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Added Gene and BioFeature to sheet_order and removed references to Ta… #130

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merged 7 commits into from May 13, 2019
Merged

Added Gene and BioFeature to sheet_order and removed references to Ta… #130

merged 7 commits into from May 13, 2019

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aschroed
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@aschroed aschroed commented May 8, 2019

…rget from docs

@aschroed aschroed requested a review from KorayKirli May 8, 2019 19:38
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Coverage Status

Coverage decreased (-0.2%) to 85.195% when pulling ef57b12 on add_biofeat_gene into 0c893ad on master.

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coveralls commented May 8, 2019 •
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Coverage Status

Coverage increased (+0.1%) to 85.506% when pulling f792dce on add_biofeat_gene into 0c893ad on master.

sbreiff
sbreiff reviewed May 9, 2019
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doc/metadata_submission.md Outdated
@@ -264,7 +264,7 @@ The scripts accepts the following parameters:.

**To get the complete list of relevant sheets in one workbook:**

get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type ExperimentRepliseq --type Target --type GenomicRegion --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile AllItems.xls
get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type ExperimentRepliseq --type BioFeature --type GenomicRegion --type Gene --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile AllItems.xls
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We might want to update this a bit more to make it less outdated (ex. TreatmentAgent instead of TreatmentChemical, remove FileSet). Could also just replace with --type all or one of the preset options (--type hic)

sbreiff
sbreiff reviewed May 9, 2019
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wranglertools/4DNWranglerTools.egg-info/PKG-INFO Outdated
*Full list*
~~~~
python3 get_field_info.py --type Publication --type Document --type Vendor --type Protocol --type ProtocolsCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type File --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type Image --outfile AllItems.xls --order

python3 get_field_info.py --type Publication --type Document --type Vendor --type Protocol --type ProtocolsCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type File --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type BioFeature --type GenomicRegion --type ExperimentSet --type Image --outfile AllItems.xls --order
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other sheets worth updating as well?

@aschroed
made some updates to docs and preset values to replace references to …
ad0db84 
…target with biofeature and gene
@aschroed
Adding option and functionality so import-item fields are excluded fo…
48699c0 
…r non-admins
@aschroed
Added some tests for new functionality; while doing so found a couple…
bcd2ea4 
… of bugs in build_field_list function having to do with embedded objects that were not arrays and 'array of string' field_type typo
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On top of adding BioFeature and Gene and removing Target and references to it in code and docs.

  • permission: import_item fields are now excluded from sheets unless admin

  • if admin but want to have those fields excluded can use --noadmin option (has no effect for regular users)

  • suggested_enum values are now included in Choices row if 'include_enums' option is True

  • also found a couple of bugs in 'build_field_list' function

  • one that prevented embedded objects that were not members of lists from having their properties included as columns eg. 'format_specification' in file_format

  • another that was a typo in 'array of string' that would prevent enum values being showed as Choices

@KorayKirli KorayKirli merged commit 6e6a2b4 into master May 13, 2019
@KorayKirli KorayKirli deleted the add_biofeat_gene branch May 13, 2019 18:33
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