[wip] Csv converter

[djarecka]

These are the first versions of converter from/to csv file. I'm not sure where should they be, but for now opening this pr for the discussion.

Examples of usage and output:

• yaml2csv converter: running python utils/yaml2csv.py --yaml linkml-schema/kbmodel.yaml --output kb_csv.csv gives kb_csv.csv

• csv2yaml converter: running python utils/csv2yaml.py --csv Donor_Metadata.csv --output donor.yaml --header head.yaml (where Donor_Metadata.csv comes from the repo, and head.yaml provides just the typical linkml settings) gives:

  yaml file content

default_prefix: bican
default_range: string
id: https://identifiers.org/brain-bican/kb-model
imports:
- linkml:types
- biolink:biolink-model
name: kb-model
prefixes:
  bican: https://identifiers.org/brain-bican/vocab/
  biolink: https://w3id.org/biolink/vocab/
  linkml: https://w3id.org/linkml/
  ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
  schema: http://schema.org/
  spdx: http://spdx.org/rdf/terms#
classes:
  Diagnoses:
    attributes:
      clinical_brain_diagnosis:
        description: Clinical Brain Diagnosis Available
      clinical_brain_diagnosis_code:
        description: Clinical Brain Diagnosis Code
      clinical_brain_diagnosis_confidence_level:
        description: Clinical Brain Diagnosis Confidence Level
      genetic_diagnosis:
        description: Genetic Diagnosis Available
      genetic_diagnosis_code:
        description: Genetic Diagnosis Code
      genetic_diagnosis_confidence_level:
        description: Genetic Diagnosis Confidence Level
      non_brain_diagnosis:
        description: Non Brain Diagnosis Available
      non_brain_diagnosis_code:
        description: Non Brain Diagnosis Code
      non_brain_diagnosis_confidence_level:
        description: Non Brain Diagnosis Confidence Level
  Family History:
    attributes:
      condition_type:
        description: Condition Type
      condition_type_specify:
        description: Condition Type Specify
      family_history_available:
        description: Family History Available
      relative_type:
        description: Relative Type
      relative_type_specify:
        description: Relative Type Specify
  General Specimen Data:
    attributes:
      antemortem_mri_available:
        description: Antemortem MRI Available
      brain_weight:
        description: Brain Weight Measurement
        range: integer
      hemisphere:
        description: Hemisphere
      left_hemisphere_preparation:
        description: Left Hemisphere Preparation
      left_hemisphere_preparation_specify:
        description: Left Hemisphere Preparation Specify
      ph:
        description: pH
        range: float
      photo_2d_available:
        description: Photo 2d Available
      post_mortem_interval:
        description: Post Mortem Interval
        range: float
      postmortem_mri_available:
        description: Postmortem MRI Available
      postmortem_mri_type:
        description: Postmortem MRI Type
      right_hemisphere_preparation:
        description: Right Hemisphere Preparation
      right_hemisphere_preparation_specify:
        description: Right Hemisphere Preparation Specify
      rin:
        description: RIN
        range: float
      rin_testing_organization:
        description: RIN Testing Organization
      rin_tissue_source:
        description: RIN Tissue Source
      rine:
        description: RINe
        range: float
      rine_testing_organization:
        description: RINe Testing Organization
      rine_tissue_source:
        description: RINe Tissue Source
      scan_3d_available:
        description: Scan 3d Available
      weighed_type:
        description: Brain Tissue Weighed Type
  General Subject Fields:
    attributes:
      age_of_death:
        description: Age Value (Years)
        range: integer
      autopsy_report:
        description: Autopsy Report
      birth_country_name:
        description: Birth Country Name
      cause_of_death:
        description: Cause of Death
      cause_of_death_code:
        description: Cause of Death Code
      donor_source:
        description: Donor Source
      education_years_number:
        description: Education Years Number
        range: integer
      ethnicity:
        description: Ethnicity
      family_income_range:
        description: Family Income Range
      gender:
        description: Gender at Time of Death
      handedness:
        description: Handedness
      informant_interview_performed:
        description: Informant Interview Performed
      informant_questionnaire_completed:
        description: Informant Questionnaire Completed
      informant_relationship:
        description: Informant Relationship
      informant_relationship_specify:
        description: Informant Relationship Specify
      manner_of_death:
        description: Manner of Death
      marital_status:
        description: Marital or Partner Status ATOD
      medical_records_available:
        description: Medical Records Available
      medical_records_reviewed:
        description: Medical Records Reviewed
      primary_language:
        description: Primary Language Code
      race:
        description: Race
      repository:
        description: Repository
      secondary_language:
        description: Secondary Language Code
      sex:
        description: Sex at Birth
      sex_orientation:
        description: Sexual Orientation at Time of Death
      subject_id:
        description: Local Donor ID
      year_of_death:
        description: Date of Death
  Infant Medical History:
    attributes:
      apgar_10_minute_score:
        description: APGAR Ten Minute Score
        range: integer
      apgar_10_minute_score_available:
        description: APGAR Ten Minute Score Available
      apgar_5_minute_score:
        description: APGAR Five Minute Score
        range: integer
      apgar_5_minute_score_available:
        description: APGAR Five Minute Score Available
      birth_weight_lbs:
        description: Birth Weight Value (lbs)
        range: float
      birth_weight_oz:
        description: Birth Weight Value (oz)
        range: float
      gestational_age_value_days:
        description: Gestational Age Value (days)
        range: integer
      gestational_age_value_weeks:
        description: Gestational Age Value (weeks)
        range: integer
  Infectious Disease Testing:
    attributes:
      test_name:
        description: Test Name
      test_result:
        description: Result
      tissue_source:
        description: Testing Tissue Source
  Neuropathological Diagnoses:
    attributes:
      aging:
        description: Aging
      aging_type:
        description: Aging Type
      aging_type_specify:
        description: Aging Type Specify
      artifacts:
        description: Artifacts
      artifacts_type:
        description: Artifacts Type
      artifacts_type_specify:
        description: Artifacts Type Specify
      developmental:
        description: Developmental
      developmental_type_specify:
        description: Developmental Type Specify
      infectious:
        description: Infectious
      infectious_type_specify:
        description: Infectious Type Specify
      inflammatory:
        description: Inflammatory
      inflammatory_type_specify:
        description: Inflammatory Type Specify
      neoplastic:
        description: Neoplastic
      neoplastic_type:
        description: Neoplastic Type
      neoplastic_type_specify:
        description: Neoplastic Type Specify
      neurodegenerative:
        description: Neurodegenerative
      neurodegenerative_type:
        description: Neurodegenerative Type
      neurodegenerative_type_specify:
        description: Neurodegenerative Type Specify
      traumatic:
        description: Traumatic
      traumatic_type:
        description: Traumatic Type
      traumatic_type_specify:
        description: Traumatic Type Specify
      vascular:
        description: Vascular
      vascular_type:
        description: Vascular Type
      vascular_type_specify:
        description: Vascular Type Specify
  Non-Brain Specimen Collected:
    attributes:
      non_brain_tissue_available:
        description: Non-Brain Tissue Available
      tissue_type:
        description: Tissue Type
      tissue_type_details:
        description: Tissue Type Details
  Perinatal Neurologic Events:
    attributes:
      perinatal_neurologic_event_type:
        description: Perinatal Neurologic Event Type
      perinatal_neurologic_event_type_specify:
        description: Perinatal Neurologic Event Type Specify
  Toxicology Screening:
    attributes:
      drugs_found:
        description: Drugs Found
      drugs_found_specify:
        description: Drugs Found Specify
      toxicology_report_level:
        description: Toxicology Report level
      toxicology_result:
        description: Toxicology Result
      toxicology_units:
        description: Toxicology Units

[djarecka]

this PR will be closed and I will reopen with new version to avoid adding automatically generated files (GA actions has been changed)