JIRA Ticket: https://ctds-planx.atlassian.net/browse/ELW-4

gdcdictionary/schema_test.py

@@ -23,7 +23,7 @@
 
 def load_yaml_schema(path):
     with open(path, 'r') as f:
-        return yaml.load(f)
+        return yaml.load(f, Loader=yaml.FullLoader)
 CUR_DIR = os.path.dirname(os.path.realpath(__file__))
 DATA_DIR = os.path.join(CUR_DIR, 'examples')
 project1 = load_yaml_schema(os.path.join(CUR_DIR, 'schemas/projects/project1.yaml'))

gdcdictionary/schemas/demographic.yaml

@@ -4,7 +4,7 @@ id: "demographic"
 title: Demographic
 type: object
 nodeTerms: null
-namespace: https://nci-crdc-demo.datacommons.io/
+namespace: https://elwazi-demo.planx-pla.net/
 category: clinical
 program: '*'
 project: '*'
@@ -42,26 +42,14 @@ properties:
 
   $ref: "_definitions.yaml#/ubiquitous_properties"
 
-  age_range:
+  age:
     description: Range of ages for the subject. The age range should not include ages
       over 89 years.
     type: string
 
-  cause_of_death:
-    description: Text term to identify the cause of death for a patient.
-    type: string
-
-  days_to_birth:
-    description: Time interval from a person’s date of birth to the date of initial
-      pathologic diagnosis, represented as a calculated negative number of days.
-    type: integer
-    maximum: 0
-    minimum: -32872
-
-  days_to_death:
-    description: Time interval from a person’s date of death to the date of initial
-      pathologic diagnosis, represented as a calculated number of days.
-    type: integer
+  bmi:
+    description:  Subject Body Mass Index (kg/m^2)
+    type: number
 
   ethnicity:
     term:
@@ -83,6 +71,16 @@ properties:
       - unknown
       - unspecified
 
+  marital_status:
+    description: current relationship status of subject
+    enum:
+      - No regular partner
+      - Separated
+      - Primary regular partner
+      - Widowed
+      - Married
+      - Unknown
+
   race:
     term:
       $ref: "_terms.yaml#/race"

gdcdictionary/schemas/exposure.yaml

@@ -0,0 +1,93 @@
+$schema: "http://json-schema.org/draft-04/schema#"
+
+id: "exposure"
+title: Envorinmental Exposure
+type: object
+nodeTerms: null
+namespace: https://elwazi-demo.planx-pla.net/
+category: clinical
+program: '*'
+project: '*'
+description:  Environmental factors that the patient has been exposed to that contribute to current diagnosis
+additionalProperties: false
+submittable: true
+validators: null
+
+systemProperties:
+  - id
+  - project_id
+  - state
+  - created_datetime
+  - updated_datetime
+
+links:
+  - name: subjects
+    backref: exposures
+    label: describes
+    target_type: subject
+    multiplicity: many_to_one
+    required: true
+
+required:
+  - submitter_id
+  - type
+  - subjects
+
+uniqueKeys:
+  - [id]
+  - [project_id, submitter_id]
+
+properties:
+
+  $ref: "_definitions.yaml#/ubiquitous_properties"
+
+  contraceptive:
+    description:  type of contraception used
+    enum:
+      - Condoms
+      - Hysterectomy
+      - Implant
+      - Injectable
+      - IUCD
+      - Oral
+      - Tubal ligation
+      - unknown
+      E
+  electricity:
+    description: Electricity at residence
+    type: string
+
+  sexual_intercourse:
+    decsription:  Sexual intercourse in the past three months
+    type: string
+
+  tap_water:
+    description:  Tap Water at residence
+    type: string
+
+  travel_time:
+    desription:  travel time from residence to clinic
+    enum:
+      - Less than 30 minutes
+      - 30-60 minutes
+      - 1-2 hours
+      - Greater than 2 hours
+      - unknown
+
+  use_condom:
+    description:  Frequency of condom use
+    enum:
+      - Always
+      - Sometimes
+      - Never
+      - unknown
+
+  use_familyplanning
+    description: Use family planning methods
+    enum:
+      - Yes
+      - No
+      - unknown
+
+  subjects:
+    $ref: "_definitions.yaml#/to_one"

gdcdictionary/schemas/medical_history.yaml

@@ -0,0 +1,182 @@
+$schema: "http://json-schema.org/draft-04/schema#"
+
+id: "medical_history"
+title: Medical_history
+type: object
+nodeTerms: null
+namespace: https://elwazi-demo.planx-pla.net/
+category: clinical
+program: '*'
+project: '*'
+description: Data obtained from the patient about past conditions
+additionalProperties: false
+submittable: true
+validators: null
+
+systemProperties:
+  - id
+  - project_id
+  - state
+  - created_datetime
+  - updated_datetime
+
+links:
+  - name: subjects
+    backref: demographics
+    label: describes
+    target_type: subject
+    multiplicity: one_to_one
+    required: true
+
+required:
+  - submitter_id
+  - type
+  - subjects
+
+uniqueKeys:
+  - [id]
+  - [project_id, submitter_id]
+
+properties:
+
+  $ref: "_definitions.yaml#/ubiquitous_properties"
+
+  arv_treatment:
+    description:  subject currently taking antiretroviral arv_treatment
+    enum:
+      - Yes
+      - No
+      - unknown
+
+  additional_children:
+    description: Does subject want additional children
+    enum:
+      - Yes
+      - No
+      - Not sure
+      - unknown
+
+  breastfeeding:
+    description:  Is Subject current breastfeeding
+    enum:
+      - Yes
+      - No
+      - unknown
+
+  cd4_count:
+    description: CD4 Lymphocyte cd4_count
+    type: number
+
+  cough:
+    description:  patient reports cough for more than two weeks
+    enum:
+      - Yes
+      - No
+      - unknown
+
+  fever:
+    description:  patient reports fever for more than two weeks
+    enum:
+      - Yes
+      - No
+      - unknown
+
+  HIV_treatment_regimen:
+    description: ARV regiment or line of arv_treatment
+    enum:
+      - EFV based
+      - Lpv/r
+      - ATV/r
+      - RTV based
+      - other
+      - unknown
+
+  lost_weight:
+    description:  patient reports weight loss in past month
+    enum:
+      - Yes
+      - No
+      - unknown
+
+    night_sweats:
+      description:  patient reports experiencing night sweats
+      enum:
+        - Yes
+        - No
+        - unknown
+
+  number_children_choice:
+    description:  number of children subject would to have alive
+    type: integer
+
+  pregnancy_desire:
+    description: Does subject want to become pregnant ever
+    enum:
+      - Yes
+      - No
+      - unknown
+
+  tb_treament:
+    description: Received treatment for TB in last three months
+    enum:
+      - Yes
+      - No
+      - unknown
+
+  tell_partner_HIV_status:
+    description: Did subject inform partner of HIV hpv_status
+    enum:
+      - Yes
+      - No
+      - unknown
+
+  new_pregnancy:
+    description: New pregnancy at followup
+    type: string
+
+  new_pregnancy_outcome:
+    description: Outcome of new pregnancy
+    enum:
+      - Abortion/miscarriage < 20 weeks
+      - Congenital anomalies
+      - Live birth
+      - Low birth weight <2500g
+      - Preterm delivery <37 weeks
+      - Stillbirth/intrauterine fetal death >20 weeks
+      - unknown
+
+  number_additional_children:
+    description: How many more children would subject like to have
+    type: integer
+
+
+  test_partner_hiv_stat:
+    description: Does subject know if partner tested for hiv_positive
+    enum:
+      - Yes
+      - No
+      - unknown
+
+
+  total_pregnancies:
+    description:  Total number of pregnancies reported by subjects
+    type:  integer
+
+  viral_load:
+    description: HIV viral load from blood specimen
+    enum:
+      - <200 cp/ml
+      - >1000 cp/ml
+      - 200-399 cp/ml
+      - 400-1000 cp/ml
+      - Undetectable
+      - unknown
+
+  who_clinical_classification:
+    description:  WHO clinical classification of HIV status 1 - Asymptomatic, 2 - symptomatic 3 -
+    enum:
+      - 1
+      - 2
+      - 3
+      - 4
+      - unknown

gdcdictionary/schemas/study.yaml

@@ -4,7 +4,7 @@ id: "study"
 title: Study
 type: object
 nodeTerms: null
-namespace: https://nci-crdc-demo.datacommons.io/
+namespace: https://elwazi-demo.planx-pla.net/
 category: administrative
 program: '*'
 project: '*'
@@ -43,41 +43,11 @@ properties:
 
   $ref: "_definitions.yaml#/ubiquitous_properties"
 
-  analytical_fraction:
-    description: Type of peptide or protein enrichment
-    type: string
-
   data_description:
     description: Brief description of the data being provided for this study. Free
       text
     type: string
 
-  experiment_type:
-    description: General strategy used for differential analysis
-    type: string
-
-  is_clinical_trial:
-    description: Flag that indicates whether this is a clinical trial study
-    type: boolean
-
-  study_completeness:
-    description: Description of data status. 0=Descriptive data and results as originally
-      received from the data provider. 1=Includes updates to the original data submission
-      short of completeness. 2=Complete set of descriptive data and results, as ascertained
-      by curator.
-    enum:
-      - '0'
-      - '1'
-      - '2'
-
-  study_description:
-    description: A brief description of the study being performed. Free text
-    type: string
-
-  study_design:
-    description: Summary of the goals the study is designed to discover. General description
-      of the study's place in relation to a clinical application.
-    type: string
 
   study_doi:
     description: Digital object identifier (DOI) is a type of persistent identifier