CEDAR Artifact Library

This library various tools to work with CEDAR model artifacts (templates, elements, fields, and template instances).

Primarily, the library provides a Java API to work with CEDAR artifacts.

The library uses this API to support the conversion of artifacts to and from various serializations.

Currently, it supports (1) the reading of artifacts from their JSON Schema and JSON-LD serializations, (2) the writing of JSON Schema and YAML serializations of templates, elements and fields, and (3) the writing of Excel, TSV, CSV, YAML, and UBKG serializations of templates.

Reading Schema Artifacts

The library provides a class to convert the Jackson Library ObjectNode class representation of a JSON object containing a JSON Schema serialization of CEDAR artifacts to a Java representation of those artifacts.

A class called JsonSchemaArtifactReader provides methods to generate Java representations of templates, elements and fields from their JSON Schema representation.

For example, assuming we used the Jackson Library to read a JSON document containing a JSON Schema representation of a CEDAR template, we can generate a Java representation as follows:

// Obtain an instance of a Jackson Library ObjectNode class
// containing a JSON Schema representation of a CEDAR template
ObjectNode objectNode = ...
// Generate an instance of the JsonSchemaArtifactReader class
JsonSchemaArtifactReader artifactReader = new JsonSchemaArtifactReader();
// Generate a Java representation of the CEDAR template 
TemplateSchemaArtifact templateSchemaArtifact 
  = artifactReader.readTemplateSchemaArtifact(objectNode);

The TemplateSchemaArtifact contains a full representation of a CEDAR template.

The JsonSchemaArtifactReader class also provides methods to read CEDAR element, field and instance artifacts.

Serializing Schema Artifacts

Currently, the following serializations are supported: JSON Schema, YAML, Excel, CSV, TSV, and UBKG.

Serializing to JSON Schema

A class called JsonSchemaArtifactRenderer provides methods to serialize CEDAR schema artifacts to JSON Schema.

Again, the ObjectNode class from the Jackson Library is used to represent JSON documents.

For example, we can generate a JSON Schema serialization for a CEDAR template as follows:

// Obtain instance of TemplateSchemaArtifact class
TemplateSchemaArtifact templateSchemaArtifact = ...
// Generate a Jackson Library ObjectNode instance containing a JSON Schema representation of the template
ObjectNode rendering 
  = jsonArtifactRenderer.renderTemplateSchemaArtifact(templateSchemaArtifact);

Serializing to YAML

A class called YamlArtifactRenderer provides methods to serialize CEDAR schema artifacts to YAML.

For example, we can generate a YAML serialization of a CEDAR template as follows:

// Set to 'false' for a complete YAML representation of an artifact, 'true' for a condensed representation
boolean isCompact = false;
// Create the renderer
YamlArtifactRenderer yamlArtifactRenderer = new YamlArtifactRenderer(isCompact);
// Generate a map containing a YAML representation of the template
LinkedHashMap<String, Object> yamlRendering 
  = yamlArtifactRenderer.renderTemplateSchemaArtifact(templateSchemaArtifact);

This map can be written to a file using the Jackson Library as follows:

YAMLFactory yamlFactory = new YAMLFactory()
          disable(YAMLGenerator.Feature.WRITE_DOC_START_MARKER).
          enable(YAMLGenerator.Feature.MINIMIZE_QUOTES).
          enable(YAMLGenerator.Feature.INDENT_ARRAYS_WITH_INDICATOR).
          disable(YAMLGenerator.Feature.SPLIT_LINES);
ObjectMapper mapper = new ObjectMapper(yamlFactory);

LinkedHashMap<String, Object> yamlRendering 
  = yamlRenderer.renderTemplateSchemaArtifact(templateSchemaArtifact);

mapper.writeValue([file], yamlRendering);

Serializing Templates to Excel

A class called ExcelArtifactRenderer provides methods to serialize CEDAR templates to Excel.

Only top-level fields in templates will be serialized. All nested elements will be ignored.

The Apache POI library Workbook class is used to store the generated Excel representation.

Using the ExcelArtifactRendered, we can generate a YAML serialization of a CEDAR template as follows:

// Pass a CEDAR terminology server endpoint (e.g., https://terminology.metadatacenter.org/bioportal/integrated-search/) with a CEDAR API key
ExcelArtifactRenderer renderer
  = new ExcelArtifactRenderer(terminologyServerIntegratedSearchEndpoint, terminologyServerAPIKey);

// Generate an Apache POI Workbook rendering, starting at column 0 and row 0
Workbook workbook = renderer.render(templateSchemaArtifact, 0, 0);

Serializing Templates to TSV

A utility class is provided that can take the above Excel rendering and generate a TSV from it.

For example, to generate a TSV from the first sheeet of the above workbook:

StringBuffer tsvBuffer = SpreadSheetUtil.convertSheetToTsv(workbook.getSheetAt(0));

This string buffer can be written to a file as follows:

    try (BufferedWriter writer = new BufferedWriter(new FileWriter([file]))) {
      writer.write(tsvBuffer.toString());
    } catch (IOException e) {
      ...
    }

Serializing Templates to CSV

Again, a utility class is provided that can take the above Excel rendering and generate a CSV from it.

For example, to generate a CSV from the first sheeet of the above workbook:

StringBuffer csvBuffer = SpreadSheetUtil.convertSheetToCsv(workbook.getSheetAt(0));

Creating Templates

CEDAR templates are represented using the TemplateSchemaArtifact class. This class provides a complete specification of a CEDAR template.

A companion builder class can be used to create a template.

For example, to create a minimal template with a name and description, we can use the library as follows:

TemplateSchemaArtifact templateSchemaArtifact = TemplateSchemaArtifact.builder()
  .withName("Study")
  .withDescription("A template describing a study")
  .build();

Creating Elements

CEDAR elements are represented using the ElementSchemaArtifact class.

Again, a companion builder class can be used to create an element.

For example, to create a minimal element with a name and description, we can use the library as follows:

ElementSchemaArtifact elementSchemaArtifact = ElementSchemaArtifact.builder()
  .withName("Address")
  .withDescription("An element describing an address")
  .build();

This element can be added as a child to a template as follows:

TemplateSchemaArtifact templateSchemaArtifact = TemplateSchemaArtifact.builder()
  .withName("Study")
  .withDescription("A template describing a study")
  .withElementSchema(elementSchemaArtifact)
  .build();

Creating Fields

Currently, CEDAR provides the following types of fields: text, temporal, numeric, controlled term, text area, phone number, email, radio, list, link, image, YouTube, section break, rich text, and attribute-value.

A class called FieldSchemaArtifact represents all of these field types.

Since each field has specific characteristics, a custom builder is provided to contruct each field type.

Creating Text Fields

A builder supplied by a class called TextField can be used to create a CEDAR text field.

With this class we can create a text field representing a study name with a minimum length of 2 and a maximum length of 10 as follows:

TextField textField = TextField.builder().
      withName("Study ID").
      withDescription("Field representing the ID of a study).
      withMinLength(2).
      withMaxLength(10).
      build();

This field can be added as a child to a template as follows:

TemplateSchemaArtifact templateSchemaArtifact = TemplateSchemaArtifact.builder()
  .withName("Study")
  .withDescription("A template describing a study")
  .withFieldSchema(fieldSchemaArtifact);
  .build();

Creating Numeric Fields

A builder supplied by a class called NumericField can be used to create a CEDAR numeric fields.

In CEDAR, numeric fields can be one of XML Schema Datatypes decimal, integer, long, byte, short, int, float and double. An enumeration called NumericType can be used to specify this type on field creation. Numeric fields also allow the optional specification of minimum and maximum values, and of a default value.

An example numeric field representing the percentage of a treatment completed and with a default of 0% could be created as follows:

    NumericField numericField = NumericField.builder().
      withName("Treatment Completed %").
      withDescription("Please enter the percentage of the treatment that has been completed").
      withNumericType(NumericType.INTEGER).
      withMinValue(0).
      withMaxValue(100).
      withDefaultValue(0).
      build();

Creating Temporal Fields

A builder supplied by a class called TemporalField can be used to create a CEDAR temporal fields.

In CEDAR, temporal fields can represent a time value, a date value, and a datetime value. An enumerated type called TemporalType can be used to specify this type when creating a temporal field. Similarly, the desired granularity and whether a 12- or 24-hour presentation is desired can be opitionally be specified; an enumeration called TemporalGranularity can be used to specify the format, and an enumeration called InputTimeFormat for the latter. Finally, a temporal field may optionally be configured to display time zone information.

An example temporal field representing the time of a patient visit recorded with the accuracy of minutes and presented in 24-hour format with time zone information displayed could be created as follows:

    TemporalField temporalField = TemporalField.builder().
      withName("Patient Visit Time").
      withTemporalType(TemporalType.DATETIME).
      withTemporalGranularity(TemporalGranularity.MINUTES).
      withInputTimeFormat(InputTimeFormat.TWENTY_FOUR_HOURS).
      withTimeZoneEnabled(true).
      build();

Creating Controlled Term Fields

A builder supplied by a class called ControlledTermField can be used to create a CEDAR controlled term fields.

Controlled term fields can have four possible value types: classes, ontologies, ontology branches, and value sets.

The builder class has methods withClassValueConstraint, withOntologyValueConstraint, withBranchValueConstraint, and withValueSetValueConstraint to allow specification of these types.

Here, for example, is the builder being used to create a field with all four types:

    String name = "Disease";
    String description = "Please enter a disease";

    URI ontologyUri = URI.create("https://data.bioontology.org/ontologies/DOID");
    String ontologyAcronym = "DOID";
    String ontologyName = "Human Disease Ontology";
    URI branchUri = URI.create("http://purl.bioontology.org/ontology/SNOMEDCT/64572001");

    String branchAcronym = "SNOMEDCT";
    String branchName = "Disease";
    String branchSource = "SNOMEDCT";

    URI classUri = URI.create("http://purl.bioontology.org/ontology/LNC/LA19711-3");
    String classSource = "LOINC";
    String classLabel= "Human";
    String classPrefLabel = "Human";
    ValueType classValueType = ValueType.ONTOLOGY_CLASS;

    URI valueSetUri = URI.create("https://cadsr.nci.nih.gov/metadata/CADSR-VS/77d61de250089d223d7153a4283e738043a15707");
    String valueSetCollection = "CADSR-VS";
    String valueSetName = "Stable Disease";

    ControlledTermField controlledTermField = ControlledTermField.builder().
      withName("Disease").
      withOntologyValueConstraint(ontologyUri, ontologyAcronym, ontologyName).
      withBranchValueConstraint(branchUri, branchSource, branchAcronym, branchName, 3).
      withClassValueConstraint(classUri, classSource, classLabel, classPrefLabel, classValueType).
      withValueSetValueConstraint(valueSetUri, valueSetCollection, valueSetName).
      build();

Creating Radio Fields

A builder supplied by a class called RadioField can be used to create a CEDAR radio field.

A list of options can be supplied when creating a radio field. Whether an option is selected by default can also be indicated.

For example, we can create a radio field representing a question with options Yes/No/Maybe, with Maybe selected by default as follows:

    RadioField radioField = RadioField.builder().
      withName("Covid-19 Status").
      withDescription("Have you had Covid-19?").
      withOption("Yes").
      withOption("No").
      withOption("Maybe", true).
      build();

Creating List Fields

A builder supplied by a class called ListField can be used to create a CEDAR list field.

A list of options can be supplied when creation a list field. Whether an option is selected by default can also be indicated.

Using this class, we can create a list field representing a question with options Moderna/Pfizer/None, with None selected by default as follows:

    ListField listField = ListField.builder().
      withName("Covid-19 Vaccine").
      withDescription("Which vaccine provider did you use?").
      withOption("Moderna").
      withOption("Pfizer").
      withOption("None", true).
      build();

Creating Checkbox Fields

A builder supplied by a class called CheckboxField can be used to create a CEDAR checkbox field.

When creating a checkbox field, a list of options can be supplied. Whether an option is selected by default can also be indicated.

For example, we can create a checkbox field representing a question with options Yes/No/Don't Know, with Don't Know salected by default as follows:

    CheckboxField checkboxField = CheckboxField.builder().
      withName("DTAP Status").
      withDescription("Are you up-to-date on your DTAP vaccination?").
      withOption("Yes").
      withOption("No").
      withOption("Don't Know", true).
      build();

Creating Link Fields

A builder supplied by a class called LinkField can be used to create a CEDAR link field.

Using this class, we can create a link field as follows:

    LinkField linkField = LinkField.builder().
      withName("Institution Home Page").
      withDescription("Please enter your institution's home page").
      withDefaultValue(URI.create("https://stanford.edu"), "Stanford")
      build();

A default value can be specified using the withDefaultValue builder method. This method must be supplied with the URI of the default value and a user-friendly label for it.

Creating Phone Number Fields

A builder supplied by a class called PhoneNumberField can be used to create a CEDAR phone number field.

Using this class, we can create a phone number field as follows:

    PhoneNumber phoneNumber = PhoneNumberField.builder().
      withName("Phone Number").
      withDescription("Please enter your phone number").
      build();

Creating Email Fields

A builder supplied by a class called EmailField can be used to create a CEDAR email field.

Using this class, we can create an email field as follows:

    EmailField emailField = EmailField.builder().
      withName("Email Address").
      withDescription("Please enter your email address").
      build();

Creating Text Area Fields

A builder supplied by a class called TextAreaField can be used to create a CEDAR text area fields.

For example, to create a text area field representing a study description with a minimum lengtth of 20 and a maximum length of 10000 we can do the following:

TextAreaField textAreaField = TextAreaField.builder().
      withName("Study Description").
      withDescription("Field representing the description of a study).
      withMinLength(20).
      withMaxLength(1000).
      build();

Creating Attribute-Value Fields

A builder supplied by a class called AttributeValueTextBuilder can be used to create a CEDAR attribute-value fields.

Using this class, we can create an atribute-value field as follows:

FieldSchemaArtifact fieldSchemaArtifact = FieldSchemaArtifact.attributeValueFieldBuilder().
      withName("Additional Patient Characteristics").
      build();

Creating Section Break Fields

A builder supplied by a class called SectionBreakField can be used to create a CEDAR section break fields.

Using this class, we can create a section break field as follows:

SectionBreakField sectionBreakField = SectionBreakField.builder().
      withName("Patient Details Section").
      withContent("This section of the form contains details about a patient").
      build();

Creating Image Fields

A builder supplied by a class called ImageField can be used to create a CEDAR image fields.

Using this class, we can create an image field as follows:

ImageField imageField = ImageField.builder().
      withName("Patient Picture").
      withContent("link to image").
      build();

Creating Image Fields

A builder supplied by a class called YouTubeField can be used to create a CEDAR YouTube fields.

Using this class, we can create a YouTube field as follows:

YouTubeField youTubeField = YouTubeField.builder().
      withName("Patient Video").
      withContent("link to video").
      build();

Creating Rich Text Fields

A builder supplied by a class called RichTextField can be used to create a CEDAR rich text fields.

Using this class, we can create a rich text field as follows:

RichTextField richTextField = RichTextField.builder().
      withName("Patient Video").
      withContent("<http> ....").
      build();

Generating Excel, TSV, and YAML Serializations of CEDAR Templates

To generate an Excel spreadsheet from a CEDAR template stored in a file:

    mvn exec:java@template2excel 
      -Dexec.args="-f <input_template_filename> 
                   -e <output_Excel_filename> 
                   -s https://terminology.metadatacenter.org/bioportal/integrated-search/ 
                   -k <CEDAR API key>"

To generate an Excel spreadsheet from a CEDAR template stored on the main CEDAR system:

    mvn exec:java@template2excel 
      -Dexec.args="-i <template_iri> 
                   -e <output_Excel_filename> 
                   -s https://terminology.metadatacenter.org/bioportal/integrated-search/ 
                   -r https://resource.metadatacenter.org/templates/ 
                   -k <CEDAR API key>"

e.g.,

    mvn exec:java@template2excel 
      -Dexec.args="-i https://repo.metadatacenter.org/templates/22bc762a-5020-419d-b170-24253ed9e8d9 
                   -e Sample.xlsx 
                   -s https://terminology.metadatacenter.org/bioportal/integrated-search/ 
                   -r https://resource.metadatacenter.org/templates/ 
                   -k <CEDAR API key>"

This will retrieve a JSON Schema-based template from CEDAR and convert it into an Excel file.

To generate a TSV file from a CEDAR template stored in a file:

mvn exec:java@template2tsv
  -Dexec.args="-f <input_template_filename> 
               -t <output_TSV_filename> 
               -s https://terminology.metadatacenter.org/bioportal/integrated-search/ 
               -k <CEDAR API key>"

To generate a TSV file from a CEDAR template stored on the main CEDAR system:

    mvn exec:java@template2tsv 
      -Dexec.args="-i <artifact_iri> 
                   -t <output_TSV_filename> 
                   -s https://terminology.metadatacenter.org/bioportal/integrated-search/ 
                   -r https://resource.metadatacenter.org/templates/ 
                   -k <CEDAR API key>"

To generate a YAML file from a CEDAR template stored in a file:

mvn exec:java@artifact-convertor 
  -Dexec.args="-tsf <input_artifact_filename> -yf -f <output_filename>"

This will read a JSON-Schema-based template and convert it into a YAML file. If the optional -cy argument is present then a compact YAML rendering of the artifact is generated; otherwise the full form is produced.

If the -f option is omitted the YAML is written to the console.

Other file-based options are -esf for element schema artifacts, -fsf for field schema artifacts, and -tif for template instance artifacts.

To generate a YAML file from a CEDAR template stored on the main CEDAR system:

    mvn exec:java@artifact-convertor 
      -Dexec.args="-tsi <artifact_iri> 
                   -yf
                   -f <output_YAML_filename> 
                   -r https://resource.metadatacenter.org
                   -k <CEDAR API key>"

Other IRI-based options are `-esi` for element schema artifacts, `-fsi` for field schema artifacts, and `-tii` for template instance artifacts.

If the `-y` option is omitted the output is written to the console.

To generate a JSON Schema file from a CEDAR template stored in a file:

    mvn exec:java@artifact-convertor 
      -Dexec.args="-tsf <input_artifact_filename> -jf -f <output_filename>"

This will read a JSON-Schema-based template,convert it to JSON Schema and write it into a file.

Building the Library

To build the code in this repository you must have the following items installed:

Java 17
A tool for checking out a Git repository.
Apache's Maven.

First build the CEDAR parent project and the CEDAR Model Library.

Get a copy of the latest code:

git clone https://github.com/metadatacenter/cedar-artifact-library.git

Change into the cedar-artifact-library directory:

cd cedar-artifact-library

Then build it with Maven:

mvn clean install

Name		Name	Last commit message	Last commit date
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.run		.run
src		src
.gitignore		.gitignore
README.md		README.md
license.txt		license.txt
pom.xml		pom.xml

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Repository files navigation

CEDAR Artifact Library

Reading Schema Artifacts

Serializing Schema Artifacts

Serializing to JSON Schema

Serializing to YAML

Serializing Templates to Excel

Serializing Templates to TSV

Serializing Templates to CSV

Creating Templates

Creating Elements

Creating Fields

Creating Text Fields

Creating Numeric Fields

Creating Temporal Fields

Creating Controlled Term Fields

Creating Radio Fields

Creating List Fields

Creating Checkbox Fields

Creating Link Fields

Creating Phone Number Fields

Creating Email Fields

Creating Text Area Fields

Creating Attribute-Value Fields

Creating Section Break Fields

Creating Image Fields

Creating Image Fields

Creating Rich Text Fields

Generating Excel, TSV, and YAML Serializations of CEDAR Templates

Building the Library

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CEDAR Artifact Library

Reading Schema Artifacts

Serializing Schema Artifacts

Serializing to JSON Schema

Serializing to YAML

Serializing Templates to Excel

Serializing Templates to TSV

Serializing Templates to CSV

Creating Templates

Creating Elements

Creating Fields

Creating Text Fields

Creating Numeric Fields

Creating Temporal Fields

Creating Controlled Term Fields

Creating Radio Fields

Creating List Fields

Creating Checkbox Fields

Creating Link Fields

Creating Phone Number Fields

Creating Email Fields

Creating Text Area Fields

Creating Attribute-Value Fields

Creating Section Break Fields

Creating Image Fields

Creating Image Fields

Creating Rich Text Fields

Generating Excel, TSV, and YAML Serializations of CEDAR Templates

Building the Library

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