Pre-cleanup commit of Sample and SampleDataSource
-- SampleDataSource has all reader functionality disabled
This commit is contained in:
Mark DePristo
parent
4d31673cc5
commit
e197dcd1f3
|
|
@ -14,6 +14,13 @@ import java.util.Map;
|
|||
* Time: 3:31:38 PM
|
||||
*/
|
||||
public class Sample implements java.io.Serializable {
|
||||
private final static String MOTHER = "mother";
|
||||
private final static String FATHER = "father";
|
||||
private final static String GENDER = "gender";
|
||||
private final static String POPULATION = "population";
|
||||
private final static String FAMILY = "familyId";
|
||||
private final static String AFFECTION = "affection";
|
||||
private final static String QUANT_TRAIT = "quantTrait";
|
||||
|
||||
private final String id;
|
||||
|
||||
|
|
@ -31,6 +38,18 @@ public class Sample implements java.io.Serializable {
|
|||
UNKNOWN
|
||||
}
|
||||
|
||||
public enum Affection {
|
||||
/** Status is unknown */
|
||||
UNKNOWN,
|
||||
/** Suffers from the disease */
|
||||
AFFECTED,
|
||||
/** Unaffected by the disease */
|
||||
UNAFFECTED,
|
||||
/** A quantitative trait: value of the trait is stored elsewhere */
|
||||
QUANTITATIVE
|
||||
}
|
||||
public final static double UNSET_QUANTITIATIVE_TRAIT_VALUE = Double.NaN;
|
||||
|
||||
public Sample(String id) {
|
||||
/* if (id == null) {
|
||||
throw new StingException("Error creating sample: sample ID cannot be null");
|
||||
|
|
@ -46,30 +65,21 @@ public class Sample implements java.io.Serializable {
|
|||
return properties;
|
||||
}
|
||||
|
||||
public void setProperties(Map<String, Object> properties) {
|
||||
this.properties = (HashMap) properties;
|
||||
}
|
||||
|
||||
public Map<String,Sample> getRelationships() {
|
||||
return Collections.unmodifiableMap(this.relationships);
|
||||
}
|
||||
|
||||
@Deprecated
|
||||
public void setSampleFileEntry(boolean value) {
|
||||
this.hasSampleFileEntry = value;
|
||||
}
|
||||
|
||||
@Deprecated
|
||||
public boolean hasSAMFileEntry() {
|
||||
return this.hasSAMFileEntry;
|
||||
}
|
||||
|
||||
@Deprecated
|
||||
public void setSAMFileEntry(boolean value) {
|
||||
this.hasSAMFileEntry = value;
|
||||
}
|
||||
|
||||
public boolean hasSampleFileEntry() {
|
||||
return this.hasSampleFileEntry;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get one property
|
||||
* @param key key of property
|
||||
|
|
@ -91,11 +101,11 @@ public class Sample implements java.io.Serializable {
|
|||
throw new StingException("The same key cannot exist as a property and a relationship");
|
||||
}
|
||||
|
||||
if (key.equals("gender") && value.getClass() != Gender.class) {
|
||||
if (key.equals(GENDER) && value.getClass() != Gender.class) {
|
||||
throw new StingException("'gender' property must be of type Sample.Gender");
|
||||
}
|
||||
|
||||
if (key.equals("population") && value.getClass() != String.class) {
|
||||
if (key.equals(POPULATION) && value.getClass() != String.class) {
|
||||
throw new StingException("'population' property must be of type String");
|
||||
}
|
||||
|
||||
|
|
@ -129,7 +139,7 @@ public class Sample implements java.io.Serializable {
|
|||
* @return sample object with relationship mother, if exists, or null
|
||||
*/
|
||||
public Sample getMother() {
|
||||
return getRelationship("mother");
|
||||
return getRelationship(MOTHER);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -137,7 +147,7 @@ public class Sample implements java.io.Serializable {
|
|||
* @return sample object with relationship father, if exists, or null
|
||||
*/
|
||||
public Sample getFather() {
|
||||
return getRelationship("father");
|
||||
return getRelationship(FATHER);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -145,29 +155,29 @@ public class Sample implements java.io.Serializable {
|
|||
* @return property of key "gender" - must be of type Gender
|
||||
*/
|
||||
public Gender getGender() {
|
||||
return (Gender) properties.get("gender");
|
||||
return (Gender) properties.get(GENDER);
|
||||
}
|
||||
|
||||
public String getPopulation() {
|
||||
return (String) properties.get("population");
|
||||
return (String) properties.get(POPULATION);
|
||||
}
|
||||
|
||||
public String getFamilyId() {
|
||||
return (String) properties.get("familyId");
|
||||
return (String) properties.get(FAMILY);
|
||||
}
|
||||
|
||||
/**
|
||||
* @return True if sample is male, false if female, unknown, or null
|
||||
*/
|
||||
public boolean isMale() {
|
||||
return properties.get("gender") == Gender.MALE;
|
||||
return properties.get(GENDER) == Gender.MALE;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return True if sample is female, false if male, unknown or null
|
||||
*/
|
||||
public boolean isFemale() {
|
||||
return properties.get("gender") == Gender.MALE;
|
||||
return properties.get(GENDER) == Gender.MALE;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -104,266 +104,265 @@ public class SampleDataSource {
|
|||
* Parse one sample file and integrate it with samples that are already there
|
||||
* Fail quickly if we find any errors in the file
|
||||
*/
|
||||
public void addFile(File sampleFile) {
|
||||
|
||||
BufferedReader reader;
|
||||
try {
|
||||
reader = new BufferedReader(new FileReader(sampleFile));
|
||||
}
|
||||
catch (IOException e) {
|
||||
throw new StingException("Could not open sample file " + sampleFile.getAbsolutePath(), e);
|
||||
}
|
||||
|
||||
// set up YAML reader - a "Constructor" creates java object from YAML and "Loader" loads the file
|
||||
Constructor con = new Constructor(SampleFileParser.class);
|
||||
TypeDescription desc = new TypeDescription(SampleFileParser.class);
|
||||
desc.putListPropertyType("propertyDefinitions", PropertyDefinition.class);
|
||||
desc.putListPropertyType("sampleAliases", SampleAlias.class);
|
||||
con.addTypeDescription(desc);
|
||||
Yaml yaml = new Yaml(con);
|
||||
|
||||
// SampleFileParser stores an object representation of a sample file - this is what we'll parse
|
||||
SampleFileParser parser;
|
||||
try {
|
||||
parser = (SampleFileParser) yaml.load(reader);
|
||||
}
|
||||
catch (Exception e) {
|
||||
throw new StingException("There was a syntactic error with the YAML in sample file " + sampleFile.getAbsolutePath(), e);
|
||||
}
|
||||
|
||||
// check to see which validation options were built into the file
|
||||
boolean restrictProperties = parser.getAllowedProperties() != null;
|
||||
boolean restrictRelationships = parser.getAllowedRelationships() != null;
|
||||
boolean restrictPropertyValues = parser.getPropertyDefinitions() != null;
|
||||
|
||||
// propertyValues stores the values that are allowed for a given property
|
||||
HashMap<String, HashSet> propertyValues = null;
|
||||
if (restrictPropertyValues) {
|
||||
propertyValues = new HashMap<String, HashSet>();
|
||||
for (PropertyDefinition def : parser.getPropertyDefinitions()) {
|
||||
HashSet<String> set = new HashSet<String>();
|
||||
for (String value : def.getValues()) {
|
||||
set.add(value);
|
||||
}
|
||||
propertyValues.put(def.getProperty(), set);
|
||||
}
|
||||
}
|
||||
|
||||
// make sure the aliases are valid
|
||||
validateAliases(parser);
|
||||
|
||||
// loop through each sample in the file - a SampleParser stores an object that will become a Sample
|
||||
for (SampleParser sampleParser : parser.getSamples()) {
|
||||
|
||||
try {
|
||||
// step 1: add the sample if it doesn't already exist
|
||||
Sample sample = getSampleById(sampleParser.getId());
|
||||
if (sample == null) {
|
||||
sample = new Sample(sampleParser.getId());
|
||||
}
|
||||
addSample(sample);
|
||||
sample.setSampleFileEntry(true);
|
||||
|
||||
// step 2: add the properties
|
||||
if (sampleParser.getProperties() != null) {
|
||||
for (String property : sampleParser.getProperties().keySet()) {
|
||||
|
||||
// check that property is allowed
|
||||
if (restrictProperties) {
|
||||
if (!isPropertyValid(property, parser.getAllowedProperties())) {
|
||||
throw new StingException(property + " is an invalid property. It is not included in the list " +
|
||||
"of allowed properties.");
|
||||
}
|
||||
}
|
||||
|
||||
// next check that the value is allowed
|
||||
if (restrictPropertyValues) {
|
||||
if (!isValueAllowed(property, sampleParser.getProperties().get(property), propertyValues)) {
|
||||
throw new StingException("The value of property '" + property + "' is invalid. " +
|
||||
"It is not included in the list of allowed values for this property.");
|
||||
}
|
||||
}
|
||||
|
||||
// next check that there isn't already a conflicting property there
|
||||
if (sample.getProperty(property) != null &&
|
||||
sample.getProperty(property) != sampleParser.getProperties().get(property))
|
||||
{
|
||||
throw new StingException(property + " is a conflicting property!");
|
||||
}
|
||||
|
||||
// checks are passed - now add the property!
|
||||
saveProperty(sample, property, sampleParser.getProperties().get(property));
|
||||
}
|
||||
}
|
||||
|
||||
// step 3: add the relationships
|
||||
if (sampleParser.getRelationships() != null) {
|
||||
for (String relationship : sampleParser.getRelationships().keySet()) {
|
||||
String relativeId = sampleParser.getRelationships().get(relationship);
|
||||
if (relativeId == null) {
|
||||
throw new StingException("The relationship cannot be null");
|
||||
}
|
||||
|
||||
// first check that it's not invalid
|
||||
if (restrictRelationships) {
|
||||
if (!isRelationshipValid(relationship, parser.getAllowedRelationships())) {
|
||||
throw new StingException(relationship + " is an invalid relationship");
|
||||
}
|
||||
}
|
||||
|
||||
// next check that there isn't already a conflicting property there
|
||||
if (sample.getRelationship(relationship) != null) {
|
||||
if (sample.getRelationship(relationship).getId() != sampleParser.getProperties().get(relationship)) {
|
||||
throw new StingException(relationship + " is a conflicting relationship!");
|
||||
}
|
||||
// if the relationship is already set - and consistent with what we're reading now - no need to continue
|
||||
else {
|
||||
continue;
|
||||
}
|
||||
}
|
||||
|
||||
// checks are passed - now save the relationship
|
||||
saveRelationship(sample, relationship, relativeId);
|
||||
}
|
||||
}
|
||||
} catch (Exception e) {
|
||||
throw new StingException("An error occurred while loading this sample from the sample file: " +
|
||||
sampleParser.getId(), e);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private boolean isValueAllowed(String key, Object value, HashMap<String, HashSet> valuesList) {
|
||||
|
||||
// if the property values weren't specified for this property, then any value is okay
|
||||
if (!valuesList.containsKey(key)) {
|
||||
return true;
|
||||
}
|
||||
|
||||
// if this property has enumerated values, it must be a string
|
||||
else if (value.getClass() != String.class)
|
||||
return false;
|
||||
|
||||
// is the value specified or not?
|
||||
else if (!valuesList.get(key).contains(value))
|
||||
return false;
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Makes sure that the aliases are valid
|
||||
* Checks that 1) no string is used as both a main ID and an alias;
|
||||
* 2) no alias is used more than once
|
||||
* @param parser
|
||||
*/
|
||||
private void validateAliases(SampleFileParser parser) {
|
||||
|
||||
// no aliases sure validate
|
||||
if (parser.getSampleAliases() == null)
|
||||
return;
|
||||
|
||||
HashSet<String> mainIds = new HashSet<String>();
|
||||
HashSet<String> otherIds = new HashSet<String>();
|
||||
|
||||
for (SampleAlias sampleAlias : parser.getSampleAliases()) {
|
||||
mainIds.add(sampleAlias.getMainId());
|
||||
for (String otherId : sampleAlias.getOtherIds()) {
|
||||
if (mainIds.contains(otherId))
|
||||
throw new StingException(String.format("The aliases in your sample file are invalid - the alias %s cannot " +
|
||||
"be both a main ID and an other ID", otherId));
|
||||
|
||||
if (!otherIds.add(otherId))
|
||||
throw new StingException(String.format("The aliases in your sample file are invalid - %s is listed as an " +
|
||||
"alias more than once.", otherId));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private boolean isPropertyValid(String property, String[] allowedProperties) {
|
||||
|
||||
// is it a special property that is always allowed?
|
||||
for (String allowedProperty : specialProperties) {
|
||||
if (property.equals(allowedProperty))
|
||||
return true;
|
||||
}
|
||||
|
||||
// is it in the allowed properties list?
|
||||
for (String allowedProperty : allowedProperties) {
|
||||
if (property.equals(allowedProperty))
|
||||
return true;
|
||||
}
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
private boolean isRelationshipValid(String relationship, String[] allowedRelationships) {
|
||||
|
||||
// is it a special relationship that is always allowed?
|
||||
for (String allowedRelationship : specialRelationships) {
|
||||
if (relationship.equals(allowedRelationship))
|
||||
return true;
|
||||
}
|
||||
|
||||
// is it in the allowed properties list?
|
||||
for (String allowedRelationship : allowedRelationships) {
|
||||
if (relationship.equals(allowedRelationship))
|
||||
return true;
|
||||
}
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
/**
|
||||
* Saves a property as the correct type
|
||||
* @param key property key
|
||||
* @param value property value, as read from YAML parser
|
||||
* @return property value to be stored
|
||||
*/
|
||||
private void saveProperty(Sample sample, String key, Object value) {
|
||||
|
||||
// convert gender to the right type, if it was stored as a String
|
||||
if (key.equals("gender")) {
|
||||
if (((String) value).toLowerCase().equals("male")) {
|
||||
value = Sample.Gender.MALE;
|
||||
}
|
||||
else if (((String) value).toLowerCase().equals("female")) {
|
||||
value = Sample.Gender.FEMALE;
|
||||
}
|
||||
else if (((String) value).toLowerCase().equals("unknown")) {
|
||||
value = Sample.Gender.UNKNOWN;
|
||||
}
|
||||
else if (value != null) {
|
||||
throw new StingException("'gender' property must be male, female, or unknown.");
|
||||
}
|
||||
}
|
||||
try {
|
||||
sample.setProperty(key, value);
|
||||
}
|
||||
catch (Exception e) {
|
||||
throw new StingException("Could not save property " + key, e);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Saves a relationship as the correct type
|
||||
* @param key relationship key
|
||||
* @param relativeId sample ID string of the relative
|
||||
* @return relationship value to be stored
|
||||
*/
|
||||
private void saveRelationship(Sample sample, String key, String relativeId) {
|
||||
|
||||
// get the reference that we'll store as the value
|
||||
Sample relative = getSampleById(relativeId);
|
||||
|
||||
// create sample object for the relative, if necessary
|
||||
if (relative == null) {
|
||||
relative = new Sample(relativeId);
|
||||
addSample(relative);
|
||||
}
|
||||
sample.setRelationship(key, relative);
|
||||
}
|
||||
public void addFile(File sampleFile) {}
|
||||
//
|
||||
// BufferedReader reader;
|
||||
// try {
|
||||
// reader = new BufferedReader(new FileReader(sampleFile));
|
||||
// }
|
||||
// catch (IOException e) {
|
||||
// throw new StingException("Could not open sample file " + sampleFile.getAbsolutePath(), e);
|
||||
// }
|
||||
//
|
||||
// // set up YAML reader - a "Constructor" creates java object from YAML and "Loader" loads the file
|
||||
// Constructor con = new Constructor(SampleFileParser.class);
|
||||
// TypeDescription desc = new TypeDescription(SampleFileParser.class);
|
||||
// desc.putListPropertyType("propertyDefinitions", PropertyDefinition.class);
|
||||
// desc.putListPropertyType("sampleAliases", SampleAlias.class);
|
||||
// con.addTypeDescription(desc);
|
||||
// Yaml yaml = new Yaml(con);
|
||||
//
|
||||
// // SampleFileParser stores an object representation of a sample file - this is what we'll parse
|
||||
// SampleFileParser parser;
|
||||
// try {
|
||||
// parser = (SampleFileParser) yaml.load(reader);
|
||||
// }
|
||||
// catch (Exception e) {
|
||||
// throw new StingException("There was a syntactic error with the YAML in sample file " + sampleFile.getAbsolutePath(), e);
|
||||
// }
|
||||
//
|
||||
// // check to see which validation options were built into the file
|
||||
// boolean restrictProperties = parser.getAllowedProperties() != null;
|
||||
// boolean restrictRelationships = parser.getAllowedRelationships() != null;
|
||||
// boolean restrictPropertyValues = parser.getPropertyDefinitions() != null;
|
||||
//
|
||||
// // propertyValues stores the values that are allowed for a given property
|
||||
// HashMap<String, HashSet> propertyValues = null;
|
||||
// if (restrictPropertyValues) {
|
||||
// propertyValues = new HashMap<String, HashSet>();
|
||||
// for (PropertyDefinition def : parser.getPropertyDefinitions()) {
|
||||
// HashSet<String> set = new HashSet<String>();
|
||||
// for (String value : def.getValues()) {
|
||||
// set.add(value);
|
||||
// }
|
||||
// propertyValues.put(def.getProperty(), set);
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// // make sure the aliases are valid
|
||||
// validateAliases(parser);
|
||||
//
|
||||
// // loop through each sample in the file - a SampleParser stores an object that will become a Sample
|
||||
// for (SampleParser sampleParser : parser.getSamples()) {
|
||||
//
|
||||
// try {
|
||||
// // step 1: add the sample if it doesn't already exist
|
||||
// Sample sample = getSampleById(sampleParser.getId());
|
||||
// if (sample == null) {
|
||||
// sample = new Sample(sampleParser.getId());
|
||||
// }
|
||||
// addSample(sample);
|
||||
// sample.setSampleFileEntry(true);
|
||||
//
|
||||
// // step 2: add the properties
|
||||
// if (sampleParser.getProperties() != null) {
|
||||
// for (String property : sampleParser.getProperties().keySet()) {
|
||||
//
|
||||
// // check that property is allowed
|
||||
// if (restrictProperties) {
|
||||
// if (!isPropertyValid(property, parser.getAllowedProperties())) {
|
||||
// throw new StingException(property + " is an invalid property. It is not included in the list " +
|
||||
// "of allowed properties.");
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// // next check that the value is allowed
|
||||
// if (restrictPropertyValues) {
|
||||
// if (!isValueAllowed(property, sampleParser.getProperties().get(property), propertyValues)) {
|
||||
// throw new StingException("The value of property '" + property + "' is invalid. " +
|
||||
// "It is not included in the list of allowed values for this property.");
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// // next check that there isn't already a conflicting property there
|
||||
// if (sample.getProperty(property) != null &&
|
||||
// sample.getProperty(property) != sampleParser.getProperties().get(property))
|
||||
// {
|
||||
// throw new StingException(property + " is a conflicting property!");
|
||||
// }
|
||||
//
|
||||
// // checks are passed - now add the property!
|
||||
// saveProperty(sample, property, sampleParser.getProperties().get(property));
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// // step 3: add the relationships
|
||||
// if (sampleParser.getRelationships() != null) {
|
||||
// for (String relationship : sampleParser.getRelationships().keySet()) {
|
||||
// String relativeId = sampleParser.getRelationships().get(relationship);
|
||||
// if (relativeId == null) {
|
||||
// throw new StingException("The relationship cannot be null");
|
||||
// }
|
||||
//
|
||||
// // first check that it's not invalid
|
||||
// if (restrictRelationships) {
|
||||
// if (!isRelationshipValid(relationship, parser.getAllowedRelationships())) {
|
||||
// throw new StingException(relationship + " is an invalid relationship");
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// // next check that there isn't already a conflicting property there
|
||||
// if (sample.getRelationship(relationship) != null) {
|
||||
// if (sample.getRelationship(relationship).getId() != sampleParser.getProperties().get(relationship)) {
|
||||
// throw new StingException(relationship + " is a conflicting relationship!");
|
||||
// }
|
||||
// // if the relationship is already set - and consistent with what we're reading now - no need to continue
|
||||
// else {
|
||||
// continue;
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// // checks are passed - now save the relationship
|
||||
// saveRelationship(sample, relationship, relativeId);
|
||||
// }
|
||||
// }
|
||||
// } catch (Exception e) {
|
||||
// throw new StingException("An error occurred while loading this sample from the sample file: " +
|
||||
// sampleParser.getId(), e);
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// private boolean isValueAllowed(String key, Object value, HashMap<String, HashSet> valuesList) {
|
||||
//
|
||||
// // if the property values weren't specified for this property, then any value is okay
|
||||
// if (!valuesList.containsKey(key)) {
|
||||
// return true;
|
||||
// }
|
||||
//
|
||||
// // if this property has enumerated values, it must be a string
|
||||
// else if (value.getClass() != String.class)
|
||||
// return false;
|
||||
//
|
||||
// // is the value specified or not?
|
||||
// else if (!valuesList.get(key).contains(value))
|
||||
// return false;
|
||||
//
|
||||
// return true;
|
||||
// }
|
||||
//
|
||||
// /**
|
||||
// * Makes sure that the aliases are valid
|
||||
// * Checks that 1) no string is used as both a main ID and an alias;
|
||||
// * 2) no alias is used more than once
|
||||
// * @param parser
|
||||
// */
|
||||
// private void validateAliases(SampleFileParser parser) {
|
||||
//
|
||||
// // no aliases sure validate
|
||||
// if (parser.getSampleAliases() == null)
|
||||
// return;
|
||||
//
|
||||
// HashSet<String> mainIds = new HashSet<String>();
|
||||
// HashSet<String> otherIds = new HashSet<String>();
|
||||
//
|
||||
// for (SampleAlias sampleAlias : parser.getSampleAliases()) {
|
||||
// mainIds.add(sampleAlias.getMainId());
|
||||
// for (String otherId : sampleAlias.getOtherIds()) {
|
||||
// if (mainIds.contains(otherId))
|
||||
// throw new StingException(String.format("The aliases in your sample file are invalid - the alias %s cannot " +
|
||||
// "be both a main ID and an other ID", otherId));
|
||||
//
|
||||
// if (!otherIds.add(otherId))
|
||||
// throw new StingException(String.format("The aliases in your sample file are invalid - %s is listed as an " +
|
||||
// "alias more than once.", otherId));
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// private boolean isPropertyValid(String property, String[] allowedProperties) {
|
||||
//
|
||||
// // is it a special property that is always allowed?
|
||||
// for (String allowedProperty : specialProperties) {
|
||||
// if (property.equals(allowedProperty))
|
||||
// return true;
|
||||
// }
|
||||
//
|
||||
// // is it in the allowed properties list?
|
||||
// for (String allowedProperty : allowedProperties) {
|
||||
// if (property.equals(allowedProperty))
|
||||
// return true;
|
||||
// }
|
||||
//
|
||||
// return false;
|
||||
// }
|
||||
//
|
||||
// private boolean isRelationshipValid(String relationship, String[] allowedRelationships) {
|
||||
//
|
||||
// // is it a special relationship that is always allowed?
|
||||
// for (String allowedRelationship : specialRelationships) {
|
||||
// if (relationship.equals(allowedRelationship))
|
||||
// return true;
|
||||
// }
|
||||
//
|
||||
// // is it in the allowed properties list?
|
||||
// for (String allowedRelationship : allowedRelationships) {
|
||||
// if (relationship.equals(allowedRelationship))
|
||||
// return true;
|
||||
// }
|
||||
//
|
||||
// return false;
|
||||
// }
|
||||
//
|
||||
// /**
|
||||
// * Saves a property as the correct type
|
||||
// * @param key property key
|
||||
// * @param value property value, as read from YAML parser
|
||||
// * @return property value to be stored
|
||||
// */
|
||||
// private void saveProperty(Sample sample, String key, Object value) {
|
||||
//
|
||||
// // convert gender to the right type, if it was stored as a String
|
||||
// if (key.equals("gender")) {
|
||||
// if (((String) value).toLowerCase().equals("male")) {
|
||||
// value = Sample.Gender.MALE;
|
||||
// }
|
||||
// else if (((String) value).toLowerCase().equals("female")) {
|
||||
// value = Sample.Gender.FEMALE;
|
||||
// }
|
||||
// else if (((String) value).toLowerCase().equals("unknown")) {
|
||||
// value = Sample.Gender.UNKNOWN;
|
||||
// }
|
||||
// else if (value != null) {
|
||||
// throw new StingException("'gender' property must be male, female, or unknown.");
|
||||
// }
|
||||
// }
|
||||
// try {
|
||||
// sample.setProperty(key, value);
|
||||
// }
|
||||
// catch (Exception e) {
|
||||
// throw new StingException("Could not save property " + key, e);
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// /**
|
||||
// * Saves a relationship as the correct type
|
||||
// * @param key relationship key
|
||||
// * @param relativeId sample ID string of the relative
|
||||
// * @return relationship value to be stored
|
||||
// */
|
||||
// private void saveRelationship(Sample sample, String key, String relativeId) {
|
||||
//
|
||||
// // get the reference that we'll store as the value
|
||||
// Sample relative = getSampleById(relativeId);
|
||||
//
|
||||
// // create sample object for the relative, if necessary
|
||||
// if (relative == null) {
|
||||
// relative = new Sample(relativeId);
|
||||
// addSample(relative);
|
||||
// }
|
||||
// sample.setRelationship(key, relative);
|
||||
// }
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue