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Merge pull request #332 from bento-platform/develop
v2.12 - documentation, new public config, improved overview computation, add debugger for vs code
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| { | ||
| // Use IntelliSense to learn about possible attributes. | ||
| // Hover to view descriptions of existing attributes. | ||
| // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 | ||
|
|
||
| "version": "0.2.0", | ||
| "configurations": [ | ||
| { | ||
| "name": "Python: Run Django", | ||
| "type": "python", | ||
| "request": "launch", | ||
| "program": "${workspaceFolder}/manage.py", | ||
| "console": "integratedTerminal", | ||
| "args": [ | ||
| "runserver", | ||
| "--noreload", | ||
| "--nothreading" | ||
| ], | ||
| "django": true | ||
| }, | ||
| { | ||
| "name": "Python: Attach Debugger", | ||
| "type": "python", | ||
| "request": "attach", | ||
| "port": 5678, | ||
| "host": "0.0.0.0" | ||
| }, | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,31 +1,114 @@ | ||
| { | ||
| "sex": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "male", | ||
| "female" | ||
| ], | ||
| "title": "Sex" | ||
| }, | ||
| "extra_properties": { | ||
| "smoking": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "Non-smoker", | ||
| "Smoker", | ||
| "Former smoker", | ||
| "Passive smoker", | ||
| "Not specified" | ||
| ], | ||
| "title": "Smoking" | ||
| "overview": [ | ||
| { | ||
| "section_title": "Demographics", | ||
| "charts": [ | ||
| {"field": "age", "chart_type": "bar"}, | ||
| {"field": "sex", "chart_type": "pie"}, | ||
| {"field": "date_of_consent", "chart_type": "bar"}, | ||
| {"field": "mobility", "chart_type": "bar"}, | ||
| {"field": "lab_test_result_value", "chart_type": "bar"} | ||
| ] | ||
| }, | ||
| { | ||
| "section_title": "Experiments", | ||
| "charts": [ | ||
| {"field": "experiment_type", "chart_type": "pie"} | ||
| ] | ||
| } | ||
| ], | ||
| "search": [ | ||
| { | ||
| "section_title": "Demographics", | ||
| "fields": ["age", "sex", "date_of_consent", "lab_test_result_value"] | ||
| } | ||
| ], | ||
| "fields": { | ||
| "age": { | ||
| "mapping": "individual/age_numeric", | ||
| "title": "Age", | ||
| "description": "Age at arrival", | ||
| "datatype": "number", | ||
| "config": { | ||
| "bin_size": 10, | ||
| "taper_left": 10, | ||
| "taper_right": 100, | ||
| "units": "years", | ||
| "minimum": 0, | ||
| "maximum": 100 | ||
| } | ||
| }, | ||
| "sex": { | ||
| "mapping": "individual/sex", | ||
| "title": "Sex", | ||
| "description": "Sex at birth", | ||
| "datatype": "string", | ||
| "config": { | ||
| "enum": null | ||
| } | ||
| }, | ||
| "experiment_type": { | ||
| "mapping": "experiment/experiment_type", | ||
| "title": "Experiment Types", | ||
| "description": "Types of experiments performed on a sample", | ||
| "datatype": "string", | ||
| "config": { | ||
| "enum": ["DNA Methylation", "mRNA-Seq", "smRNA-Seq", "RNA-Seq", "WES", "Other"] | ||
| } | ||
| }, | ||
| "date_of_consent": { | ||
| "mapping": "individual/extra_properties/date_of_consent", | ||
| "title": "Verbal consent date", | ||
| "description": "Date of initial verbal consent(participant, legal representative or tutor), yyyy-mm-dd", | ||
| "datatype": "date", | ||
| "config": { | ||
| "bin_by": "month" | ||
| } | ||
| }, | ||
| "type_partic": { | ||
| "mapping": "individual/extra_properties/type_partic", | ||
| "title": "Participant type", | ||
| "description": "Has the patient been hospitalized or is the patient seen on as an outpatient?", | ||
| "datatype": "string", | ||
| "config": { | ||
| "enum": [ | ||
| "Hospitalized", | ||
| "Outpatient" | ||
| ] | ||
| } | ||
| }, | ||
| "mobility": { | ||
| "mapping": "individual/extra_properties/mobility", | ||
| "title": "Functional status", | ||
| "description": "Mobility", | ||
| "datatype": "string", | ||
| "config": { | ||
| "enum": [ | ||
| "I have no problems in walking about", | ||
| "I have slight problems in walking about", | ||
| "I have moderate problems in walking about", | ||
| "I have severe problems in walking about", | ||
| "I am unable to walk about" | ||
| ] | ||
| } | ||
| }, | ||
| "lab_test_result_value": { | ||
| "mapping": "individual/extra_properties/lab_test_result_value", | ||
| "title": "Lab Test Result", | ||
| "description": "This acts as a placeholder for numeric values", | ||
| "datatype": "number", | ||
| "config": { | ||
| "bin_size": 50, | ||
| "taper_left": 50, | ||
| "taper_right": 800, | ||
| "minimum": 0, | ||
| "maximum": 1000, | ||
| "units": "mg/L" | ||
| } | ||
| } | ||
| }, | ||
| "death": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "Alive", | ||
| "Deceased" | ||
| ], | ||
| "title": "Death" | ||
| "rules": { | ||
| "count_threshold": 5, | ||
| "max_query_parameters": 2 | ||
| } | ||
| } | ||
| } | ||
| } |
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