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Submission Check

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vdancik edited this page Jan 5, 2017 · 3 revisions

What should be checked before submission can be loaded to the Dashboard

dashboard-CV-per-template.txt:

  • observation_tier, template_name, observation_summary, submission_name, submission_description, project, submission_story, submission_story_rank, submission_center, and principal_investigator are not null (story_title is allowed to be null)

  • observation_tier is 1, 2, or 3

  • column references in observation_summary are in dashboard-CV-per-column.txt

  • submission_name format is [datestamp]-[template_name]

  • submission_story is TRUE or FALSE

  • submission_story_rank are consecutive integers (starting with 1) when submission_story is TRUE and zero when submission_story is FALSE.

  • submission_center and principal_investigator match centers on https://ocg.cancer.gov/programs/ctd2/centers

dashboard-CV-per-column.txt:

  • template_name matches template_name in dashboard-CV-per-template.txt

  • subject is one of: gene, transcript, shrna, protein, compound, cell_sample, tissue_sample, animal_model

  • evidence is one of: numeric, label, file, url

  • either subject or evidence must be specified, but not both

  • role is always specified and conforms to controlled vocabulary:

'gene': {'target','biomarker','oncogene','perturbagen','master regulator','candidate master regulator','interactor','background'},

'shrna': {'perturbagen'},

'tissue_sample': {'metastasis','disease','tissue'},

'cell_sample': {'cell line'},

'compound': {'candidate drug','perturbagen','metabolite','control compound'},

'animal_model': {'strain'},

'numeric': {'measured','observed','computed','background'},

'label': {'measured','observed','computed','species','background'},

'file': {'literature','measured','observed','computed','written','background'},

'url': {'measured','computed','reference','resource','link'}

  • mime_type is specified when evidence is file, empty otherwise

  • numeric units are optional when evidence is numeric, empty otherwise

  • display_text can contain only ASCII characters, no unicode characters or newlines

submission text files:

  • the file name and the folder name match submission_name

  • column names match column names in dashboard-CV-per-column.txt

  • subject, evidence, role, mime_type, numeric_units, and display_text rows should match dashboard-CV-per-column.txt (this is not necessary for the upload, but may indicate that change in a submission did not propagate to the dashboard-CV-per-column tab)

  • the submission does not contain trailing empty rows or columns

  • submission_name format is [datestamp]-[template_name], where datestamp consists of submission_date digits

  • submission_date format is four-digit year, two-digit month, and two-digit day separated by periods

  • template_name matches template_name in dashboard-CV-per-template.txt

  • data in subject columns match their corresponding background data

  • data in file columns match existing files

  • data in url columns contain valid and existing hyperlinks or appropriate lower-tier evidence references

Note: all text contains only ASCII characters, unicode and newline characters are not allowed; all text comparisons are case sensitive

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