Attention

This repo is an adaption of https://github.com/ssec-jhu/biospecdb. Images present within this documentation may not entirely reflect the exact working content of this application.

Welcome to biodb’s documentation!

biodb is a Django application for collecting patient biosample and spectroscopy data.

Contents

• User Manual
  • Contents
    • Login and Accounts
      • Registration
      • Permissions
      • Login
      • Password Reset
      • User Profile
    • Dataset Catalog
      • Usage
      • Fields
      • Computing Data File Integrity
    • Data Collection
      • Usage
      • Viewing
      • Downloading
      • Adding
      • Editing
      • Deleting
      • Patients
      • Visits
      • Observations
      • BioSamples
      • ArrayData
      • Bulk Data Uploads
    • SQL Explorer
      • Usage
      • Playground
      • Charts
      • Schema
      • New Query
• Installation
• Deployment
• Management
• API
  • Data Catalog Model
    • catalog.models.Dataset
      • Dataset
        • Dataset.id
        • Dataset.query
        • Dataset.sql
        • Dataset.version
        • Dataset.name
        • Dataset.description
        • Dataset.file
        • Dataset.app_version
        • Dataset.sha256
        • Dataset.n_rows
        • Dataset.data_sha256
        • Dataset.array_data_filenames
        • Dataset.__init__()
  • Data Collection Model
    • Patient & Visit
      • uploader.models.Patient
        • Patient
          • Patient.patient_id
          • Patient.patient_cid
          • Patient.center
          • Patient.__init__()
      • uploader.models.Visit
        • Visit
          • Visit.patient
          • Visit.previous_visit
          • Visit.days_observed
          • Visit.__init__()
    • BioSample
      • uploader.models.BioSampleType
        • BioSampleType
          • BioSampleType.name
          • BioSampleType.__init__()
      • uploader.models.BioSample
        • BioSample
          • BioSample.visit
          • BioSample.sample_cid
          • BioSample.sample_study_id
          • BioSample.sample_study_name
          • BioSample.sample_type
          • BioSample.sample_processing
          • BioSample.sample_extraction
          • BioSample.sample_extraction_tube
          • BioSample.centrifuge_time
          • BioSample.centrifuge_rpm
          • BioSample.freezing_temp
          • BioSample.thawing_temp
          • BioSample.thawing_time
          • BioSample.freezing_time
          • BioSample.__init__()
    • Observations
      • uploader.models.Observable
        • Observable
          • Observable.category
          • Observable.name
          • Observable.description
          • Observable.alias
          • Observable.value_class
          • Observable.value_choices
          • Observable.validator
          • Observable.center
          • Observable.__init__()
      • uploader.models.Observation
        • Observation
          • Observation.visit
          • Observation.observable
          • Observation.days_observed
          • Observation.observable_value
          • Observation.__init__()
    • ArrayData
      • uploader.models.Instrument
        • Instrument
          • Instrument.id
          • Instrument.cid
          • Instrument.manufacturer
          • Instrument.model
          • Instrument.serial_number
          • Instrument.center
          • Instrument.__init__()
      • uploader.models.ArrayMeasurementType
        • ArrayMeasurementType
          • ArrayMeasurementType.name
          • ArrayMeasurementType.__init__()
      • uploader.models.ArrayData
        • ArrayData
          • ArrayData.id
          • ArrayData.data
          • ArrayData.instrument
          • ArrayData.bio_sample
          • ArrayData.measurement_type
          • ArrayData.measurement_id
          • ArrayData.acquisition_time
          • ArrayData.resolution
          • ArrayData.power
          • ArrayData.pressure
          • ArrayData.date
          • ArrayData.__init__()
    • Bulk Data Uploads
      • uploader.models.UploadedFile
        • UploadedFile
          • UploadedFile.meta_data_file
          • UploadedFile.array_data_file
          • UploadedFile.center
          • UploadedFile.__init__()
    • Quality Control Annotations
      • biodb.qc.qcfilter.QcFilter
        • QcFilter
          • QcFilter.__init__()
      • uploader.models.QCAnnotator
        • QCAnnotator
          • QCAnnotator.name
          • QCAnnotator.fully_qualified_class_name
          • QCAnnotator.value_type
          • QCAnnotator.description
          • QCAnnotator.default
          • QCAnnotator.__init__()
      • uploader.models.QCAnnotation
        • QCAnnotation
          • QCAnnotation.value
          • QCAnnotation.annotator
          • QCAnnotation.array_data
          • QCAnnotation.__init__()
  • SQL Explorer Model
    • Query Model
      • explorer.models.Query
        • Query
          • Query.__init__()
    • Data Exporters
      • uploader.exporters.CSVExporter
        • CSVExporter
          • CSVExporter.__init__()
      • uploader.exporters.ExcelExporter
        • ExcelExporter
          • ExcelExporter.__init__()
      • uploader.exporters.JSONExporter
        • JSONExporter
          • JSONExporter.__init__()
      • uploader.exporters.ZipArrayDataMixin
        • ZipArrayDataMixin
          • ZipArrayDataMixin.__init__()
    • Charts
      • uploader.charts.get_pie_chart
        • get_pie_chart()
      • uploader.charts.get_line_chart
        • get_line_chart()
    • SQL
      • biodb.apps.uploader.sql
  • User Model API
    • user.models.Center
      • Center
        • Center.id
        • Center.name
        • Center.country
        • Center.__init__()
    • user.models.User
      • User
        • User.username
        • User.first_name
        • User.last_name
        • User.email
        • User.center
        • User.is_staff
        • User.is_active
        • User.date_joined
        • User.is_sqluser_view
        • User.is_sqluser_change
        • User.is_catalogviewer
        • User.__init__()
  • IO & File Storage Utilities
    • biodb.apps.uploader.io
    • biodb.apps.uploader.loaddata
  • General Utility
    • biodb.util