS464EKT/', None),
 ('/annotations/ENCSR790GQB/', None),
 ('/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/', None),
 ('/pipelines/', None),
 ('/pipelines/ENCPL210QWH/', None),
 ('/pipelines/ENCPL002LPE/', None),
 ('/pipelines/ENCPL002LSE/', None),
 ('/rna-seq/long-rnas/', None),
 ('/pipelines/ENCPL337CSA/', None),
 ('/rna-seq/small-rnas/', None),
 ('/pipelines/ENCPL444CYA/', None),
 ('/microrna/microrna-seq/', None),
 ('/pipelines/ENCPL278BTI/', None),
 ('/microrna/microrna-counts/', None),
 ('/pipelines/ENCPL122WIM/', None),
 ('/rampage/', None),
 ('/pipelines/ENCPL220NBH/', None),
 ('/pipelines/ENCPL272XAE/', None),
 ('/pipelines/ENCPL272XAE/', None),
 ('/chip-seq/histone/', None),
 ('/pipelines/ENCPL138KID/', None),
 ('/pipelines/ENCPL493SGC/', None),
 ('/chip-seq/transcription_factor/', None),
 ('/pipelines/ENCPL001DNS/', None),
 ('/pipelines/ENCPL002DNS/', None),
 ('/data-standards/dnase-seq/', None),
 ('/atac-seq/', None),
 ('/pipelines/ENCPL985BLO/', None),
 ('/data/annotations/', None),
 ('/help/rest-api/', None),
 ('/about/experiment-guidelines/', None),
 ('/data-standards/terms/', None)]

Both check_permissions and check_trackhubs use find_differences with custom actions:



In [13]:

    
qa.check_permissions_default_actions









    Out[13]:





[('/experiments/ENCSR524OCB/', None),
 ('/experiments/ENCSR000EFT/', None),
 ('/biosamples/ENCBS643IYW/', None),
 ('/experiments/ENCSR466YGC/', None),
 ('/experiments/ENCSR255XZG/', None),
 ('/experiments/ENCSR115BCB/', None),
 ('/files/ENCFF752JWY/', None),
 ('/targets/2L52.1-celegans/', None),
 ('/targets/CG15455-dmelanogaster/', None),
 ('/software/dnase-eval-bam-se/', None),
 ('/software/atac-seq-software-tools/', None),
 ('/software/trimAdapters.py/', None),
 ('/software/bigwigaverageoverbed/', None),
 ('/pipelines/ENCPL493SGC/', None),
 ('/pipelines/ENCPL035XIO/', None),
 ('/pipelines/ENCPL568PWV/', None),
 ('/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/', None),
 ('/pipelines/ENCPL734EDH/', None),
 ('/pipelines/ENCPL983UFZ/', None),
 ('/pipelines/ENCPL631XPY/', None),
 ('/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/', None),
 ('/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/', None),
 ('/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/', None),
 ('/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/', None),
 ('/internal-data-use-policy/', None),
 ('/tutorials/encode-users-meeting-2016/logistics/', None),
 ('/2017-06-09-release/', None)]



In [33]:

    
qa.check_trackhubs_default_actions









    Out[33]:





[('/experiments/ENCSR502NRF/', qancode.OpenUCSCGenomeBrowserGRCh38),
 ('/experiments/ENCSR502NRF/', qancode.OpenUCSCGenomeBrowserHG19),
 ('/experiments/ENCSR985KAT/', qancode.OpenUCSCGenomeBrowserHG19),
 ('/experiments/ENCSR426UUG/', qancode.OpenUCSCGenomeBrowserGRCh38),
 ('/experiments/ENCSR293WTN/', qancode.OpenUCSCGenomeBrowserMM9),
 ('/experiments/ENCSR335LKF/', qancode.OpenUCSCGenomeBrowserMM10),
 ('/experiments/ENCSR922ESH/', qancode.OpenUCSCGenomeBrowserDM3),
 ('/experiments/ENCSR671XAK/', qancode.OpenUCSCGenomeBrowserDM6),
 ('/experiments/ENCSR422XRE/', qancode.OpenUCSCGenomeBrowserCE10),
 ('/experiments/ENCSR686FKU/', qancode.OpenUCSCGenomeBrowserCE11),
 ('/publication-data/ENCSR764APB/', qancode.OpenUCSCGenomeBrowserHG19),
 ('/projects/ENCSR295OIE/', qancode.OpenUCSCGenomeBrowserHG19),
 ('/annotations/ENCSR212BHV/', qancode.OpenUCSCGenomeBrowserHG19),
 ('/experiments/ENCSR000CJR/', qancode.OpenUCSCGenomeBrowserHG19),
 ('/search/?type=Experiment&assembly=hg19&target.investigated_as=RNA+binding+protein&assay_title=ChIP-seq&replicates.library.biosample.biosample_type=primary+cell',
  qancode.OpenUCSCGenomeBrowserHG19),
 ('/search/?type=Experiment&assembly=GRCh38&assay_title=shRNA+RNA-seq&target.investigated_as=transcription+factor&month_released=October%2C+2014',
  qancode.OpenUCSCGenomeBrowserGRCh38),
 ('/search/?type=Experiment&assembly=mm9&assay_title=Repli-chip',
  qancode.OpenUCSCGenomeBrowserMM9),
 ('/search/?type=Experiment&assembly=mm10&assay_title=microRNA-seq&month_released=January%2C+2016',
  qancode.OpenUCSCGenomeBrowserMM10),
 ('/search/?type=Experiment&assembly=dm3&status=released&replicates.library.biosample.biosample_type=whole+organisms&assay_title=total+RNA-seq',
  qancode.OpenUCSCGenomeBrowserDM3),
 ('/search/?type=Experiment&assembly=dm6&replicates.library.biosample.life_stage=wandering+third+instar+larva',
  qancode.OpenUCSCGenomeBrowserDM6),
 ('/search/?type=Experiment&assembly=ce10&target.investigated_as=transcription+factor&replicates.library.biosample.life_stage=L4+larva',
  qancode.OpenUCSCGenomeBrowserCE10),
 ('/search/?type=Experiment&assembly=ce11&target.investigated_as=recombinant+protein&replicates.library.biosample.life_stage=late+embryonic&replicates.library.biosample.life_stage=L4+larva',
  qancode.OpenUCSCGenomeBrowserCE11),
 ('/search/?searchTerm=hippocampus&type=Experiment',
  qancode.OpenUCSCGenomeBrowserHG19)]

Want to check server response time?

Use check_response_time

Allows you to specify:

List of URLs (by default production and RC)
List of item_types/subpages (by default None)
Sample size (number of GET requests to make)

Outputs mean internal server response time ± standard deviation (in milliseconds) by category:

es_time - time spent in Elasticsearch
render_time - time spent in JavaScript/React
wsgi_time - time spent in Python
queue_time - time spent waiting for Apache to pass request to Python
total time - sum of above

Based on time values in X-Stats field returned by response header.



In [8]:

    
qa.check_response_time(item_types=[None, '/antibodies/ENCAB284TTY', '/search/?type=Experiment'], n=20)









    



Checking response time

*** item_type: None
------------------------ https://www.encodeproject.org -------------------------
Average es_time: 20.147 ± 19.571 ms (n=20)
Average queue_time: 0.984 ± 0.527 ms (n=20)
Average render_time: 8.907 ± 2.877 ms (n=20)
Average wsgi_time: 37.488 ± 19.335 ms (n=20)
Average total time: 67.526 ± 39.132 ms (n=20)
-------------------------- https://test.encodedcc.org --------------------------
Average es_time: 5.857 ± 0.666 ms (n=20)
Average queue_time: 1.186 ± 0.725 ms (n=20)
Average render_time: 8.309 ± 1.849 ms (n=20)
Average wsgi_time: 24.428 ± 3.475 ms (n=20)
Average total time: 39.78 ± 5.404 ms (n=20)


*** item_type: /antibodies/ENCAB284TTY
------------- https://www.encodeproject.org/antibodies/ENCAB284TTY -------------
Average es_time: 13.652 ± 10.334 ms (n=20)
Average queue_time: 0.982 ± 0.225 ms (n=20)
Average render_time: 22.442 ± 5.261 ms (n=20)
Average wsgi_time: 50.668 ± 11.051 ms (n=20)
Average total time: 87.744 ± 21.643 ms (n=20)
-------------- https://test.encodedcc.org/antibodies/ENCAB284TTY ---------------
Average es_time: 6.987 ± 1.348 ms (n=20)
Average queue_time: 1.669 ± 2.29 ms (n=20)
Average render_time: 22.203 ± 3.836 ms (n=20)
Average wsgi_time: 44.543 ± 5.451 ms (n=20)
Average total time: 75.401 ± 10.369 ms (n=20)


*** item_type: /search/?type=Experiment
------------ https://www.encodeproject.org/search/?type=Experiment -------------
Average es_time: 121.146 ± 29.87 ms (n=20)
Average queue_time: 0.927 ± 0.123 ms (n=20)
Average render_time: 164.732 ± 30.525 ms (n=20)
Average wsgi_time: 307.0 ± 46.385 ms (n=20)
Average total time: 593.806 ± 92.238 ms (n=20)
-------------- https://test.encodedcc.org/search/?type=Experiment --------------
Average es_time: 75.404 ± 12.153 ms (n=20)
Average queue_time: 1.699 ± 1.61 ms (n=20)
Average render_time: 142.664 ± 10.118 ms (n=20)
Average wsgi_time: 243.058 ± 16.591 ms (n=20)
Average total time: 462.825 ± 31.675 ms (n=20)

Want to check external requests against RC?

Use check_requests

Semi-exhaustive grid search of patching/posting/viewing different objects with different statuses:

- As users:
    * Public
    * View-only lab (encoded.test@gmail.com)
    * Lab submitter (encoded.test2@gmail.com)
    * Disabled account (encoded.test3@gmail.com)
    * View-only admin (encoded.test4@gmail.com)
    * Admin
- Overlap with backend pytests and check_permissions()



In [14]:

    
qa.check_requests()









    



Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR082IHY/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR082IHY/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR082IHY/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR524OCB/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR524OCB/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR524OCB/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR524OCB/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR524OCB/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR524OCB/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000EFT/ with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000EFT/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000EFT/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000EFT/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000EFT/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000EFT/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/biosamples/ENCBS643IYW/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/biosamples/ENCBS643IYW/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/biosamples/ENCBS643IYW/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/biosamples/ENCBS643IYW/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/biosamples/ENCBS643IYW/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/biosamples/ENCBS643IYW/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/libraries/ENCLB220SGE/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/libraries/ENCLB220SGE/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/libraries/ENCLB220SGE/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/libraries/ENCLB220SGE/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/libraries/ENCLB220SGE/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/libraries/ENCLB220SGE/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR466YGC/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR466YGC/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR466YGC/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR466YGC/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR466YGC/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR466YGC/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR255XZG/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR255XZG/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR255XZG/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR255XZG/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR255XZG/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR255XZG/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR115BCB/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR115BCB/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR115BCB/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR115BCB/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR115BCB/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR115BCB/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/files/ENCFF851EYG/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/files/ENCFF851EYG/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/files/ENCFF851EYG/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/files/ENCFF851EYG/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/files/ENCFF851EYG/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/files/ENCFF851EYG/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/targets/2L52.1-celegans/ with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/targets/2L52.1-celegans/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/targets/2L52.1-celegans/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/targets/2L52.1-celegans/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/targets/2L52.1-celegans/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/targets/2L52.1-celegans/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/dnase-eval-bam-se/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/dnase-eval-bam-se/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/dnase-eval-bam-se/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/dnase-eval-bam-se/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/dnase-eval-bam-se/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/dnase-eval-bam-se/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/atac-seq-software-tools/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/atac-seq-software-tools/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/atac-seq-software-tools/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/atac-seq-software-tools/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/atac-seq-software-tools/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/atac-seq-software-tools/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/trimAdapters.py/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/trimAdapters.py/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/trimAdapters.py/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/trimAdapters.py/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/trimAdapters.py/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/trimAdapters.py/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/bigwigaverageoverbed/ with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/bigwigaverageoverbed/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/bigwigaverageoverbed/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/bigwigaverageoverbed/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/bigwigaverageoverbed/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/software/bigwigaverageoverbed/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL493SGC/ with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL493SGC/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL493SGC/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL493SGC/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL493SGC/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL493SGC/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL035XIO/ with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL035XIO/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL035XIO/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL035XIO/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL035XIO/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL035XIO/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL568PWV/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL568PWV/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL568PWV/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL568PWV/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL568PWV/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL568PWV/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL855QIE/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL855QIE/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL855QIE/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL855QIE/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL855QIE/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL855QIE/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL983UFZ/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL983UFZ/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL983UFZ/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL983UFZ/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL983UFZ/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL983UFZ/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL631XPY/ with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL631XPY/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL631XPY/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL631XPY/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL631XPY/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL631XPY/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/ with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/internal-data-use-policy/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/internal-data-use-policy/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/internal-data-use-policy/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/internal-data-use-policy/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/internal-data-use-policy/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/internal-data-use-policy/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/tutorials/encode-users-meeting-2016/logistics/ with None as user Public
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/tutorials/encode-users-meeting-2016/logistics/ with None as user encoded.test@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/tutorials/encode-users-meeting-2016/logistics/ with None as user encoded.test2@gmail.com
Expected: 403
Actual: 403
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/tutorials/encode-users-meeting-2016/logistics/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/tutorials/encode-users-meeting-2016/logistics/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/tutorials/encode-users-meeting-2016/logistics/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/2017-06-09-release/ with None as user Public
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/2017-06-09-release/ with None as user encoded.test@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/2017-06-09-release/ with None as user encoded.test2@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/2017-06-09-release/ with None as user encoded.test3@gmail.com
Expected: 401
Actual: 401
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/2017-06-09-release/ with None as user encoded.test4@gmail.com
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to get https://v60rc1-master.demo.encodedcc.org/2017-06-09-release/ with None as user admin
Expected: 200
Actual: 200
GET SUCCESSFUL

Trying to post https://v60rc1-master.demo.encodedcc.org/experiments/ with {'target': '/targets/SMAD6-human/', 'references': ['PMID:18229687', 'PMID:25677182'], 'lab': '/labs/thomas-gingeras/', 'description': 'test post experiment', 'biosample_term_name': 'Stromal cell of bone marrow', 'biosample_term_id': 'CL:0010001', 'award': '/awards/U41HG006992/', 'biosample_type': 'primary cell', 'assay_term_name': 'ChIP-seq'} as user Public
Expected: 400
Actual: 400
POST SUCCESSFUL

Trying to post https://v60rc1-master.demo.encodedcc.org/experiments/ with {'target': '/targets/SMAD6-human/', 'references': ['PMID:18229687', 'PMID:25677182'], 'lab': '/labs/thomas-gingeras/', 'description': 'test post experiment', 'biosample_term_name': 'Stromal cell of bone marrow', 'biosample_term_id': 'CL:0010001', 'award': '/awards/U41HG006992/', 'biosample_type': 'primary cell', 'assay_term_name': 'ChIP-seq'} as user encoded.test2@gmail.com
Expected: 201
Actual: 201
POST SUCCESSFUL

Trying to post https://v60rc1-master.demo.encodedcc.org/experiments/ with {'target': '/targets/SMAD6-human/', 'references': ['PMID:18229687', 'PMID:25677182'], 'lab': '/labs/thomas-gingeras/', 'description': 'test post experiment', 'biosample_term_name': 'Stromal cell of bone marrow', 'biosample_term_id': 'CL:0010001', 'award': '/awards/U41HG006992/', 'biosample_type': 'primary cell', 'assay_term_name': 'ChIP-seq'} as user admin
Expected: 201
Actual: 201
POST SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'description': 'test'} as user Public
Expected: 400
Actual: 400
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'description': 'test'} as user encoded.test4@gmail.com
Expected: 403
Actual: 403
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'status': 'deleted'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'status': 'archived'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'status': 'proposed'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'status': 'ready for review'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'status': 'released'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'status': 'started'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'status': 'submitted'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000CUS/ with {'status': 'replaced'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR035DLJ/ with {'alternate_accessions': ['ENCSR000CUS']} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR035DLJ/ with {'alternate_accessions': []} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/35f91f16-dcef-4ab2-90bd-3928b0db9a60 with {'status': 'revoked'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/files/ENCFF002BYE/ with {'status': 'deleted'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/files/ENCFF002BYE/ with {'status': 'in progress'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/files/ENCFF002BYE/ with {'status': 'released'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/files/ENCFF002BYE/ with {'status': 'replaced'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/4dc1fbd3-6692-42fa-b710-03eaba9263c1 with {'status': 'revoked'} as user admin
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR524OCB/ with {'status': 'submitted'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR524OCB/ with {'status': 'submitted'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000EFT/ with {'status': 'revoked'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR000EFT/ with {'status': 'revoked'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/biosamples/ENCBS643IYW/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/biosamples/ENCBS643IYW/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/libraries/ENCLB220SGE/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/libraries/ENCLB220SGE/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR466YGC/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR466YGC/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR255XZG/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR255XZG/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR115BCB/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/experiments/ENCSR115BCB/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/files/ENCFF851EYG/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/files/ENCFF851EYG/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 200
Actual: 200
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/targets/2L52.1-celegans/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/targets/2L52.1-celegans/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/software/dnase-eval-bam-se/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/software/dnase-eval-bam-se/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/software/atac-seq-software-tools/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/software/atac-seq-software-tools/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/software/trimAdapters.py/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/software/trimAdapters.py/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/software/bigwigaverageoverbed/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/software/bigwigaverageoverbed/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL493SGC/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL493SGC/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL035XIO/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL035XIO/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL568PWV/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL568PWV/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL855QIE/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL855QIE/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL983UFZ/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL983UFZ/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL631XPY/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/pipelines/ENCPL631XPY/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/internal-data-use-policy/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 403
Actual: 403
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/internal-data-use-policy/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 403
Actual: 403
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/tutorials/encode-users-meeting-2016/logistics/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 403
Actual: 403
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/tutorials/encode-users-meeting-2016/logistics/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 403
Actual: 403
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/2017-06-09-release/ with {'status': 'in progress'} as user encoded.test@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL

Trying to patch https://v60rc1-master.demo.encodedcc.org/2017-06-09-release/ with {'status': 'in progress'} as user encoded.test2@gmail.com
Expected: 422
Actual: 422
PATCH SUCCESSFUL



In [15]:

    
qa.check_requests_default_actions









    Out[15]:





{'get': [('/experiments/ENCSR082IHY/',
   [None],
   [('Public', 403), ('encoded.test2@gmail.com', 403), ('admin', 200)]),
  ('/experiments/ENCSR000CUS',
   [None],
   [('Public', 200), ('encoded.test2@gmail.com', 200), ('admin', 200)]),
  ('/experiments/ENCSR524OCB/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/experiments/ENCSR000EFT/',
   [None],
   [('Public', 200),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/biosamples/ENCBS643IYW/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/libraries/ENCLB220SGE/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/experiments/ENCSR466YGC/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/experiments/ENCSR255XZG/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/experiments/ENCSR115BCB/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/files/ENCFF851EYG/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/targets/2L52.1-celegans/',
   [None],
   [('Public', 200),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/software/dnase-eval-bam-se/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/software/atac-seq-software-tools/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/software/trimAdapters.py/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/software/bigwigaverageoverbed/',
   [None],
   [('Public', 200),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/pipelines/ENCPL493SGC/',
   [None],
   [('Public', 200),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/pipelines/ENCPL035XIO/',
   [None],
   [('Public', 200),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/pipelines/ENCPL568PWV/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/pipelines/ENCPL855QIE/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/pipelines/ENCPL983UFZ/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/pipelines/ENCPL631XPY/',
   [None],
   [('Public', 200),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/',
   [None],
   [('Public', 200),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/internal-data-use-policy/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/tutorials/encode-users-meeting-2016/logistics/',
   [None],
   [('Public', 403),
    ('encoded.test@gmail.com', 403),
    ('encoded.test2@gmail.com', 403),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)]),
  ('/2017-06-09-release/',
   [None],
   [('Public', 200),
    ('encoded.test@gmail.com', 200),
    ('encoded.test2@gmail.com', 200),
    ('encoded.test3@gmail.com', 401),
    ('encoded.test4@gmail.com', 200),
    ('admin', 200)])],
 'patch': [('/experiments/ENCSR000CUS/',
   [{'description': 'test'}],
   [('Public', 400), ('encoded.test4@gmail.com', 403)]),
  ('/experiments/ENCSR000CUS/',
   [{'status': 'deleted'},
    {'status': 'archived'},
    {'status': 'proposed'},
    {'status': 'ready for review'},
    {'status': 'released'},
    {'status': 'started'},
    {'status': 'submitted'},
    {'status': 'replaced'}],
   [('admin', 200)]),
  ('/experiments/ENCSR035DLJ/',
   [{'alternate_accessions': ['ENCSR000CUS']}, {'alternate_accessions': []}],
   [('admin', 200)]),
  ('35f91f16-dcef-4ab2-90bd-3928b0db9a60',
   [{'status': 'revoked'}],
   [('admin', 200)]),
  ('/files/ENCFF002BYE/',
   [{'status': 'deleted'},
    {'status': 'in progress'},
    {'status': 'released'},
    {'status': 'replaced'}],
   [('admin', 200)]),
  ('4dc1fbd3-6692-42fa-b710-03eaba9263c1',
   [{'status': 'revoked'}],
   [('admin', 200)]),
  ('/experiments/ENCSR524OCB/',
   [{'status': 'submitted'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/experiments/ENCSR000EFT/',
   [{'status': 'revoked'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/biosamples/ENCBS643IYW/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 200)]),
  ('/libraries/ENCLB220SGE/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/experiments/ENCSR466YGC/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/experiments/ENCSR255XZG/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/experiments/ENCSR115BCB/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/files/ENCFF851EYG/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 200)]),
  ('/targets/2L52.1-celegans/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/software/dnase-eval-bam-se/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/software/atac-seq-software-tools/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/software/trimAdapters.py/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/software/bigwigaverageoverbed/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/pipelines/ENCPL493SGC/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/pipelines/ENCPL035XIO/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/pipelines/ENCPL568PWV/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/pipelines/e02448b1-9706-4e7c-b31b-78c921d58f0b/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/pipelines/ENCPL855QIE/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/pipelines/ENCPL983UFZ/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/pipelines/ENCPL631XPY/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/publications/b2e859e6-3ee7-4274-90be-728e0faaa8b9/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/publications/a4db2c6d-d1a3-4e31-b37b-5cc7d6277548/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/publications/16c77add-1bfb-424b-8cab-498ac1e5f6ed/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/publications/da2f7542-3d99-48f6-a95d-9907dd5e2f81/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)]),
  ('/internal-data-use-policy/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 403), ('encoded.test2@gmail.com', 403)]),
  ('/tutorials/encode-users-meeting-2016/logistics/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 403), ('encoded.test2@gmail.com', 403)]),
  ('/2017-06-09-release/',
   [{'status': 'in progress'}],
   [('encoded.test@gmail.com', 422), ('encoded.test2@gmail.com', 422)])],
 'post': [('/experiments/',
   [{'assay_term_name': 'ChIP-seq',
     'award': '/awards/U41HG006992/',
     'biosample_term_id': 'CL:0010001',
     'biosample_term_name': 'Stromal cell of bone marrow',
     'biosample_type': 'primary cell',
     'description': 'test post experiment',
     'lab': '/labs/thomas-gingeras/',
     'references': ['PMID:18229687', 'PMID:25677182'],
     'target': '/targets/SMAD6-human/'}],
   [('Public', 400), ('encoded.test2@gmail.com', 201), ('admin', 201)])]}

Quick check that important scripts from pyencoded-tools still work?

Use check_tools

Runs script from command line against RC with basic arguments and ensures no errors thrown:

This is a very surface-level check



In [18]:

    
qa.check_tools()









    



Running ENCODE_get_fields.py
/Users/keenan/anaconda/bin/python ENCODE_get_fields.py --key current_rc  --infile ENCSR000CUS --field status
ENCODE_GET_FIELDS.PY SUCCESSFUL
Running ENCODE_patch_set.py
/Users/keenan/anaconda/bin/python ENCODE_patch_set.py --key current_rc --accession ENCSR000CUS --field status --data revoked
ENCODE_PATCH_SET.PY SUCCESSFUL
Running ENCODE_release.py
/Users/keenan/anaconda/bin/python ENCODE_release.py --key current_rc --infile ENCSR000CUS
ENCODE_RELEASE.PY SUCCESSFUL
Running ENCODE_submit_files.py
/Users/keenan/anaconda/bin/python ENCODE_submit_files.py permissions_qa_scripts/Test_submit_files.csv --key current_rc
ENCODE_SUBMIT_FILES.PY SUCCESSFUL

Notebook formatting

Load QANCODE

Instantiate QANCODE object with release candidate URL

QANCODE methods

Three main areas of functionality

1. Crawl website and scrape/download data

2. Compare screenshots between production and RC

3. Submit RC to external (non-browser) requests

Want to compare facet numbers between production and RC?

Use compare_facets

Default list of item_types for compare_facets:

Want to check that downloads work?

Use check_downloads

Download BED file from page (single file)

Download documents from antibody page (multiple files)

Default action list for check_downloads:

Want to highlight differences between pages?

Use find_differences

Default list of action_tuples for find_differences:

Both check_permissions and check_trackhubs use find_differences with custom actions:

Want to check server response time?

Use check_response_time

Want to check external requests against RC?

Use check_requests

Quick check that important scripts from pyencoded-tools still work?

Use check_tools