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This package includes java objects for all items in the Physical Information File (PIF),
http://www.citrine.io/pif. Files formatted in the PIF schema can be serialized and deserialized using
included methods.
package io.citrine.jpif.obj.system;
import com.fasterxml.jackson.annotation.JsonAnySetter;
import com.fasterxml.jackson.annotation.JsonGetter;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonSetter;
import com.fasterxml.jackson.annotation.JsonSubTypes;
import com.fasterxml.jackson.annotation.JsonTypeInfo;
import com.fasterxml.jackson.annotation.JsonTypeName;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import io.citrine.jpif.obj.common.Classification;
import io.citrine.jpif.obj.common.Id;
import io.citrine.jpif.obj.common.License;
import io.citrine.jpif.obj.common.Person;
import io.citrine.jpif.obj.common.Pio;
import io.citrine.jpif.obj.common.ProcessStep;
import io.citrine.jpif.obj.common.Property;
import io.citrine.jpif.obj.common.Quantity;
import io.citrine.jpif.obj.common.Rcl;
import io.citrine.jpif.obj.common.Reference;
import io.citrine.jpif.obj.common.Source;
import io.citrine.jpif.obj.merge.MergeStrategy;
import io.citrine.jpif.obj.merge.PioReflection;
import io.citrine.jpif.obj.system.chemical.ChemicalSystem;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* Base representation for all systems.
*
* Supported fields:
*
* - uid - Permanent ID associated with this record.
*
- names - Names of the system.
*
- ids - List of {@link Id}s of the system.
*
- classifications - List of {@link Classification}s of the system.
*
- source - {@link Source} of the system.
*
- quantity - {@link Quantity} of the system.
*
- properties - List of measured or calculated properties ({@link Property}) of the system.
*
- preparation - List of preparation steps ({@link ProcessStep}) describing the making of the system.
*
- subSystems - List of sub-systems ({@link System}) of the system.
*
- references - List of {@link Reference}s with information about the system.
*
- contacts - List of contacts ({@link Person}) for information about the system.
*
- licenses - List of {@link License}s that apply to the system.
*
- tags - List of strings with tags that apply to the system.
*
*
* @author Kyle Michel
*/
@JsonTypeName("system")
@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "category")
@JsonSubTypes( {
@JsonSubTypes.Type(value = System.class),
@JsonSubTypes.Type(value = ChemicalSystem.class),
@JsonSubTypes.Type(name = "system.chemical.alloy", value = ChemicalSystem.class), // Legacy support
@JsonSubTypes.Type(name = "system.chemical.alloy.phase", value = ChemicalSystem.class)}) // Legacy support
public class System extends Rcl {
/**
* Set the unique ID for this system.
*
* @param uid String with the unique id.
* @return This object.
*/
@JsonSetter(value = "uid")
public System setUid(final String uid) {
this.uid = uid;
return this;
}
/**
* Get the PIF ID for this system.
*
* @return String with the PIF ID for this system.
*/
@JsonGetter(value = "uid")
public String getUid() {
return this.uid;
}
/**
* Set the list of names of this system.
*
* @param names List of strings with the names of this system.
*/
@JsonSetter(value = "names")
protected void setNames(final List names) { // Private since only Jackson should use it
this.names = names;
}
/**
* Set the list of names of this system.
*
* @param name List of strings with the names of this system.
*/
@JsonSetter(value = "name")
protected void setName(final List name) { // Private since only Jackson should use it
setNames(name);
}
/**
* Add a name for this system.
*
* @param name String with the name to add.
* @return This object.
*/
public System addName(final String name) {
if (this.names == null) {
this.names = new ArrayList<>();
}
this.names.add(name);
return this;
}
/**
* Insert a single name for this value.
*
* @param index Index at which to insert the input name.
* @param name String with the name to add.
* @return This object.
*/
public System addName(final int index, final String name) {
if (this.names == null) {
this.names = new ArrayList<>();
}
this.names.add(index, name);
return this;
}
/**
* Remove a name from the system.
*
* @param name String with the name to remove.
* @return True if the name was removed.
*/
public boolean removeName(final String name) {
return (this.names != null) && this.names.remove(name);
}
/**
* Get the number of names for this system.
*
* @return Number of names for this system.
*/
public int numNames() {
return (this.names == null) ? 0 : this.names.size();
}
/**
* Get a name for this system at a set index.
*
* @param index Index of the name to get.
* @return String with the name at the input index.
* @throws IndexOutOfBoundsException if the index is out of range of the names list.
*/
@JsonIgnore
public String getName(final int index) {
if (this.names == null) {
throw new IndexOutOfBoundsException("Attempting to access name " + index + " of " + this.numNames());
}
return this.names.get(index);
}
/**
* Get an {@link Iterable} object to iterate over names of this system.
*
* @return {@link Iterable} object for iterating over names of this system.
*/
public Iterable names() {
return (this.names == null) ? Collections.emptyList() : this.names;
}
/**
* Get the list of names for this system.
*
* @return List of strings with names for this system.
*/
@JsonGetter(value = "names")
protected List getNames() { // Private since only Jackson should use it
return this.names;
}
/**
* Set the list of IDs of this system.
*
* @param ids List of {@link Id} objects with the IDs of this system.
*/
@JsonSetter(value = "ids")
@JsonDeserialize(contentUsing = Id.Deserializer.class)
protected void setIds(final List ids) { // Private since only Jackson should use it
this.ids = ids;
}
/**
* Set the list of IDs of this system.
*
* @param id List of {@link Id} objects with the IDs of this system.
*/
@JsonSetter(value = "id")
@JsonDeserialize(contentUsing = Id.Deserializer.class)
protected void setId(final List id) { // Private since only Jackson should use it
setIds(id);
}
/**
* Add an ID for this system.
*
* @param id {@link Id} object with the ID to add.
* @return This object.
*/
public System addId(final Id id) {
if (this.ids == null) {
this.ids = new ArrayList<>();
}
this.ids.add(id);
return this;
}
/**
* Insert a single ID for this system.
*
* @param index Index at which to insert the input ID.
* @param id {@link Id} object to add to this system.
* @return This object.
*/
public System addId(final int index, final Id id) {
if (this.ids == null) {
this.ids = new ArrayList<>();
}
this.ids.add(index, id);
return this;
}
/**
* Remove an ID from the system.
*
* @param id {@link Id} object to delete.
* @return True if the object was removed.
*/
public boolean removeId(final Id id) {
return (this.ids != null) && this.ids.remove(id);
}
/**
* Get the number of IDs for this system.
*
* @return Number of IDs for this system.
*/
public int numIds() {
return (this.ids == null) ? 0 : this.ids.size();
}
/**
* Get an ID for this system at a set index.
*
* @param index Index of the ID to get.
* @return {@link Id} object with the ID at the input index.
* @throws IndexOutOfBoundsException if the index is out of range of the IDs list.
*/
@JsonIgnore
public Id getId(final int index) {
if (this.ids == null) {
throw new IndexOutOfBoundsException("Attempting to access ID " + index + " of " + this.numIds());
}
return this.ids.get(index);
}
/**
* Get an {@link Iterable} object to iterate over IDs of this system.
*
* @return {@link Iterable} object for iterating over IDs of this system.
*/
public Iterable ids() {
return (this.ids == null) ? Collections.emptyList() : this.ids;
}
/**
* Get the list of IDs for this system.
*
* @return List of {@link Id} objects with IDs for this system.
*/
@JsonGetter(value = "ids")
protected List getIds() { // Private since only Jackson should use it
return this.ids;
}
/**
* Set the list of classifications of this system.
*
* @param classifications List of {@link Classification} objects with the classifications of this system.
*/
@JsonSetter(value = "classifications")
@JsonDeserialize(contentUsing = Classification.Deserializer.class)
protected void setClassifications(final List classifications) { // Private since only Jackson should
// use it
this.classifications = classifications;
}
/**
* Set the list of classifications of this system.
*
* @param classification List of {@link Classification} objects with the classifications of this system.
*/
@JsonSetter(value = "classification")
@JsonDeserialize(contentUsing = Classification.Deserializer.class)
protected void setClassification(final List classification) { // Private since only Jackson should
// use it
setClassifications(classification);
}
/**
* Add an classification for this system.
*
* @param classification {@link Classification} object with the classification to add.
* @return This object.
*/
public System addClassification(final Classification classification) {
if (this.classifications == null) {
this.classifications = new ArrayList<>();
}
this.classifications.add(classification);
return this;
}
/**
* Insert a single classification for this system.
*
* @param index Index at which to insert the input classification.
* @param classification {@link Classification} object to add to this system.
* @return This object.
*/
public System addClassification(final int index, final Classification classification) {
if (this.classifications == null) {
this.classifications = new ArrayList<>();
}
this.classifications.add(index, classification);
return this;
}
/**
* Remove an classification from the system.
*
* @param classification {@link Classification} object to delete.
* @return True if the object was removed.
*/
public boolean removeClassification(final Classification classification) {
return (this.classifications != null) && this.classifications.remove(classification);
}
/**
* Get the number of classifications for this system.
*
* @return Number of classifications for this system.
*/
public int numClassifications() {
return (this.classifications == null) ? 0 : this.classifications.size();
}
/**
* Get an classification for this system at a set index.
*
* @param index Index of the classification to get.
* @return {@link Classification} object with the classification at the input index.
* @throws IndexOutOfBoundsException if the index is out of range of the classifications list.
*/
@JsonIgnore
public Classification getClassification(final int index) {
if (this.classifications == null) {
throw new IndexOutOfBoundsException("Attempting to access classification " + index
+ " of " + this.numClassifications());
}
return this.classifications.get(index);
}
/**
* Get an {@link Iterable} object to iterate over classifications of this system.
*
* @return {@link Iterable} object for iterating over classifications of this system.
*/
public Iterable classifications() {
return (this.classifications == null) ? Collections.emptyList() : this.classifications;
}
/**
* Get the list of classifications for this system.
*
* @return List of {@link Classification} objects with classifications for this system.
*/
@JsonGetter(value = "classifications")
protected List getClassifications() { // Private since only Jackson should use it
return this.classifications;
}
/**
* Set the source for this system.
*
* @param source {@link Source} for this system.
* @return This object.
*/
@JsonSetter(value = "source")
@JsonDeserialize(using = Source.Deserializer.class)
public System setSource(final Source source) {
this.source = source;
return this;
}
/**
* Get the source for this system.
*
* @return {@link Source} for this system.
*/
@JsonGetter(value = "source")
public Source getSource() {
return this.source;
}
/**
* Set the quantity of this system.
*
* @param quantity {@link Quantity} of this system.
* @return This object.
*/
@JsonSetter(value = "quantity")
public System setQuantity(final Quantity quantity) {
this.quantity = quantity;
return this;
}
/**
* Get the quantity of this system.
*
* @return {@link Quantity} of this system.
*/
@JsonGetter(value = "quantity")
public Quantity getQuantity() {
return this.quantity;
}
/**
* Set the list of properties of this system.
*
* @param properties List of {@link Property} objects with the properties of this system.
*/
@JsonSetter(value = "properties")
protected void setProperties(final List properties) { // Private since only Jackson should use it
this.properties = properties;
}
/**
* Set the list of properties of this system.
*
* @param property List of {@link Property} objects with the properties of this system.
*/
@JsonSetter(value = "property")
protected void setProperty(final List property) { // Private since only Jackson should use it
setProperties(property);
}
/**
* Add a property for this system.
*
* @param property {@link Property} object with the property to add.
* @return This object.
*/
public System addProperty(final Property property) {
if (this.properties == null) {
this.properties = new ArrayList<>();
}
this.properties.add(property);
return this;
}
/**
* Insert a single property for this system.
*
* @param index Index at which to insert the input property.
* @param property {@link Property} object to add to this system.
* @return This object.
*/
public System addProperty(final int index, final Property property) {
if (this.properties == null) {
this.properties = new ArrayList<>();
}
this.properties.add(index, property);
return this;
}
/**
* Remove a property from the system.
*
* @param property {@link Property} object to delete.
* @return True if the object was removed.
*/
public boolean removeProperty(final Property property) {
return (this.properties != null) && this.properties.remove(property);
}
/**
* Get the number of properties for this system.
*
* @return Number of properties for this system.
*/
public int numProperties() {
return (this.properties == null) ? 0 : this.properties.size();
}
/**
* Get a property for this system at a set index.
*
* @param index Index of the property to get.
* @return {@link Property} object with the property at the input index.
* @throws IndexOutOfBoundsException if the index is out of range of the properties list.
*/
@JsonIgnore
public Property getProperty(final int index) {
if (this.properties == null) {
throw new IndexOutOfBoundsException("Attempting to access property " + index
+ " of " + this.numProperties());
}
return this.properties.get(index);
}
/**
* Get an {@link Iterable} object to iterate over properties of this system.
*
* @return {@link Iterable} object for iterating over properties of this system.
*/
public Iterable properties() {
return (this.properties == null) ? Collections.emptyList() : this.properties;
}
/**
* Get the list of properties for this system.
*
* @return List of {@link Property} objects with properties for this system.
*/
@JsonGetter(value = "properties")
protected List getProperties() { // Private since only Jackson should use it
return this.properties;
}
/**
* Set the list of preparation steps of this system.
*
* @param preparation List of {@link ProcessStep} objects with the processing steps of this system.
*/
@JsonSetter(value = "preparation")
protected void setPreparation(final List preparation) { // Private since only Jackson should use it
this.preparation = preparation;
}
/**
* Set the list of preparation steps of this system.
*
* @param preparations List of {@link ProcessStep} objects with the processing steps of this system.
*/
@JsonSetter(value = "preparations")
protected void setPreparations(final List preparations) { // Private since only Jackson should use it
setPreparation(preparations);
}
/**
* Add a preparation step for this system.
*
* @param preparation {@link ProcessStep} object with the preparation step to add.
* @return This object.
*/
public System addPreparation(final ProcessStep preparation) {
if (this.preparation == null) {
this.preparation = new ArrayList<>();
}
this.preparation.add(preparation);
return this;
}
/**
* Insert a single preparation step for this system.
*
* @param index Index at which to insert the input preparation step.
* @param preparation {@link ProcessStep} object to add to this system.
* @return This object.
*/
public System addPreparation(final int index, final ProcessStep preparation) {
if (this.preparation == null) {
this.preparation = new ArrayList<>();
}
this.preparation.add(index, preparation);
return this;
}
/**
* Remove a preparation step from the system.
*
* @param preparation {@link ProcessStep} object to delete.
* @return True if the object was removed.
*/
public boolean removePreparation(final ProcessStep preparation) {
return (this.preparation != null) && this.preparation.remove(preparation);
}
/**
* Get the number of preparation steps for this system.
*
* @return Number of preparation steps for this system.
*/
public int numPreparation() {
return (this.preparation == null) ? 0 : this.preparation.size();
}
/**
* Get a preparation step for this system at a set index.
*
* @param index Index of the preparation step to get.
* @return {@link ProcessStep} object with the preparation step at the input index.
* @throws IndexOutOfBoundsException if the index is out of range of the preparation list.
*/
@JsonIgnore
public ProcessStep getPreparation(final int index) {
if (this.preparation == null) {
throw new IndexOutOfBoundsException("Attempting to access preparation " + index + " of "
+ this.numPreparation());
}
return this.preparation.get(index);
}
/**
* Get the list of preparation steps for this system.
*
* @return List of {@link ProcessStep} objects with preparation steps for this system.
*/
@JsonGetter(value = "preparation")
protected List getPreparation() { // Private since only Jackson should use it
return this.preparation;
}
/**
* Get an {@link Iterable} object to iterate over preparation steps of this system.
*
* @return {@link Iterable} object for iterating over preparation steps of this system.
*/
public Iterable preparation() {
return (this.preparation == null) ? Collections.emptyList() : this.preparation;
}
/**
* Set the list of subsystems of this system.
*
* @param subSystems List of {@link System} objects with the subsystems of this system.
*/
@JsonSetter(value = "subSystems")
protected void setSubSystems(final List subSystems) { // Private since only Jackson should use it
this.subSystems = subSystems;
}
/**
* Set the list of subsystems of this system.
*
* @param subSystem List of {@link System} objects with the subsystems of this system.
*/
@JsonSetter(value = "subSystem")
protected void setSubSystem(final List subSystem) { // Private since only Jackson should use it
setSubSystems(subSystem);
}
/**
* Add a subsystem for this system.
*
* @param subSystem {@link System} object with the subsystem to add.
* @return This object.
*/
public System addSubSystem(final System subSystem) {
if (this.subSystems == null) {
this.subSystems = new ArrayList<>();
}
this.subSystems.add(subSystem);
return this;
}
/**
* Insert a single subsystem for this system.
*
* @param index Index at which to insert the input subsystem.
* @param subSystem {@link System} object to add to this value.
* @return This object.
*/
public System addSubSystem(final int index, final System subSystem) {
if (this.subSystems == null) {
this.subSystems = new ArrayList<>();
}
this.subSystems.add(index, subSystem);
return this;
}
/**
* Remove a subsystem from the system.
*
* @param subsystem {@link System} object to delete.
* @return True if the object was removed.
*/
public boolean removeSubsystem(final System subsystem) {
return (this.subSystems != null) && this.subSystems.remove(subsystem);
}
/**
* Get the number of subsystems for this system.
*
* @return Number of subsystems for this system.
*/
public int numSubSystems() {
return (this.subSystems == null) ? 0 : this.subSystems.size();
}
/**
* Get a subsystem for this system at a set index.
*
* @param index Index of the subsystem to get.
* @return {@link System} object with the subsystem at the input index.
* @throws IndexOutOfBoundsException if the index is out of range of the subsystem list.
*/
@JsonIgnore
public System getSubSystem(final int index) {
if (this.subSystems == null) {
throw new IndexOutOfBoundsException("Attempting to access subsystem " + index
+ " of " + this.numSubSystems());
}
return this.subSystems.get(index);
}
/**
* Get an {@link Iterable} object to iterate over subsystems of this system.
*
* @return {@link Iterable} object for iterating over subsystems of this system.
*/
public Iterable subSystems() {
return (this.subSystems == null) ? Collections.emptyList() : this.subSystems;
}
/**
* Get the list of subsystems for this system.
*
* @return List of {@link System} objects with subsystems for this system.
*/
@JsonGetter(value = "subSystems")
protected List getSubSystems() { // Private since only Jackson should use it
return this.subSystems;
}
@Override
public System addReference(final Reference reference) {
super.addReference(reference);
return this;
}
@Override
public System addReference(final int index, final Reference reference) {
super.addReference(index, reference);
return this;
}
@Override
public System addContact(final Person contact) {
super.addContact(contact);
return this;
}
@Override
public System addContact(final int index, final Person contact) {
super.addContact(index, contact);
return this;
}
@Override
public System addLicense(final License license) {
super.addLicense(license);
return this;
}
@Override
public System addLicense(final int index, final License license) {
super.addLicense(index, license);
return this;
}
@Override
public System addTag(final String tag) {
super.addTag(tag);
return this;
}
@Override
public System addTag(final int index, final String tag) {
super.addTag(index, tag);
return this;
}
@Override
@JsonAnySetter
public System addUnsupportedField(final String key, final Object value) {
super.addUnsupportedField(key, value);
return this;
}
@Override
public System merge(Pio mergeFrom, MergeStrategy strategy) throws Exception {
return (System) super.merge(mergeFrom, strategy);
}
@Override
public System merge(Pio mergeFrom, MergeStrategy strategy, List ignoredFields) throws Exception {
System mergeResult = (System) super.merge(mergeFrom, strategy, ignoredFields);
// Add all fields that don't exist in `this` as unsupported fields
PioReflection fromReflection = new PioReflection(mergeFrom);
PioReflection thisReflection = new PioReflection(this);
fromReflection.getGetters().keySet().stream()
// Filter for only fields that exist in `mergeFrom` and _not_ in `this`
.filter(methodName -> !thisReflection.getGetters().keySet().contains(methodName))
.forEach(methodName -> {
String fieldName = methodName.replace("get", "");
String fixedFieldName = fieldName.substring(0, 1).toLowerCase() + fieldName.substring(1);
try {
mergeResult.addUnsupportedField(
fixedFieldName,
fromReflection.getMethod("get" + fieldName).invoke(mergeFrom)
);
} catch (IllegalAccessException e) {
e.printStackTrace();
} catch (InvocationTargetException e) {
e.printStackTrace();
}
});
return mergeResult;
}
/** Permanent ID for this system. */
private String uid;
/** List of names for this system. */
private List names;
/** List of IDs for this system. */
private List ids;
/** List of classifications for this system. */
private List classifications;
/** Source of this system. */
private Source source;
/** Quantity of this system. */
private Quantity quantity;
/** List of properties of this system. */
private List properties;
/** List of processing steps in the preparation of this system. */
private List preparation;
/** List of subsystems of this system. */
private List subSystems;
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