Dpl 917 scrna faculty input submission #4067
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… scRNA core pipeline
…s to allow multiple samples per well
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| studies: [study], | ||
| sample_metadata_attributes: { | ||
| supplier_name: sample_name, | ||
| cohort: "Cohort#{plate.human_barcode}", |
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UatActions::GeneratePlates#build_sample calls 'plate.human_barcode' 2 times
| # Ensures number of samples per occupied well is at least 1 | ||
| def num_samples_per_well | ||
| @num_samples_per_well ||= | ||
| if number_of_samples_in_each_well.present? && number_of_samples_in_each_well.to_i.positive? |
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UatActions::GeneratePlates#num_samples_per_well calls 'number_of_samples_in_each_well.to_i' 2 times
| sample.save!(validate: false) | ||
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| if num_samples_per_well > 1 | ||
| well.aliquots.create!(sample: sample, study: study, tag_depth: sample_index) |
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UatActions::GeneratePlates#save_sample calls 'well.aliquots' 2 times
| studies: [study], | ||
| sample_metadata_attributes: { | ||
| supplier_name: sample_name, | ||
| cohort: "Cohort#{plate.human_barcode}", |
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UatActions::GeneratePlates#build_sample refers to 'plate' more than self (maybe move it to another class?)
| } | ||
| ) | ||
| sample.save!(validate: false) | ||
| num_samples_per_well.times { |sample_index| create_sample(plate, well, sample_index + 1) } |
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UatActions::GeneratePlates#construct_wells contains iterators nested 2 deep
| sample_name = "sample_#{sample_index}_#{plate.human_barcode}_#{well.map.description}" | ||
| sample = build_sample(sample_name, plate) | ||
| save_sample(sample, well, sample_index) | ||
| rescue ActiveRecord::RecordInvalid => e |
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UatActions::GeneratePlates#create_sample has the variable name 'e'
| # Ensures number of samples per occupied well is at least 1 | ||
| def num_samples_per_well | ||
| @num_samples_per_well ||= | ||
| if number_of_samples_in_each_well.present? && number_of_samples_in_each_well.to_i.positive? |
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UatActions::TestSubmission#num_samples_per_well calls 'number_of_samples_in_each_well.to_i' 2 times
| # The well layout is set to 'Random'. | ||
| # The number of samples in each well is set to num_samples_per_well. | ||
| # @return [UatActions::GeneratePlates] the configured plate generator | ||
| def setup_generator |
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UatActions::TestSubmission#setup_generator has approx 6 statements
… to only create one request per well
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Code Climate has analyzed commit 8ce8f7e and detected 11 issues on this pull request. Here's the issue category breakdown:
The test coverage on the diff in this pull request is 97.8% (50% is the threshold). This pull request will bring the total coverage in the repository to 86.7% (0.0% change). View more on Code Climate. |
Closes #3901
Changes proposed in this pull request
Adds submission template for faculty input plate