The following schema fragment specifies the expected content contained within this class.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
_case;
-
- /**
- * Gets the value of the case property.
- *
- *
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a set method for the case property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getCase().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link CaseType }
- *
- *
- */
- public List getCase() {
- if (_case == null) {
- _case = new ArrayList();
- }
- return this._case;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ClientCaseInfoType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ClientCaseInfoType.java
deleted file mode 100644
index c5decd061a5..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ClientCaseInfoType.java
+++ /dev/null
@@ -1,69 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for ClientCaseInfoType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="ClientCaseInfoType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Cases" type="{}CasesType"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "ClientCaseInfoType", propOrder = {
- "cases"
-})
-public class ClientCaseInfoType {
-
- @XmlElement(name = "Cases", required = true)
- protected CasesType cases;
-
- /**
- * Gets the value of the cases property.
- *
- * @return
- * possible object is
- * {@link CasesType }
- *
- */
- public CasesType getCases() {
- return cases;
- }
-
- /**
- * Sets the value of the cases property.
- *
- * @param value
- * allowed object is
- * {@link CasesType }
- *
- */
- public void setCases(CasesType value) {
- this.cases = value;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/CopyNumberAlterationType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/CopyNumberAlterationType.java
deleted file mode 100644
index d84bfe9f121..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/CopyNumberAlterationType.java
+++ /dev/null
@@ -1,256 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
-
-
-/**
- * Java class for copy-number-alterationType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="copy-number-alterationType">
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="copy-number" type="{http://www.w3.org/2001/XMLSchema}byte" />
- * <attribute name="gene" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="number-of-exons" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="position" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="ratio" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "copy-number-alterationType", propOrder = {
- "value"
-})
-public class CopyNumberAlterationType {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "copy-number")
- protected Byte copyNumber;
- @XmlAttribute(name = "gene")
- protected String gene;
- @XmlAttribute(name = "number-of-exons")
- protected String numberOfExons;
- @XmlAttribute(name = "position")
- protected String position;
- @XmlAttribute(name = "ratio")
- protected Float ratio;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "type")
- protected String type;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the copyNumber property.
- *
- * @return
- * possible object is
- * {@link Byte }
- *
- */
- public Byte getCopyNumber() {
- return copyNumber;
- }
-
- /**
- * Sets the value of the copyNumber property.
- *
- * @param value
- * allowed object is
- * {@link Byte }
- *
- */
- public void setCopyNumber(Byte value) {
- this.copyNumber = value;
- }
-
- /**
- * Gets the value of the gene property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getGene() {
- return gene;
- }
-
- /**
- * Sets the value of the gene property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGene(String value) {
- this.gene = value;
- }
-
- /**
- * Gets the value of the numberOfExons property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNumberOfExons() {
- return numberOfExons;
- }
-
- /**
- * Sets the value of the numberOfExons property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setNumberOfExons(String value) {
- this.numberOfExons = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getPosition() {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setPosition(String value) {
- this.position = value;
- }
-
- /**
- * Gets the value of the ratio property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getRatio() {
- return ratio;
- }
-
- /**
- * Sets the value of the ratio property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setRatio(Float value) {
- this.ratio = value;
- }
-
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
-
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/CopyNumberAlterationsType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/CopyNumberAlterationsType.java
deleted file mode 100644
index 08d5a596fb6..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/CopyNumberAlterationsType.java
+++ /dev/null
@@ -1,81 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElementRef;
-import javax.xml.bind.annotation.XmlMixed;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for copy-number-alterationsType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="copy-number-alterationsType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="copy-number-alteration" type="{}copy-number-alterationType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "copy-number-alterationsType", propOrder = {
- "content"
-})
-public class CopyNumberAlterationsType {
-
- @XmlElementRef(name = "copy-number-alteration", type = JAXBElement.class, required = false)
- @XmlMixed
- protected List content;
-
- /**
- * Gets the value of the content property.
- *
- *
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a set method for the content property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getContent().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * {@link JAXBElement }{@code <}{@link CopyNumberAlterationType }{@code >}
- *
- *
- */
- public List getContent() {
- if (content == null) {
- content = new ArrayList();
- }
- return this.content;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/MetricType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/MetricType.java
deleted file mode 100644
index 606e8166492..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/MetricType.java
+++ /dev/null
@@ -1,175 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
-
-
-/**
- * Java class for metricType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="metricType">
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="criterion" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "metricType", propOrder = {
- "value"
-})
-public class MetricType {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "criterion")
- protected String criterion;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "value")
- protected String metricTypeValue;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the criterion property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCriterion() {
- return criterion;
- }
-
- /**
- * Sets the value of the criterion property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCriterion(String value) {
- this.criterion = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
-
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
-
- /**
- * Gets the value of the metricTypeValue property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMetricTypeValue() {
- return metricTypeValue;
- }
-
- /**
- * Sets the value of the metricTypeValue property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMetricTypeValue(String value) {
- this.metricTypeValue = value;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/MetricsType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/MetricsType.java
deleted file mode 100644
index 293f16a880b..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/MetricsType.java
+++ /dev/null
@@ -1,74 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for metricsType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="metricsType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="metric" type="{}metricType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "metricsType", propOrder = {
- "metric"
-})
-public class MetricsType {
-
- protected List metric;
-
- /**
- * Gets the value of the metric property.
- *
- *
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a set method for the metric property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getMetric().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link MetricType }
- *
- *
- */
- public List getMetric() {
- if (metric == null) {
- metric = new ArrayList();
- }
- return this.metric;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ObjectFactory.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ObjectFactory.java
deleted file mode 100644
index d97ab4cd32a..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ObjectFactory.java
+++ /dev/null
@@ -1,219 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.annotation.XmlElementDecl;
-import javax.xml.bind.annotation.XmlRegistry;
-import javax.xml.namespace.QName;
-
-
-/**
- * This object contains factory methods for each
- * Java content interface and Java element interface
- * generated in the org.foundation.data package.
- * An ObjectFactory allows you to programatically
- * construct new instances of the Java representation
- * for XML content. The Java representation of XML
- * content can consist of schema derived interfaces
- * and classes representing the binding of schema
- * type definitions, element declarations and model
- * groups. Factory methods for each of these are
- * provided in this class.
- *
- */
-@XmlRegistry
-public class ObjectFactory {
-
- private final static QName _ClientCaseInfo_QNAME = new QName("", "ClientCaseInfo");
- private final static QName _VariantReportTypeRearrangementsRearrangement_QNAME = new QName("", "rearrangement");
- private final static QName _SampleTypeComment_QNAME = new QName("", "comment");
- private final static QName _CopyNumberAlterationsTypeCopyNumberAlteration_QNAME = new QName("", "copy-number-alteration");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.foundation.data
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link VariantReportType }
- *
- */
- public VariantReportType createVariantReportType() {
- return new VariantReportType();
- }
-
- /**
- * Create an instance of {@link ClientCaseInfoType }
- *
- */
- public ClientCaseInfoType createClientCaseInfoType() {
- return new ClientCaseInfoType();
- }
-
- /**
- * Create an instance of {@link CopyNumberAlterationsType }
- *
- */
- public CopyNumberAlterationsType createCopyNumberAlterationsType() {
- return new CopyNumberAlterationsType();
- }
-
- /**
- * Create an instance of {@link CasesType }
- *
- */
- public CasesType createCasesType() {
- return new CasesType();
- }
-
- /**
- * Create an instance of {@link CaseType }
- *
- */
- public CaseType createCaseType() {
- return new CaseType();
- }
-
- /**
- * Create an instance of {@link RearrangementsType }
- *
- */
- public RearrangementsType createRearrangementsType() {
- return new RearrangementsType();
- }
-
- /**
- * Create an instance of {@link SamplesType }
- *
- */
- public SamplesType createSamplesType() {
- return new SamplesType();
- }
-
- /**
- * Create an instance of {@link MetricsType }
- *
- */
- public MetricsType createMetricsType() {
- return new MetricsType();
- }
-
- /**
- * Create an instance of {@link QualityControlType }
- *
- */
- public QualityControlType createQualityControlType() {
- return new QualityControlType();
- }
-
- /**
- * Create an instance of {@link ShortVariantsType }
- *
- */
- public ShortVariantsType createShortVariantsType() {
- return new ShortVariantsType();
- }
-
- /**
- * Create an instance of {@link MetricType }
- *
- */
- public MetricType createMetricType() {
- return new MetricType();
- }
-
- /**
- * Create an instance of {@link ShortVariantType }
- *
- */
- public ShortVariantType createShortVariantType() {
- return new ShortVariantType();
- }
-
- /**
- * Create an instance of {@link RearrangementType }
- *
- */
- public RearrangementType createRearrangementType() {
- return new RearrangementType();
- }
-
- /**
- * Create an instance of {@link SampleType }
- *
- */
- public SampleType createSampleType() {
- return new SampleType();
- }
-
- /**
- * Create an instance of {@link CopyNumberAlterationType }
- *
- */
- public CopyNumberAlterationType createCopyNumberAlterationType() {
- return new CopyNumberAlterationType();
- }
-
- /**
- * Create an instance of {@link VariantReportType.Rearrangements }
- *
- */
- public VariantReportType.Rearrangements createVariantReportTypeRearrangements() {
- return new VariantReportType.Rearrangements();
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link ClientCaseInfoType }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "", name = "ClientCaseInfo")
- public JAXBElement createClientCaseInfo(ClientCaseInfoType value) {
- return new JAXBElement(_ClientCaseInfo_QNAME, ClientCaseInfoType.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link RearrangementType }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "", name = "rearrangement", scope = VariantReportType.Rearrangements.class)
- public JAXBElement createVariantReportTypeRearrangementsRearrangement(RearrangementType value) {
- return new JAXBElement(_VariantReportTypeRearrangementsRearrangement_QNAME, RearrangementType.class, VariantReportType.Rearrangements.class, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "", name = "comment", scope = SampleType.class)
- public JAXBElement createSampleTypeComment(String value) {
- return new JAXBElement(_SampleTypeComment_QNAME, String.class, SampleType.class, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link CopyNumberAlterationType }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "", name = "copy-number-alteration", scope = CopyNumberAlterationsType.class)
- public JAXBElement createCopyNumberAlterationsTypeCopyNumberAlteration(CopyNumberAlterationType value) {
- return new JAXBElement(_CopyNumberAlterationsTypeCopyNumberAlteration_QNAME, CopyNumberAlterationType.class, CopyNumberAlterationsType.class, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "", name = "comment", scope = RearrangementType.class)
- public JAXBElement createRearrangementTypeComment(String value) {
- return new JAXBElement(_SampleTypeComment_QNAME, String.class, RearrangementType.class, value);
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/QualityControlType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/QualityControlType.java
deleted file mode 100644
index 1491c951df7..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/QualityControlType.java
+++ /dev/null
@@ -1,97 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for quality-controlType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="quality-controlType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="metrics" type="{}metricsType"/>
- * </sequence>
- * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "quality-controlType", propOrder = {
- "metrics"
-})
-public class QualityControlType {
-
- @XmlElement(required = true)
- protected MetricsType metrics;
- @XmlAttribute(name = "status")
- protected String status;
-
- /**
- * Gets the value of the metrics property.
- *
- * @return
- * possible object is
- * {@link MetricsType }
- *
- */
- public MetricsType getMetrics() {
- return metrics;
- }
-
- /**
- * Sets the value of the metrics property.
- *
- * @param value
- * allowed object is
- * {@link MetricsType }
- *
- */
- public void setMetrics(MetricsType value) {
- this.metrics = value;
- }
-
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
-
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/RearrangementType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/RearrangementType.java
deleted file mode 100644
index a877d356cb9..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/RearrangementType.java
+++ /dev/null
@@ -1,298 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElementRef;
-import javax.xml.bind.annotation.XmlMixed;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for rearrangementType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="rearrangementType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="in-frame" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="other-gene" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="supporting-read-pairs" type="{http://www.w3.org/2001/XMLSchema}short" />
- * <attribute name="targeted-gene" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "rearrangementType", propOrder = {
- "content"
-})
-public class RearrangementType {
-
- @XmlElementRef(name = "comment", type = JAXBElement.class, required = false)
- @XmlMixed
- protected List content;
- @XmlAttribute(name = "description")
- protected String description;
- @XmlAttribute(name = "in-frame")
- protected String inFrame;
- @XmlAttribute(name = "other-gene")
- protected String otherGene;
- @XmlAttribute(name = "pos1")
- protected String pos1;
- @XmlAttribute(name = "pos2")
- protected String pos2;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "supporting-read-pairs")
- protected Short supportingReadPairs;
- @XmlAttribute(name = "targeted-gene")
- protected String targetedGene;
-
- /**
- * Gets the value of the content property.
- *
- *
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a set method for the content property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getContent().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * {@link JAXBElement }{@code <}{@link String }{@code >}
- *
- *
- */
- public List getContent() {
- if (content == null) {
- content = new ArrayList();
- }
- return this.content;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the inFrame property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getInFrame() {
- return inFrame;
- }
-
- /**
- * Sets the value of the inFrame property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setInFrame(String value) {
- this.inFrame = value;
- }
-
- /**
- * Gets the value of the otherGene property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getOtherGene() {
- return otherGene;
- }
-
- /**
- * Sets the value of the otherGene property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setOtherGene(String value) {
- this.otherGene = value;
- }
-
- /**
- * Gets the value of the pos1 property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getPos1() {
- return pos1;
- }
-
- /**
- * Sets the value of the pos1 property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setPos1(String value) {
- this.pos1 = value;
- }
-
- /**
- * Gets the value of the pos2 property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getPos2() {
- return pos2;
- }
-
- /**
- * Sets the value of the pos2 property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setPos2(String value) {
- this.pos2 = value;
- }
-
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
-
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
-
- /**
- * Gets the value of the supportingReadPairs property.
- *
- * @return
- * possible object is
- * {@link Short }
- *
- */
- public Short getSupportingReadPairs() {
- return supportingReadPairs;
- }
-
- /**
- * Sets the value of the supportingReadPairs property.
- *
- * @param value
- * allowed object is
- * {@link Short }
- *
- */
- public void setSupportingReadPairs(Short value) {
- this.supportingReadPairs = value;
- }
-
- /**
- * Gets the value of the targetedGene property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTargetedGene() {
- return targetedGene;
- }
-
- /**
- * Sets the value of the targetedGene property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTargetedGene(String value) {
- this.targetedGene = value;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/RearrangementsType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/RearrangementsType.java
deleted file mode 100644
index 4538e6334ca..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/RearrangementsType.java
+++ /dev/null
@@ -1,74 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for rearrangementsType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="rearrangementsType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="rearrangement" type="{}rearrangementType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "rearrangementsType", propOrder = {
- "rearrangement"
-})
-public class RearrangementsType {
-
- protected List rearrangement;
-
- /**
- * Gets the value of the rearrangement property.
- *
- *
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a set method for the rearrangement property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getRearrangement().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link RearrangementType }
- *
- *
- */
- public List getRearrangement() {
- if (rearrangement == null) {
- rearrangement = new ArrayList();
- }
- return this.rearrangement;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/SampleType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/SampleType.java
deleted file mode 100644
index 1741619f8f4..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/SampleType.java
+++ /dev/null
@@ -1,163 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElementRef;
-import javax.xml.bind.annotation.XmlMixed;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for sampleType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="sampleType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="bait-set" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="mean-exon-depth" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sampleType", propOrder = {
- "content"
-})
-public class SampleType {
-
- @XmlElementRef(name = "comment", type = JAXBElement.class, required = false)
- @XmlMixed
- protected List content;
- @XmlAttribute(name = "bait-set")
- protected String baitSet;
- @XmlAttribute(name = "mean-exon-depth")
- protected Float meanExonDepth;
- @XmlAttribute(name = "name")
- protected String name;
-
- /**
- * Gets the value of the content property.
- *
- *
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a set method for the content property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getContent().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * {@link JAXBElement }{@code <}{@link String }{@code >}
- *
- *
- */
- public List getContent() {
- if (content == null) {
- content = new ArrayList();
- }
- return this.content;
- }
-
- /**
- * Gets the value of the baitSet property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getBaitSet() {
- return baitSet;
- }
-
- /**
- * Sets the value of the baitSet property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setBaitSet(String value) {
- this.baitSet = value;
- }
-
- /**
- * Gets the value of the meanExonDepth property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMeanExonDepth() {
- return meanExonDepth;
- }
-
- /**
- * Sets the value of the meanExonDepth property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMeanExonDepth(Float value) {
- this.meanExonDepth = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/SamplesType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/SamplesType.java
deleted file mode 100644
index ce0bb233240..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/SamplesType.java
+++ /dev/null
@@ -1,69 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for samplesType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="samplesType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sample" type="{}sampleType"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "samplesType", propOrder = {
- "sample"
-})
-public class SamplesType {
-
- @XmlElement(required = true)
- protected SampleType sample;
-
- /**
- * Gets the value of the sample property.
- *
- * @return
- * possible object is
- * {@link SampleType }
- *
- */
- public SampleType getSample() {
- return sample;
- }
-
- /**
- * Sets the value of the sample property.
- *
- * @param value
- * allowed object is
- * {@link SampleType }
- *
- */
- public void setSample(SampleType value) {
- this.sample = value;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ShortVariantType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ShortVariantType.java
deleted file mode 100644
index 051d2c300ba..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ShortVariantType.java
+++ /dev/null
@@ -1,337 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
-
-
-/**
- * Java class for short-variantType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="short-variantType">
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="cds-effect" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="depth" type="{http://www.w3.org/2001/XMLSchema}short" />
- * <attribute name="functional-effect" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gene" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="percent-reads" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="position" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="protein-effect" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="strand" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="transcript" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "short-variantType", propOrder = {
- "value"
-})
-public class ShortVariantType {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "cds-effect")
- protected String cdsEffect;
- @XmlAttribute(name = "depth")
- protected Short depth;
- @XmlAttribute(name = "functional-effect")
- protected String functionalEffect;
- @XmlAttribute(name = "gene")
- protected String gene;
- @XmlAttribute(name = "percent-reads")
- protected Float percentReads;
- @XmlAttribute(name = "position")
- protected String position;
- @XmlAttribute(name = "protein-effect")
- protected String proteinEffect;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "strand")
- protected String strand;
- @XmlAttribute(name = "transcript")
- protected String transcript;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the cdsEffect property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCdsEffect() {
- return cdsEffect;
- }
-
- /**
- * Sets the value of the cdsEffect property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCdsEffect(String value) {
- this.cdsEffect = value;
- }
-
- /**
- * Gets the value of the depth property.
- *
- * @return
- * possible object is
- * {@link Short }
- *
- */
- public Short getDepth() {
- return depth;
- }
-
- /**
- * Sets the value of the depth property.
- *
- * @param value
- * allowed object is
- * {@link Short }
- *
- */
- public void setDepth(Short value) {
- this.depth = value;
- }
-
- /**
- * Gets the value of the functionalEffect property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFunctionalEffect() {
- return functionalEffect;
- }
-
- /**
- * Sets the value of the functionalEffect property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFunctionalEffect(String value) {
- this.functionalEffect = value;
- }
-
- /**
- * Gets the value of the gene property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getGene() {
- return gene;
- }
-
- /**
- * Sets the value of the gene property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGene(String value) {
- this.gene = value;
- }
-
- /**
- * Gets the value of the percentReads property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getPercentReads() {
- return percentReads;
- }
-
- /**
- * Sets the value of the percentReads property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setPercentReads(Float value) {
- this.percentReads = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getPosition() {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setPosition(String value) {
- this.position = value;
- }
-
- /**
- * Gets the value of the proteinEffect property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getProteinEffect() {
- return proteinEffect;
- }
-
- /**
- * Sets the value of the proteinEffect property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setProteinEffect(String value) {
- this.proteinEffect = value;
- }
-
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
-
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
-
- /**
- * Gets the value of the strand property.
- *
- * @return
- * possible object is
- * {@link Byte }
- *
- */
- public String getStrand() {
- return strand;
- }
-
- /**
- * Sets the value of the strand property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStrand(String value) {
- this.strand = value;
- }
-
- /**
- * Gets the value of the transcript property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTranscript() {
- return transcript;
- }
-
- /**
- * Sets the value of the transcript property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTranscript(String value) {
- this.transcript = value;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ShortVariantsType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ShortVariantsType.java
deleted file mode 100644
index 97c836fedaf..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/ShortVariantsType.java
+++ /dev/null
@@ -1,76 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for short-variantsType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="short-variantsType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="short-variant" type="{}short-variantType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "short-variantsType", propOrder = {
- "shortVariant"
-})
-public class ShortVariantsType {
-
- @XmlElement(name = "short-variant")
- protected List shortVariant;
-
- /**
- * Gets the value of the shortVariant property.
- *
- *
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a set method for the shortVariant property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getShortVariant().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link ShortVariantType }
- *
- *
- */
- public List getShortVariant() {
- if (shortVariant == null) {
- shortVariant = new ArrayList();
- }
- return this.shortVariant;
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/VariantReportType.java b/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/VariantReportType.java
deleted file mode 100644
index 12a82553d12..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/foundation/jaxb/VariantReportType.java
+++ /dev/null
@@ -1,341 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
-// See http://java.sun.com/xml/jaxb
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2014.08.05 at 10:50:18 AM EDT
-//
-
-
-package org.mskcc.cbio.foundation.jaxb;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlElementRef;
-import javax.xml.bind.annotation.XmlMixed;
-import javax.xml.bind.annotation.XmlType;
-
-
-/**
- * Java class for variant-reportType complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType name="variant-reportType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="samples" type="{}samplesType"/>
- * <element name="quality-control" type="{}quality-controlType"/>
- * <element name="short-variants" type="{}short-variantsType"/>
- * <element name="copy-number-alterations" type="{}copy-number-alterationsType"/>
- * <element name="rearrangements">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="rearrangement" type="{}rearrangementType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="gender" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="pipeline-version" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="study" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "variant-reportType", propOrder = {
- "samples",
- "qualityControl",
- "shortVariants",
- "copyNumberAlterations",
- "rearrangements"
-})
-public class VariantReportType {
-
- @XmlElement(required = true)
- protected SamplesType samples;
- @XmlElement(name = "quality-control", required = true)
- protected QualityControlType qualityControl;
- @XmlElement(name = "short-variants", required = true)
- protected ShortVariantsType shortVariants;
- @XmlElement(name = "copy-number-alterations", required = true)
- protected CopyNumberAlterationsType copyNumberAlterations;
- @XmlElement(required = true)
- protected VariantReportType.Rearrangements rearrangements;
- @XmlAttribute(name = "gender")
- protected String gender;
- @XmlAttribute(name = "pipeline-version")
- protected String pipelineVersion;
- @XmlAttribute(name = "study")
- protected String study;
-
- /**
- * Gets the value of the samples property.
- *
- * @return
- * possible object is
- * {@link SamplesType }
- *
- */
- public SamplesType getSamples() {
- return samples;
- }
-
- /**
- * Sets the value of the samples property.
- *
- * @param value
- * allowed object is
- * {@link SamplesType }
- *
- */
- public void setSamples(SamplesType value) {
- this.samples = value;
- }
-
- /**
- * Gets the value of the qualityControl property.
- *
- * @return
- * possible object is
- * {@link QualityControlType }
- *
- */
- public QualityControlType getQualityControl() {
- return qualityControl;
- }
-
- /**
- * Sets the value of the qualityControl property.
- *
- * @param value
- * allowed object is
- * {@link QualityControlType }
- *
- */
- public void setQualityControl(QualityControlType value) {
- this.qualityControl = value;
- }
-
- /**
- * Gets the value of the shortVariants property.
- *
- * @return
- * possible object is
- * {@link ShortVariantsType }
- *
- */
- public ShortVariantsType getShortVariants() {
- return shortVariants;
- }
-
- /**
- * Sets the value of the shortVariants property.
- *
- * @param value
- * allowed object is
- * {@link ShortVariantsType }
- *
- */
- public void setShortVariants(ShortVariantsType value) {
- this.shortVariants = value;
- }
-
- /**
- * Gets the value of the copyNumberAlterations property.
- *
- * @return
- * possible object is
- * {@link CopyNumberAlterationsType }
- *
- */
- public CopyNumberAlterationsType getCopyNumberAlterations() {
- return copyNumberAlterations;
- }
-
- /**
- * Sets the value of the copyNumberAlterations property.
- *
- * @param value
- * allowed object is
- * {@link CopyNumberAlterationsType }
- *
- */
- public void setCopyNumberAlterations(CopyNumberAlterationsType value) {
- this.copyNumberAlterations = value;
- }
-
- /**
- * Gets the value of the rearrangements property.
- *
- * @return
- * possible object is
- * {@link VariantReportType.Rearrangements }
- *
- */
- public VariantReportType.Rearrangements getRearrangements() {
- return rearrangements;
- }
-
- /**
- * Sets the value of the rearrangements property.
- *
- * @param value
- * allowed object is
- * {@link VariantReportType.Rearrangements }
- *
- */
- public void setRearrangements(VariantReportType.Rearrangements value) {
- this.rearrangements = value;
- }
-
- /**
- * Gets the value of the gender property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getGender() {
- return gender;
- }
-
- /**
- * Sets the value of the gender property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGender(String value) {
- this.gender = value;
- }
-
- /**
- * Gets the value of the pipelineVersion property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getPipelineVersion() {
- return pipelineVersion;
- }
-
- /**
- * Sets the value of the pipelineVersion property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setPipelineVersion(String value) {
- this.pipelineVersion = value;
- }
-
- /**
- * Gets the value of the study property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStudy() {
- return study;
- }
-
- /**
- * Sets the value of the study property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStudy(String value) {
- this.study = value;
- }
-
-
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="rearrangement" type="{}rearrangementType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "content"
- })
- public static class Rearrangements {
-
- @XmlElementRef(name = "rearrangement", type = JAXBElement.class, required = false)
- @XmlMixed
- protected List content;
-
- /**
- * Gets the value of the content property.
- *
- *
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a set method for the content property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getContent().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * {@link JAXBElement }{@code <}{@link RearrangementType }{@code >}
- *
- *
- */
- public List getContent() {
- if (content == null) {
- content = new ArrayList();
- }
- return this.content;
- }
-
- }
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/Admin.java b/importer/src/main/java/org/mskcc/cbio/importer/Admin.java
deleted file mode 100644
index ffbff78f3d9..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/Admin.java
+++ /dev/null
@@ -1,963 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import org.mskcc.cbio.importer.*;
-import org.mskcc.cbio.importer.model.*;
-import org.mskcc.cbio.portal.dao.DaoCancerStudy;
-
-import org.apache.commons.cli.*;
-
-import org.apache.commons.logging.*;
-import org.apache.log4j.PropertyConfigurator;
-
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.support.ClassPathXmlApplicationContext;
-import org.springframework.mail.javamail.JavaMailSender;
-import org.springframework.mail.SimpleMailMessage;
-
-import java.io.*;
-import java.util.*;
-import java.text.SimpleDateFormat;
-
-/**
- * Class which provides command line admin capabilities
- * to the importer tool.
- */
-public class Admin implements Runnable {
-
- // our context file
- public static final String contextFile = "classpath:applicationContext-importer.xml";
-
- // date format
- public static final SimpleDateFormat PORTAL_DATE_FORMAT = new SimpleDateFormat("MM/dd/yyyy");
-
- // context
- private static final ApplicationContext context = new ClassPathXmlApplicationContext(contextFile);
-
- // our logger
- private static final Log LOG = LogFactory.getLog(Admin.class);
-
- // options var
- private static final Options options = initializeOptions();
-
- // identifiers for init db command
- private static final String PORTAL_DATABASE = "portal";
- private static final String IMPORTER_DATABASE = "importer";
-
- private int numStudiesUpdated;
-
- // parsed command line
- private CommandLine commandLine;
-
- /**
- * Method to get beans by id
- *
- * @param String beanID
- * @return Object
- */
- private static Object getBean(String beanID) {
- return context.getBean(beanID);
- }
-
- /**
- * Method to initialize our static options var
- *
- * @return Options
- */
- private static Options initializeOptions() {
-
- // create each option
- Option help = new Option("help", "Print this message.");
-
- Option initializeDatabase = (OptionBuilder.withArgName("db_name")
- .hasArg()
- .withDescription("Initialize database(s). Valid " +
- "database identifiers are: " +
- "\"" + PORTAL_DATABASE + "\" and \"" +
- IMPORTER_DATABASE + "\" or " +
- "\"" + Config.ALL + "\".")
- .create("init_db"));
-
- Option fetchData = (OptionBuilder.withArgName("data_source:run_date:update_worksheet")
- .hasArgs(3)
- .withValueSeparator(':')
- .withDescription("Fetch data from the given data_source and the given run date (mm/dd/yyyy). " +
- "Use \"" + Fetcher.LATEST_RUN_INDICATOR + "\" to retrieve the most current run or " +
- "when fetching clinical data. If fetching is from mercurial via automation, " +
- "if update_worksheet is 't', cancer study entries on the cancer_studies worksheet will be updated " +
- "or added as needed.")
- .create("fetch_data"));
-
- Option fetchReferenceData = (OptionBuilder.withArgName("reference_data")
- .hasArg()
- .withDescription("Fetch the given reference data." +
- " Use \"" + Config.ALL + "\" to retrieve all reference data.")
- .create("fetch_reference_data"));
-
- Option oncotateMAF = (OptionBuilder.withArgName("maf_file")
- .hasArg()
- .withDescription("Run the given MAF though the Oncotator and OMA tools.")
- .create("oncotate_maf"));
-
- Option oncotateAllMAFs = (OptionBuilder.withArgName("data_source")
- .hasArg()
- .withDescription("Run all MAFs in the given datasource though the Oncotator and OMA tools.")
- .create("oncotate_mafs"));
-
- Option convertData = (OptionBuilder.withArgName("portal:run_date:apply_overrides")
- .hasArgs(3)
- .withValueSeparator(':')
- .withDescription("Convert data within the importer database " +
- "from the given run date (mm/dd/yyyy), " +
- "for the given portal. If apply_overrides is 't', " +
- "overrides will be substituted for data_source data " +
- "before staging files are created.")
- .create("convert_data"));
-
- Option applyOverrides = (OptionBuilder.withArgName("portal:exclude_datatype:apply_case_lists")
- .hasArgs(3)
- .withValueSeparator(':')
- .withDescription("Replace staging files for the given portal " +
- "with any exisiting overrides. If exclude_datatype is set, " +
- "the datatype provided will not have overrides applied. If " +
- "apply_case_lists is 'f', case lists will not be copied into staging directory.")
- .create("apply_overrides"));
-
- Option generateCaseLists = (OptionBuilder.withArgName("portal")
- .hasArg()
- .withDescription("Generate case lists for existing " +
- "staging files for the given portal.")
- .create("generate_case_lists"));
-
- Option importReferenceData = (OptionBuilder.withArgName("reference_type")
- .hasArg()
- .withDescription("Import reference data for the given reference_type. "+
- "Use \"" + Config.ALL + "\" to import all reference data.")
- .create("import_reference_data"));
-
- Option importTypesOfCancer = (OptionBuilder.hasArg(false)
- .withDescription("Import types of cancer.")
- .create("import_types_of_cancer"));
-
- Option importData = (OptionBuilder.withArgName("portal:init_portal_db:init_tumor_types:ref_data")
- .hasArgs(4)
- .withValueSeparator(':')
- .withDescription("Import data for the given portal. " +
- "If init_portal_db is 't' a portal db will be created (an existing one will be clobbered. " +
- "If init_tumor_types is 't' tumor types will be imported " +
- "If ref_data is 't', all reference data will be imported prior to importing staging files.")
- .create("import_data"));
-
- Option updateStudyData = (OptionBuilder.withArgName("portal:update_worksheet:send_notification")
- .hasArgs(3)
- .withValueSeparator(':')
- .withDescription("Updates study data for the given portal. if update_worksheet is 't' " +
- "msk_automation_portal entry will be cleared. if send_notification is 't' " +
- "email will be sent to registered users within information about the updates.")
- .create("update_study_data"));
-
- Option importCaseLists = (OptionBuilder.withArgName("portal")
- .hasArgs(1)
- .withDescription("Import case lists for the given portal.")
- .create("import_case_lists"));
-
- Option copySegFiles = (OptionBuilder.withArgName("portal:seg_datatype:remote_user_name")
- .hasArgs(3)
- .withValueSeparator(':')
- .withDescription("Copy's given portal's .seg files to location used for linking to IGV " +
- "from cBio Portal web site. 'ssh-add' should be executed prior to this " +
- "command to add your identity to the authentication agent.")
- .create("copy_seg_files"));
-
- Option redeployWar = (OptionBuilder.withArgName("portal")
- .hasArg()
- .withDescription("Redeploy war for given portal. " +
- "'ssh-add' should be executed prior to this " +
- "command to add your identity to the authentication agent.")
- .create("redeploy_war"));
-
- Option deleteCancerStudy = (OptionBuilder.withArgName("cancer_study_id")
- .hasArg()
- .withDescription("Delete a cancer study matching the given cancer study id.")
- .create("delete_cancer_study"));
-
- // create an options instance
- Options toReturn = new Options();
-
- // add options
- toReturn.addOption(help);
- toReturn.addOption(initializeDatabase);
- toReturn.addOption(fetchData);
- toReturn.addOption(fetchReferenceData);
- toReturn.addOption(oncotateMAF);
- toReturn.addOption(oncotateAllMAFs);
- toReturn.addOption(convertData);
- toReturn.addOption(applyOverrides);
- toReturn.addOption(generateCaseLists);
- toReturn.addOption(importReferenceData);
- toReturn.addOption(importTypesOfCancer);
- toReturn.addOption(importData);
- toReturn.addOption(updateStudyData);
- toReturn.addOption(importCaseLists);
- toReturn.addOption(copySegFiles);
- toReturn.addOption(redeployWar);
- toReturn.addOption(deleteCancerStudy);
-
- // outta here
- return toReturn;
- }
-
- /**
- * Parses the arguments.
- *
- * @param args String[]
- */
- public void setCommandParameters(String[] args) {
-
- // create our parser
- CommandLineParser parser = new PosixParser();
-
- // parse
- try {
- commandLine = parser.parse(options, args);
- }
- catch (Exception e) {
- Admin.usage(new PrintWriter(System.out, true));
- }
- }
-
- public int getNumStudiesUpdated()
- {
- return numStudiesUpdated;
- }
-
- /*
- * Executes the desired portal commmand.
- */
- @Override
- public void run() {
-
- numStudiesUpdated = 0;
-
- // sanity check
- if (commandLine == null) {
- return;
- }
-
- try {
- // usage
- if (commandLine.hasOption("help")) {
- Admin.usage(new PrintWriter(System.out, true));
- }
- // initialize import database
- else if (commandLine.hasOption("init_db")) {
- initializeDatabase(commandLine.getOptionValue("init_db"));
- }
- // fetch
- else if (commandLine.hasOption("fetch_data")) {
- String[] values = commandLine.getOptionValues("fetch_data");
- fetchData(values[0], values[1], (values.length == 3) ? values[2] : "f");
- }
- // fetch reference data
- else if (commandLine.hasOption("fetch_reference_data")) {
- fetchReferenceData(commandLine.getOptionValue("fetch_reference_data"));
- }
- // oncotate MAF
- else if (commandLine.hasOption("oncotate_maf")) {
- oncotateMAF(commandLine.getOptionValue("oncotate_maf"));
- }
- // oncotate MAFs
- else if (commandLine.hasOption("oncotate_mafs")) {
- oncotateAllMAFs(commandLine.getOptionValue("oncotate_mafs"));
- }
- // apply overrides
- else if (commandLine.hasOption("apply_overrides")) {
- String[] values = commandLine.getOptionValues("apply_overrides");
- applyOverrides(values[0], (values.length >= 2) ? values[1] : "", (values.length == 3) ? values[2] : "");
- }
- // convert data
- else if (commandLine.hasOption("convert_data")) {
- String[] values = commandLine.getOptionValues("convert_data");
- convertData(values[0], values[1], (values.length == 3) ? values[2] : "");
- }
- // generate case lists
- else if (commandLine.hasOption("generate_case_lists")) {
- generateCaseLists(commandLine.getOptionValue("generate_case_lists"));
- }
- // import reference data
- else if (commandLine.hasOption("import_reference_data")) {
- importReferenceData(commandLine.getOptionValue("import_reference_data"));
- }
- else if (commandLine.hasOption("import_types_of_cancer")) {
- importTypesOfCancer();
- }
- // import data
- else if (commandLine.hasOption("import_data")) {
- String[] values = commandLine.getOptionValues("import_data");
- importData(values[0], values[1], values[2], values[3]);
- }
- else if (commandLine.hasOption("update_study_data")) {
- String[] values = commandLine.getOptionValues("update_study_data");
- numStudiesUpdated = updateStudyData(values[0], values[1], values[2]);
- }
-
- // import case lists
- else if (commandLine.hasOption("import_case_lists")) {
- String[] values = commandLine.getOptionValues("import_case_lists");
- importCaseLists(values[0]);
- }
- // copy seg files
- else if (commandLine.hasOption("copy_seg_files")) {
- String[] values = commandLine.getOptionValues("copy_seg_files");
- copySegFiles(values[0], values[1], values[2]);
- }
- // redeploy war
- else if (commandLine.hasOption("redeploy_war")) {
- redeployWar(commandLine.getOptionValue("redeploy_war"));
- }
- else if (commandLine.hasOption("delete_cancer_study")) {
- deleteCancerStudy(commandLine.getOptionValue("delete_cancer_study"));
- }
- else {
- Admin.usage(new PrintWriter(System.out, true));
- }
- }
- catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- /**
- * Helper function to initialize import database.
- *
- * @param databaseName String
- * @throws Exception
- */
- private void initializeDatabase(String databaseName) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("initializeDatabase(): " + databaseName);
- }
-
- boolean unknownDB = true;
- DatabaseUtils databaseUtils = (DatabaseUtils)getBean("databaseUtils");
- if (databaseName.equals(Config.ALL) || databaseName.equals(IMPORTER_DATABASE)) {
- unknownDB = false;
- databaseUtils.createDatabase(databaseUtils.getImporterDatabaseName(), true);
- }
- if (databaseName.equals(Config.ALL) || databaseName.equals(PORTAL_DATABASE)) {
- unknownDB = false;
- databaseUtils.createDatabase(databaseUtils.getPortalDatabaseName(), false);
- boolean success = databaseUtils.executeScript(databaseUtils.getPortalDatabaseName(),
- databaseUtils.getPortalDatabaseSchema(),
- databaseUtils.getDatabaseUser(),
- databaseUtils.getDatabasePassword());
- if (!success) {
- System.err.println("Error creating database schema.");
- }
- }
- if (unknownDB && LOG.isInfoEnabled()) {
- LOG.info("initializeDatabase(), unknown database: " + databaseName);
- }
-
- if (LOG.isInfoEnabled()) {
- LOG.info("initializeDatabase(), complete");
- }
- }
-
- /**
- * Helper function to get data.
- *
- * @param dataSource String
- * @param runDate String
- * @throws Exception
- */
- private void fetchData(String dataSource, String runDate, String updateWorksheet) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("fetchData(), dateSource:runDate: " + dataSource + ":" + runDate);
- }
- Boolean updateWorksheetBool = getBoolean(updateWorksheet);
-
- // create an instance of fetcher
- DataSourcesMetadata dataSourcesMetadata = getDataSourcesMetadata(dataSource);
- // fetch the given data source
- Fetcher fetcher = (Fetcher)getBean(dataSourcesMetadata.getFetcherBeanID());
- fetcher.fetch(dataSource, runDate, updateWorksheetBool);
-
- if (LOG.isInfoEnabled()) {
- LOG.info("fetchData(), complete");
- }
- }
-
- /**
- * Helper function to fetch reference data.
- *
- * @param referenceType String
- *
- * @throws Exception
- */
- private void fetchReferenceData(String referenceType) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("fetchReferenceData(), referenceType: " + referenceType);
- }
-
- // create an instance of fetcher
- Config config = (Config)getBean("config");
- Collection referenceMetadatas = config.getReferenceMetadata(referenceType);
- if (referenceMetadatas.isEmpty()) {
- if (LOG.isInfoEnabled()) {
- LOG.info("fetchReferenceData(), unknown referenceType: " + referenceType);
- }
- }
- else {
- Fetcher fetcher = (Fetcher)getBean("referenceDataFetcher");
- for (ReferenceMetadata referenceMetadata : referenceMetadatas) {
- if ((referenceType.equals(Config.ALL) && referenceMetadata.getFetch())
- || referenceMetadata.getReferenceType().equals(referenceType)) {
- if (LOG.isInfoEnabled()) {
- LOG.info("fetchReferenceData(), calling fetcher for: " + referenceMetadata.getReferenceType());
- }
- fetcher.fetchReferenceData(referenceMetadata);
- }
- }
- }
- if (LOG.isInfoEnabled()) {
- LOG.info("fetchReferenceData(), complete");
- }
- }
-
- /**
- * Helper function to oncotate the give MAF.
- *
- * @param mafFile String
- *
- * @throws Exception
- */
- private void oncotateMAF(String mafFileName) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("oncotateMAF(), mafFile: " + mafFileName);
- }
-
- // sanity check
- File mafFile = new File(mafFileName);
- if (!mafFile.exists()) {
- throw new IllegalArgumentException("cannot find the give MAF: " + mafFileName);
- }
-
- // create fileUtils object
- Config config = (Config)getBean("config");
- FileUtils fileUtils = (FileUtils)getBean("fileUtils");
-
- // create tmp file for given MAF
- File tmpMAF =
- org.apache.commons.io.FileUtils.getFile(org.apache.commons.io.FileUtils.getTempDirectory(),
- ""+System.currentTimeMillis()+".tmpMAF");
- org.apache.commons.io.FileUtils.copyFile(mafFile, tmpMAF);
-
- // oncotate the MAF (input is tmp maf, output is original maf)
- fileUtils.oncotateMAF(FileUtils.FILE_URL_PREFIX + tmpMAF.getCanonicalPath(),
- FileUtils.FILE_URL_PREFIX + mafFile.getCanonicalPath());
-
- // clean up
- if (tmpMAF.exists()) {
- org.apache.commons.io.FileUtils.forceDelete(tmpMAF);
- }
-
- if (LOG.isInfoEnabled()) {
- LOG.info("oncotateMAF(), complete");
- }
- }
-
- /**
- * Helper function to oncotate MAFs.
- *
- * @param dataSource String
- *
- * @throws Exception
- */
- private void oncotateAllMAFs(String dataSource) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("oncotateAllMAFs(), dataSource: " + dataSource);
- }
-
- // get the data source metadata object
- DataSourcesMetadata dataSourcesMetadata = getDataSourcesMetadata(dataSource);
-
- // oncotate all the files of the given data source
- FileUtils fileUtils = (FileUtils)getBean("fileUtils");
- fileUtils.oncotateAllMAFs(dataSourcesMetadata);
-
- if (LOG.isInfoEnabled()) {
- LOG.info("oncotateAllMAFs(), complete");
- }
- }
-
- /**
- * Helper function to convert data.
- *
- * @param portal String
- * @param runDate String
- * @param applyOverrides String
- *
- * @throws Exception
- */
- private void convertData(String portal, String runDate, String applyOverrides) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("convertData(), portal: " + portal);
- LOG.info("convertData(), run date: " + runDate);
- LOG.info("convertData(), apply overrides: " + applyOverrides);
- }
-
- Boolean applyOverridesBool = getBoolean(applyOverrides);
-
- // sanity check date format - doesn't work?
- PORTAL_DATE_FORMAT.setLenient(false);
- PORTAL_DATE_FORMAT.parse(runDate);
-
- // create an instance of Converter
- Converter converter = (Converter)getBean("converter");
- converter.convertData(portal, runDate, applyOverridesBool);
-
- if (LOG.isInfoEnabled()) {
- LOG.info("convertData(), complete");
- }
- }
-
- /**
- * Helper function to apply overrides to a given portal.
- *
- * @param portal String
- * @param excludeDatatype String
- * @param applyCaseLists String
- * @throws Exception
- */
- private void applyOverrides(String portal, String excludeDatatype, String applyCaseLists) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("applyOverrides(), portal: " + portal);
- LOG.info("applyOverrides(), exclude_datatype: " + excludeDatatype);
- LOG.info("applyOverrides(), apply_case_lists: " + applyCaseLists);
- }
-
- Converter converter = (Converter)getBean("converter");
- HashSet excludeDatatypes = new HashSet();
- if (excludeDatatype.length() > 0) excludeDatatypes.add(excludeDatatype);
- Boolean applyCaseListsBool = getBoolean(applyCaseLists);
- converter.applyOverrides(portal, excludeDatatypes, applyCaseListsBool);
-
- if (LOG.isInfoEnabled()) {
- LOG.info("applyOverrides(), complete");
- }
- }
-
- /**
- * Helper function to generate case lists.
- *
- * @param portal String
- *
- * @throws Exception
- */
- private void generateCaseLists(String portal) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("generateCaseLists(), portal: " + portal);
- }
-
- // create an instance of Converter
- Converter converter = (Converter)getBean("converter");
- converter.generateCaseLists(portal);
-
- if (LOG.isInfoEnabled()) {
- LOG.info("generateCaseLists(), complete");
- }
- }
-
- /**
- * Helper function to import reference data.
- *
- * @param referenceType String
- *
- * @throws Exception
- */
- private void importReferenceData(String referenceType) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("importReferenceData(), referenceType: " + referenceType);
- }
-
- // create an instance of Importer
- Config config = (Config)getBean("config");
- Collection referenceMetadatas = config.getReferenceMetadata(referenceType);
- if (referenceMetadatas.isEmpty()) {
- if (LOG.isInfoEnabled()) {
- LOG.info("importReferenceData(), unknown referenceType: " + referenceType);
- }
- }
- else {
- Importer importer = (Importer)getBean("importer");
- for (ReferenceMetadata referenceMetadata : referenceMetadatas) {
- if ((referenceType.equals(Config.ALL) && referenceMetadata.getImport()) ||
- referenceMetadata.getReferenceType().equals(referenceType)) {
- if (LOG.isInfoEnabled()) {
- LOG.info("importReferenceData(), calling import for: " + referenceMetadata.getReferenceType());
- }
- importer.importReferenceData(referenceMetadata);
- }
- }
- }
- if (LOG.isInfoEnabled()) {
- LOG.info("importReferenceData(), complete");
- }
- }
-
- /**
- * Helper function to import types of cancer.
- *
- * @param referenceType String
- *
- * @throws Exception
- */
- private void importTypesOfCancer() throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("importTypesOfCancer()");
- }
-
- Importer importer = (Importer)getBean("importer");
- importer.importTypesOfCancer();
-
- if (LOG.isInfoEnabled()) {
- LOG.info("importReferenceData(), complete");
- }
- }
-
- /**
- * Helper function to import data.
- *
- * @param portal String
- * @param initPortalDatabase String
- * @param initTumorTypes String
- * @param importReferenceData String
- *
- * @throws Exception
- */
- private void importData(String portal, String initPortalDatabase, String initTumorTypes, String importReferenceData) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("importData(), portal: " + portal);
- LOG.info("importData(), initPortalDatabase: " + initPortalDatabase);
- LOG.info("importData(), initTumorTypes: " + initTumorTypes);
- LOG.info("importData(), importReferenceData: " + importReferenceData);
- }
-
- // get booleans
- Boolean initPortalDatabaseBool = getBoolean(initPortalDatabase);
- Boolean initTumorTypesBool = getBoolean(initTumorTypes);
- Boolean importReferenceDataBool = getBoolean(importReferenceData);
-
- // create an instance of Importer
- Importer importer = (Importer)getBean("importer");
- importer.importData(portal, initPortalDatabaseBool, initTumorTypesBool, importReferenceDataBool);
-
- if (LOG.isInfoEnabled()) {
- LOG.info("importData(), complete");
- }
- }
-
- private int updateStudyData(String portal, String updateWorksheet, String sendNotification) throws Exception
- {
- if (LOG.isInfoEnabled()) {
- LOG.info("updateStudyData(), portal: " + portal);
- LOG.info("updateStudyData(), update_worksheet: " + updateWorksheet);
- }
- Boolean updateWorksheetBool = getBoolean(updateWorksheet);
- Boolean sendNotificationBool = getBoolean(sendNotification);
-
- Config config = (Config)getBean("config");
- Importer importer = (Importer)getBean("importer");
-
- Map propertyMap = new HashMap();
- propertyMap.put(CancerStudyMetadata.MSK_PORTAL_COLUMN_KEY, "");
-
- List cancerStudiesUpdated = new ArrayList();
- List cancerStudiesRemoved = new ArrayList();
-
- Collection cancerStudyMetadataToImport = config.getCancerStudyMetadata(portal);
- for (CancerStudyMetadata cancerStudyMetadata : config.getAllCancerStudyMetadata()) {
- if (portal.equals(PortalMetadata.TRIAGE_PORTAL)) {
- if (cancerStudyMetadataToImport.contains(cancerStudyMetadata)) {
- if (!DaoCancerStudy.doesCancerStudyExistByStableId(cancerStudyMetadata.getStableId())) {
- // update/add study into db
- try {
- importer.updateCancerStudy(portal, cancerStudyMetadata);
- cancerStudiesUpdated.add(cancerStudyMetadata.getStudyPath());
- }
- catch (Exception e) {
- LOG.info(e.getMessage());
- LOG.info("Error updating study: " + cancerStudyMetadata.getStableId() + ", skipping.");
- }
- }
- }
- else {
- // remove from db
- if (deleteCancerStudy(cancerStudyMetadata.getStableId())) {
- cancerStudiesRemoved.add(cancerStudyMetadata.getStudyPath());
- }
- }
- }
- else if (cancerStudyMetadataToImport.contains(cancerStudyMetadata)) {
- importer.updateCancerStudy(portal, cancerStudyMetadata);
- cancerStudiesUpdated.add(cancerStudyMetadata.getStudyPath());
- }
- if (portal.equals(PortalMetadata.MSK_AUTOMATION_PORTAL) && updateWorksheetBool
- && cancerStudyMetadataToImport.contains(cancerStudyMetadata)) {
- // For BIC, we do not want to update production again unless a new update occurs.
- // For DMP we will, so we need option to clear msk_automation_portal flag
- config.updateCancerStudyAttributes(cancerStudyMetadata.getStudyPath(), propertyMap);
- }
- }
- if (sendNotificationBool && (!cancerStudiesUpdated.isEmpty() || !cancerStudiesRemoved.isEmpty())) {
- sendNotification(portal, cancerStudiesUpdated, cancerStudiesRemoved);
- }
-
- return cancerStudiesUpdated.size() + cancerStudiesRemoved.size();
- }
-
-
-
- private void sendNotification(String portal, List cancerStudiesUpdated, List cancerStudiesRemoved)
- {
- Config config = (Config)getBean("config");
- SimpleMailMessage message = null;
- if (portal.equals(CancerStudyMetadata.MSK_PORTAL_COLUMN_KEY)) {
- message = (SimpleMailMessage)getBean("mskUpdateMessage");
- }
- else if (portal.equals(CancerStudyMetadata.TRIAGE_PORTAL_COLUMN_KEY)) {
- message = (SimpleMailMessage)getBean("triageUpdateMessage");
- }
- String body = message.getText() + "\n\n";
- SimpleMailMessage msg = new SimpleMailMessage(message);
- for (String cancerStudy : cancerStudiesUpdated) {
- CancerStudyMetadata cancerStudyMetadata = config.getCancerStudyMetadataByName(cancerStudy);
- body += cancerStudyMetadata.getStableId() + "\n";
- }
- if (!cancerStudiesRemoved.isEmpty()) {
- body += "\n\n" + "The following studies have been removed:\n\n";
- for (String cancerStudy : cancerStudiesRemoved) {
- CancerStudyMetadata cancerStudyMetadata = config.getCancerStudyMetadataByName(cancerStudy);
- body += cancerStudyMetadata.getStableId() + "\n";
- }
- }
- msg.setText(body);
- try {
- JavaMailSender mailSender = (JavaMailSender)getBean("mailSender");
- mailSender.send(msg);
- }
- catch (Exception e) {
- LOG.info("sendNotification(), error sending email notification:\n" + e.getMessage());
- }
- }
-
- /**
- *
- * @param portal
- * @throws Exception
- */
- private void importCaseLists(String portal) throws Exception {
- if (LOG.isInfoEnabled()) {
- LOG.info("importData(), portal: " + portal);
- }
-
- // create an instance of Importer
- Importer importer = (Importer)getBean("importer");
- importer.importCaseLists(portal);
-
- if (LOG.isInfoEnabled()) {
- LOG.info("importCaseLists(), complete");
- }
- }
-
- /**
- * Helper function to copy seg files for IGV linking.
- *
- * @param portalName String
- * @param segDatatype String
- * @param removeUserName String
- *
- * @throws Exception
- */
- private void copySegFiles(String portalName, String segDatatype, String remoteUserName) throws Exception {
-
- if (LOG.isInfoEnabled()) {
- LOG.info("copySegFiles(), portal: " + portalName);
- LOG.info("copySegFiles(), segDatatype: " + segDatatype);
- LOG.info("copySegFiles(), remoteUserName: " + remoteUserName);
- }
-
- Config config = (Config)getBean("config");
- Collection portalMetadatas = config.getPortalMetadata(portalName);
- Collection datatypeMetadatas = config.getDatatypeMetadata(segDatatype);
-
- // sanity check args
- if (remoteUserName.length() == 0 || portalMetadatas.isEmpty() || datatypeMetadatas.isEmpty()) {
- if (LOG.isInfoEnabled()) {
- LOG.info("copySegFiles(), error processing arguments, aborting....");
- }
- }
- else {
- // create an instance of Importer
- FileUtils fileUtils = (FileUtils)getBean("fileUtils");
- fileUtils.copySegFiles(portalMetadatas.iterator().next(),
- datatypeMetadatas.iterator().next(),
- remoteUserName);
- }
-
- if (LOG.isInfoEnabled()) {
- LOG.info("copySegFiles(), complete");
- }
- }
-
- private void redeployWar(String portalName) throws Exception
- {
- if (LOG.isInfoEnabled()) {
- LOG.info("redeployWar(), portal: " + portalName);
- }
-
- Config config = (Config)getBean("config");
- Collection portalMetadatas = config.getPortalMetadata(portalName);
-
- // sanity check args
- if (portalMetadatas.isEmpty()) {
- if (LOG.isInfoEnabled()) {
- LOG.info("redeployWar(), error processing argument, aborting....");
- }
- }
- else {
- // create an instance of Importer
- FileUtils fileUtils = (FileUtils)getBean("fileUtils");
- fileUtils.redeployWar(portalMetadatas.iterator().next());
- }
-
- if (LOG.isInfoEnabled()) {
- LOG.info("redeployWar(), complete");
- }
- }
-
- private boolean deleteCancerStudy(String cancerStudyStableId) throws Exception
- {
- if (LOG.isInfoEnabled()) {
- LOG.info("deleteCancerStudy(), study id: " + cancerStudyStableId);
- }
- if (DaoCancerStudy.doesCancerStudyExistByStableId(cancerStudyStableId)) {
- DaoCancerStudy.deleteCancerStudy(cancerStudyStableId);
- if (LOG.isInfoEnabled()) {
- LOG.info("deleteCancerStudy(), complete");
- }
- return true;
- }
- return false;
- }
-
- /**
- * Helper function to get a DataSourcesMetadata from
- * a given datasource (name).
- *
- * @param dataSource String
- * @return DataSourcesMetadata
- */
- private DataSourcesMetadata getDataSourcesMetadata(String dataSource) {
-
- DataSourcesMetadata toReturn = null;
- Config config = (Config)getBean("config");
- Collection dataSources = config.getDataSourcesMetadata(dataSource);
- if (!dataSources.isEmpty()) {
- toReturn = dataSources.iterator().next();
- }
-
- // sanity check
- if (toReturn == null) {
- throw new IllegalArgumentException("cannot instantiate a proper DataSourcesMetadata object.");
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Helper function to create boolean based on argument parameter.
- *
- * @param parameterValue String
- * @return Boolean
- */
- private Boolean getBoolean(String parameterValue) {
- if (parameterValue.length() == 0) return new Boolean("false");
- return (parameterValue.equalsIgnoreCase("t")) ? new Boolean("true") : new Boolean("false");
- }
-
- /**
- * Helper function - prints usage
- */
- public static void usage(PrintWriter writer) {
-
- HelpFormatter formatter = new HelpFormatter();
- formatter.printHelp(writer, HelpFormatter.DEFAULT_WIDTH,
- "Admin", "", options,
- HelpFormatter.DEFAULT_LEFT_PAD,
- HelpFormatter.DEFAULT_DESC_PAD, "");
- }
-
- /**
- * The big deal main.
- *
- * @param args String[]
- */
- public static void main(String[] args) throws Exception {
-
- // sanity check
- if (args.length == 0) {
- System.err.println("Missing args to Admin.");
- Admin.usage(new PrintWriter(System.err, true));
- return;
- }
-
- // configure logging
- Properties props = new Properties();
- props.load(Admin.class.getResourceAsStream("/log4j.properties"));
- PropertyConfigurator.configure(props);
-
- // process
- Admin admin = new Admin();
- try {
- admin.setCommandParameters(args);
- admin.run();
- }
- catch (Exception e) {
- e.printStackTrace();
- }
-
- System.exit(admin.getNumStudiesUpdated());
- }
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/CaseIDs.java b/importer/src/main/java/org/mskcc/cbio/importer/CaseIDs.java
deleted file mode 100644
index 60bd9e2619b..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/CaseIDs.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import org.mskcc.cbio.importer.model.DataMatrix;
-
-import java.util.Collection;
-
-/**
- * Interface used to manage case ids within import data matrices.
- */
-public interface CaseIDs {
- boolean isSampleId(String caseId);
- boolean isSampleId(int cancerStudyId, String caseId);
- boolean isNormalId(String caseId);
- boolean isTruncatedTCGAPatientId(String caseId);
- String getSampleId(String caseId);
- String getSampleId(int cancerStudyId, String caseId);
- String getPatientId(String caseId);
- String getPatientId(int cancerStudyId, String caseId);
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/Config.java b/importer/src/main/java/org/mskcc/cbio/importer/Config.java
deleted file mode 100644
index f970877b01a..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/Config.java
+++ /dev/null
@@ -1,213 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-import org.mskcc.cbio.importer.model.*;
-
-/**
- * Interface used to get/set configuration properties.
- */
-public interface Config {
-
- // const used when requesting all of something
- public static final String ALL = "all";
-
- /**
- * Gets a TumorTypeMetadata object via tumorType.
- * If tumorType == Config.ALL, all are returned.
- *
- * @param tumortype String
- * @return Collection
- */
- Collection getTumorTypeMetadata(String tumorType);
- public TCGATumorTypeMetadata getTCGATumorTypeMetadata(String oncotreeCode);
-
- /**
- * Function to get tumor types to download as String[]
- *
- * @return String[]
- */
- String[] getTumorTypesToDownload();
-
- /**
- * Gets a DatatypeMetadata object for the given datatype name.
- * If datatype == Config.ALL, all are returned.
- *
- * @param datatype String
- * @return Collection
- */
- Collection getDatatypeMetadata(String datatype);
-
- /**
- * Gets a collection of Datatype names for the given portal/cancer study.
- *
- * @param portalMetadata PortalMetadata
- * @param cancerStudyMetadata CancerStudyMetadata
- * @return Collection
- */
- Collection getDatatypeMetadata(PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata);
-
- /**
- * Function to get datatypes to download as String[].
- *
- * @param dataSourcesMetadata DataSourcesMetadata
- * @return String[]
- * @throws Exception
- */
- String[] getDatatypesToDownload(DataSourcesMetadata dataSourcesMetadata) throws Exception;
-
- /**
- * Function to determine the datatype(s)
- * of the datasource file (the file that was fetched from a datasource).
- *
- * @param dataSourcesMetadata DataSourcesMetadata
- * @param filename String
- * @return Collection
- * @throws Exception
- */
- Collection getFileDatatype(DataSourcesMetadata dataSourcesMetadata, String filename) throws Exception;
-
- /**
- * Gets a collection of CaseIDFilterMetadata.
- * If filterName == Config.ALL, all are returned.
- *
- * @param filterName String
- * @return Collection
- */
- Collection getCaseIDFilterMetadata(String filterName);
-
- /**
- * Gets a collection of CaseListMetadata.
- * If caseListFilename == Config.ALL, all are returned.
- *
- * @param caseListFilename String
- * @return Collection
- */
- Collection getCaseListMetadata(String caseListFilename);
-
- /**
- * Gets a collection of ClinicalAttributesNamespace.
- * If clinicalAttributeNamespaceColumnHeader == Config.ALL, all are returned.
- *
- * @param clinicalAttributeNamespaceColumnHeader String
- * @return Collection
- */
- Collection getClinicalAttributesNamespace(String clinicalAttributesNamespaceColumnHeader);
-
- /**
- * Gets a collection of ClinicalAttributesMetadata.
- * If clinicalAttributeColumnHeader == Config.ALL, all are returned.
- *
- * @param clinicalAttributeColumnHeader String
- * @return Collection
- */
- Collection getClinicalAttributesMetadata(String clinicalAttributeColumnHeader);
-
- /**
- * Gets a map of ClinicalAttributesMetadata (external column header key, metadata object value) given
- * a collection of "external" column header values (column headers from incoming datafiles).
- *
- * @param Collection
- * @return Map
- */
- Map getClinicalAttributesMetadata(Collection externalColumnHeaders);
-
- /**
- * Imports the given collection of bcrs if they are unknown.
- *
- * @param Collection bcrs
- */
- void importBCRClinicalAttributes(Collection bcrs);
-
- void flagMissingClinicalAttributes(String cancerStudy, String tumorType, Collection missingAttributeColumnHeaders);
-
- /**
- * Gets a PortalMetadata object given a portal name.
- * If portalName == Config.ALL, all are returned.
- *
- * @param portalName String
- * @return Collection
- */
- Collection getPortalMetadata(String portalName);
-
- /**
- * Gets ReferenceMetadata for the given referenceType.
- * If referenceType == Config.ALL, all are returned.
- *
- * @param referenceType String
- * @return Collection
- */
- Collection getReferenceMetadata(String referenceType);
-
- /**
- * Gets DataSourcesMetadata for the given dataSource. If dataSource == Config.ALL,
- * all are returned.
- *
- * @param dataSource String
- * @return Collection
- */
- Collection getDataSourcesMetadata(String dataSource);
-
- Collection getAllCancerStudyMetadata();
-
- /**
- * Gets all the cancer studies for a given portal.
- *
- * @param portal String
- * @return Collection
- */
- Collection getCancerStudyMetadata(String portalName);
-
- /**
- * Gets a CancerStudyMetadata for the given cancer study.
- *
- * @param cancerStudyName String - fully qualified path as entered on worksheet, e.g.: prad/mskcc/foundation
- * @return CancerStudyMetadata or null if not found
- */
- CancerStudyMetadata getCancerStudyMetadataByName(String cancerStudyName);
-
- /**
- * Gets FoundationMetadata.
- *
- * @return Collection
- */
- Collection getFoundationMetadata();
-
- /**
- * return the collection of icgc metadata objects
- */
- Collection getIcgcMetadata();
-
- /**
- * Returns a list of cancer study names which incorporate the supplied
- * substring. Comparisons are standardized to
- * lower case. An empty list is returned if no matches are found.
- * @param organizationName
- * @return
- */
- List findCancerStudiesBySubstring(String substring);
-
-
- void updateCancerStudyAttributes(String cancerStudy, Map properties);
- void insertCancerStudyAttributes(Map properties);
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/Converter.java b/importer/src/main/java/org/mskcc/cbio/importer/Converter.java
deleted file mode 100644
index 437a1b31229..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/Converter.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import java.util.Arrays;
-import java.util.HashSet;
-import org.mskcc.cbio.importer.model.DataMatrix;
-import org.mskcc.cbio.importer.model.PortalMetadata;
-import org.mskcc.cbio.importer.model.DatatypeMetadata;
-import org.mskcc.cbio.importer.model.CancerStudyMetadata;
-
-import java.util.Set;
-
-/**
- * Interface used to convert portal data.
- */
-public interface Converter {
-
- public static final String VALUE_DELIMITER = "\t";
- public static final String GENE_ID_COLUMN_HEADER_NAME = "Entrez_Gene_Id";
- public static final String GENE_SYMBOL_COLUMN_HEADER_NAME = "Hugo_Symbol";
- public static final String MUTATION_CASE_ID_COLUMN_HEADER = "Tumor_Sample_Barcode";
- public static final String MUTATION_CASE_LIST_META_HEADER = "sequenced_samples";
- public static final Set NON_CASE_IDS = new HashSet(
- Arrays.asList("MIRNA", "LOCUS", "ID", "GENE SYMBOL", "ENTREZ_GENE_ID", "HUGO_SYMBOL", "LOCUS ID", "CYTOBAND", "COMPOSITE.ELEMENT.REF", "HYBRIDIZATION REF"));
-
- /**
- * Converts data for the given portal.
- *
- * @param portal String
- * @param runDate String
- * @param applyOverrides Boolean
- * @throws Exception
- */
- void convertData(String portal, String runDate, Boolean applyOverrides) throws Exception;
-
- /**
- * Generates case lists for the given portal.
- *
- * @param portal String
- * @throws Exception
- */
- void generateCaseLists(String portal) throws Exception;
-
- /**
- * Applies overrides to the given portal using the given data source.
- * Any datatypes within the excludes datatypes set will not have be overridden.
- *
- * @param portal String
- * @param excludeDatatypes Set
- * @param applyCaseLists boolean
- * @throws Exception
- */
- void applyOverrides(String portal, Set excludeDatatypes, boolean applyCaseLists) throws Exception;
-
- /**
- * Creates a staging file from the given import data.
- *
- * @param portalMetadata PortalMetadata
- * @param cancerStudy CancerStudyMetadata
- * @param datatypeMetadata DatatypeMetadata
- * @param dataMatrices DataMatrix[]
- * @throws Exception
- */
- void createStagingFile(PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata,
- DatatypeMetadata datatypeMetadata, DataMatrix[] dataMatrices) throws Exception;
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/DatabaseUtils.java b/importer/src/main/java/org/mskcc/cbio/importer/DatabaseUtils.java
deleted file mode 100644
index 10a5f28a517..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/DatabaseUtils.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import javax.sql.DataSource;
-
-/**
- * Interface used to create database/database schema dynamically.
- */
-public interface DatabaseUtils {
-
- /**
- * Returns the database user credential.
- *
- * @return String
- */
- String getDatabaseUser();
-
- /**
- * Returns the database password credential.
- *
- * @return String
- */
- String getDatabasePassword();
-
- /**
- * Returns the database connection string.
- *
- * @return String
- */
- String getDatabaseConnectionString();
-
- /**
- * Returns the database schema filename.
- *
- * @return String
- */
- String getPortalDatabaseSchema();
-
- /**
- * Returns the importer database name.
- *
- * @return String
- */
- String getImporterDatabaseName();
-
- /**
- * Returns the portal database name.
- *
- * @return String
- */
- String getPortalDatabaseName();
-
- /**
- * Creates a database and optional schema.
- *
- * @param databaseName String
- * @param createSchema boolean
- */
- void createDatabase(String databaseName, boolean createSchema);
-
- /**
- * Execute the given script on the given db.
- *
- * @param databaseName String
- * @param databaseScript String
- * @param databaseUser String
- * @param databasePassword String
- */
- boolean executeScript(String databaseName, String databaseScript,
- String databaseUser, String databasePassword);
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/Fetcher.java b/importer/src/main/java/org/mskcc/cbio/importer/Fetcher.java
deleted file mode 100644
index 8addab371ea..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/Fetcher.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import org.mskcc.cbio.importer.model.ReferenceMetadata;
-
-/**
- * Interface used to retrieve portal data.
- */
-public interface Fetcher {
-
- // latest run indicator
- public static final String LATEST_RUN_INDICATOR = "latest";
-
- /**
- * Fetchers genomic data from an external datasource and
- * places in database for processing.
- *
- * @param dataSource String
- * @param desiredRunDate String
- * @throws Exception
- */
- void fetch(String dataSource, String desiredRunDate, boolean updateStudiesWorksheet) throws Exception;
-
- /**
- * Fetchers reference data from an external datasource.
- *
- * @param referenceMetadata ReferenceMetadata
- * @throws Exception
- */
- void fetchReferenceData(ReferenceMetadata referenceMetadata) throws Exception;
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/FileTransformer.java b/importer/src/main/java/org/mskcc/cbio/importer/FileTransformer.java
deleted file mode 100644
index b2dfcd57ae0..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/FileTransformer.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * Copyright (c) 2014 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
- */
-
-package org.mskcc.cbio.importer;
-
-import java.io.IOException;
-import java.nio.file.Path;
-import org.mskcc.cbio.importer.foundation.extractor.FileDataSource;
-
-/**
- *
- * @author criscuof
- */
-public interface FileTransformer {
-
- public void transform(Path aPath) throws IOException;
- public void transform(FileDataSource fds);
- public String getPrimaryIdentifier();
- public Integer getPrimaryEntityCount();
-
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/FileUtils.java b/importer/src/main/java/org/mskcc/cbio/importer/FileUtils.java
deleted file mode 100644
index 00b763d3ae5..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/FileUtils.java
+++ /dev/null
@@ -1,334 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import org.mskcc.cbio.importer.CaseIDs;
-import org.mskcc.cbio.importer.model.*;
-
-import org.apache.commons.io.LineIterator;
-
-import java.io.*;
-import java.util.*;
-
-/**
- * Interface used to access some common file utils.
- */
-public interface FileUtils {
-
- public static final String FILE_URL_PREFIX = "file://";
- public static final String CASE_LIST_DIRECTORY_NAME = "case_lists";
-
- /**
- * Computes the MD5 digest for the given file.
- * Returns the 32 digit hexadecimal.
- *
- * @param file File
- * @return String
- * @throws Exception
- */
- String getMD5Digest(File file) throws Exception;
-
- /**
- * Reads the precomputed md5 digest out of a firehose .md5 file.
- *
- * @param file File
- * @return String
- * @throws Exception
- */
- String getPrecomputedMD5Digest(File file) throws Exception;
-
- /**
- * Makes a directory, including parent directories if necessary.
- *
- * @param directory File
- * @throws Exception
- */
- void makeDirectory(File directory) throws Exception;
-
- /**
- * Checks if directory is empty
- */
- boolean directoryIsEmpty(File directory) throws Exception;
-
- /**
- * Deletes a directory recursively.
- *
- * @param directory File
- * @throws Exception
- */
- void deleteDirectory(File directory) throws Exception;
-
- /**
- * Deletes a file.
- *
- * @param file File
- * @throws Exception
- */
- void deleteFile(File file) throws Exception;
-
- /**
- * Lists all files in a given directory and its subdirectories.
- *
- * @param directory File
- * @param extensions String[]
- * @param recursize boolean
- * @return Collection
- * @throws Exception
- */
- Collection listFiles(File directory, String[] extensions, boolean recursive) throws Exception;
- Collection listFiles(File directory, String wildcard) throws Exception;
-
- /**
- * Returns the contents of the datafile as specified by ImportDataRecord
- * in an DataMatrix. May return null if there is a problem reading the file.
- *
- * methylationCorrelation matrix is set when we are processing a methlation file.
- * These files can be extremely large, so the correlation file is used to skip
- * all rows in the methylation file that do not have a corresponding row in the correlate file.
- *
- * @param importDataRecord ImportDataRecord
- * @param methylationCorrelation DataMatrix
- * @return DataMatrix
- * @throws Exception
- */
- List getDataMatrices(ImportDataRecord importDataRecord, DataMatrix methylationCorrelation) throws Exception;
-
- /**
- * Returns a list of missing caselists. Applicable to
- * manually curated studies checked into a 'studies' directory
- *
- * @param stagingDirectory String
- * @param cancerStudyMetadata CancerStudyMetadata
- * @return List
- */
- List getMissingCaseListFilenames(String rootDirectory, CancerStudyMetadata cancerStudyMetadata) throws Exception;
-
- /**
- * Generates caselists for the given cancer study. If strict is false, a check of isTumorCaseID is skipped.
- * If overwrite is set, any existing caselist file will be clobbered.
- *
- * @param overwrite boolean
- * @param strict boolean
- * @param stagingDirectory String
- * @param cancerStudyMetadata CancerStudyMetadata
- * @throws Exception
- */
- void generateCaseLists(boolean overwrite, boolean strict, String stagingDirectory, CancerStudyMetadata cancerStudyMetadata) throws Exception;
-
- /**
- * Get the case list from the staging file. If strict is false, a check of isTumorCaseID is skipped.
- *
- * @param strict boolean
- * @param caseIDs CaseIDs;
- * @param cancerStudyMetadata CancerStudyMetadata
- * @param stagingDirectory String
- * @param stagingFilename String
- * @return List
- * @throws Exception
- */
- List getCaseListFromStagingFile(boolean strict, CaseIDs caseIDs, CancerStudyMetadata cancerStudyMetadata, String stagingDirectory, String stagingFilename) throws Exception;
-
- /**
- * Creates a temporary file with the given contents.
- *
- * @param filename String
- * @param fileContent String
- * @return File
- * @throws Exception
- */
- File createTmpFileWithContents(String filename, String fileContent) throws Exception;
-
- /**
- * Creates (or overwrites) the given file with the given contents. Filename
- * is canonical path/filename.
- *
- * @param filename String
- * @param fileContent String
- * @return File
- * @throws Exception
- */
- File createFileWithContents(String filename, String fileContent) throws Exception;
- File createFileFromStream(String filename, InputStream fileContent) throws Exception;
-
- /**
- * Downloads the given file specified via url to the given canonicalDestination.
- *
- * @param uriSource String
- * @param uriDestination String
- * @throws Exception
- */
- void downloadFile(String urlSource, String urlDestination) throws Exception;
-
- /**
- * Returns a line iterator over the given file.
- *
- * @param urlFile String
- * @throws Exception
- */
- LineIterator getFileContents(String urlFile) throws Exception;
-
- /**
- * Method which writes the cancer study metadata file.
- *
- * @param stagingDirectory String
- * @param cancerStudyMetadata CancerStudyMetadata
- * @param numCases int
- * @throws Exception
- */
- void writeCancerStudyMetadataFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata, int numCases) throws Exception;
- void updateCancerStudyMetadataFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata, Map properties) throws Exception;
-
- /**
- * Method which writes a metadata file for
- * the given Datatype metadata instance.
- *
- * @param stagingDirectory String
- * @param datatypeMetadata DatatypeMetadata
- * @param numCases int
- * @throws Exception
- */
- void writeMetadataFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata, DatatypeMetadata datatypeMetadata, int numCases) throws Exception;
- void writeCopyNumberSegmentMetadataFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata,
- DatatypeMetadata datatypeMetadata, DataMatrix dataMatrix) throws Exception;
-
- /**
- * Method which writes a metadata file for the
- * given DatatypeMetadata. DataMatrix may be null.
- *
- * @param stagingDirectory String
- * @param cancerStudyMetadata CancerStudyMetadata
- * @param datatypeMetadata DatatypeMetadata
- * @param dataMatrix DataMatrix
- * @throws Exception
- *
- */
- void writeMetadataFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata,
- DatatypeMetadata datatypeMetadata, DataMatrix dataMatrix) throws Exception;
-
- /**
- * Creates a staging file (and meta file) with contents from the given DataMatrix.
- *
- * @param stagingDirectory String
- * @param cancerStudyMetadata CancerStudyMetadata
- * @param datatypeMetadata DatatypeMetadata
- * @param dataMatrix DataMatrix
- * @throws Exception
- */
- void writeStagingFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata,
- DatatypeMetadata datatypeMetadata, DataMatrix dataMatrix) throws Exception;
-
- /**
- * Creates a staging file for mutation data (and meta file) with contents from the given DataMatrix.
- * This is called when the mutation file needs to be run through the Oncotator and Mutation Assessor Tools.
- *
- * @param stagingDirectory String
- * @param cancerStudy CancerStudyMetadata
- * @param datatypeMetadata DatatypeMetadata
- * @param dataMatrix DataMatrix
- * @throws Exception
- */
- void writeMutationStagingFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata,
- DatatypeMetadata datatypeMetadata, DataMatrix dataMatrix) throws Exception;
-
- /**
- * Creates a z-score staging file from the given dependencies. It assumes that the
- * dependency - staging files have already been created.
- *
- * @param stagingDirectory String
- * @param cancerStudyMetadata CancerStudyMetadata
- * @param datatypeMetadata DatatypeMetadata
- * @param dependencies DatatypeMetadata[]
- * @throws Exception
- */
- boolean writeZScoresStagingFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata,
- DatatypeMetadata datatypeMetadata, DatatypeMetadata[] dependencies) throws Exception;
-
- /**
- * Returns an override file (if it exists) for the given portal & cancer study. The override in this case
- * is the override file that a DataMatrix is created from.
- *
- * Null is returned if an override file is not found.
- *
- * @param portalMetadata PortalMetadata
- * @param cancerStudyMetadata CancerStudyMetadata
- * @param filename String
- * @return File
- * @throws Exception
- */
- File getOverrideFile(PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, String filename) throws Exception;
-
- /**
- * If it exists, moves an override file into the proper
- * location in the given portals staging area.
- *
- * Note, filename can be the name of a file or directory (like case_lists)
- *
- * @param overrideDirectory String
- * @param stagingDirectory String
- * @param cancerStudyMetadata CancerStudyMetadata
- * @param overrideFilename String
- * @param stagingFilename String
- * @throws Exception
- */
- void applyOverride(String overrideDirectory, String stagingDirectory, CancerStudyMetadata cancerStudyMetadata,
- String overrideFilename, String stagingFilename) throws Exception;
-
- /**
- * Create a case list file from the given case list metadata file.
- *
- * @param stagingDirectory String
- * @param cancerStudyMetadata CancerStudyMetadata
- * @param caseListMetadata CaseListMetadata
- * @param caseList String[]
- * @throws Exception
- */
- void writeCaseListFile(String stagingDirectory, CancerStudyMetadata cancerStudyMetadata, CaseListMetadata caseListMetadata, String[] caseList) throws Exception;
-
- /**
- * Runs all MAFs for the given dataaSourcesMetadata through
- * the Oncotator and OMA tools.
- *
- * @param dataSourcesMetadata DataSourcesMetadata
- * @throws Exception
- */
- void oncotateAllMAFs(DataSourcesMetadata dataSourcesMetadata) throws Exception;
-
- /**
- * Runs a MAF file through the Oncotator and OMA tools.
- *
- * @param inputMAFURL String
- * @param outputMAFURL String
- * @throws Exception
- */
- void oncotateMAF(String inputMAFURL, String outputMAFURL) throws Exception;
-
- /**
- * Copy's the given portal's seg files to location used for linking to IGV from cBio Portal web site.
- *
- * @param portalMetadata PortalMetadata
- * @param datatypeMetadata DatatypeMetadata
- * @param remoteUserName String
- * @throws Exception
- */
- void copySegFiles(PortalMetadata portalMetadata, DatatypeMetadata datatypeMetadata, String remoteUserName) throws Exception;
- void redeployWar(PortalMetadata portalMetadata) throws Exception;
-
- CancerStudyMetadata createCancerStudyMetadataFromMetaStudyFile(String downloadDirectory, String studyName);
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/IDMapper.java b/importer/src/main/java/org/mskcc/cbio/importer/IDMapper.java
deleted file mode 100644
index 8c9215e7be9..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/IDMapper.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-
-import scala.Tuple2;
-
-/**
- * Interface used to map IDS.
- */
-public interface IDMapper {
-
- /**
- *
- * @param chromosome
- * @param position
- * @param strand
- * @return
- */
-
- public String findGeneNameByGenomicPosition(String chromosome, String position,String strand);
-
- /**
- * For the given symbol, return id.
- *
- * @param geneSymbol String
- * @return String
- * @throws Exception
- */
- String symbolToEntrezID(String geneSymbol) throws Exception;
-
- /**
- * For the entrezID, return symbol.
- *
- * @param entrezID String
- * @return String
- * @throws Exception
- */
- String entrezIDToSymbol(String entrezID) throws Exception;
-
- /**
- * returns the Gene Symbol and Entrez ID for a specified Ensembl ID
- * @param ensemblID
- * @return
- */
-
- Tuple2 ensemblToHugoSymbolAndEntrezID(String ensemblID);
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/Importer.java b/importer/src/main/java/org/mskcc/cbio/importer/Importer.java
deleted file mode 100644
index 506ac11830c..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/Importer.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import org.mskcc.cbio.importer.model.*;
-
-/**
- * Interface used to import portal data.
- */
-public interface Importer {
-
- /**
- * Imports data for use in the given portal.
- *
- * @param portal String
- * @param initPortalDatabase Boolean
- * @param initTumorTypes Boolean
- * @param importReferenceData Boolean
- * @throws Exception
- */
- void importData(String portal, Boolean initPortalDatabase, Boolean initTumorTypes, Boolean importReferenceData) throws Exception;
- void updateCancerStudy(String portal, CancerStudyMetadata cancerStudyMetadata) throws Exception;
-
- /**
- * Imports the given reference data.
- *
- * @param referenceMetadata ReferenceMetadata
- * @throws Exception
- */
- void importReferenceData(ReferenceMetadata referenceMetadata) throws Exception;
-
- /**
- * Imports tumor type metadata.
- */
- void importTypesOfCancer() throws Exception;
-
- void importCaseLists(String portal) throws Exception;
-
- /**
- * Imports all cancer studies found within the given directory.
- * If force is set, user will not be prompted to override existing cancer study.
- * If cancer study exists and skip is set, new study will not be imported.
- *
- * @param cancerStudyDirectoryName
- * @param skip
- * @param force
-
- */
- void importCancerStudy(String cancerStudyDirectoryName, boolean skip, boolean force) throws Exception;
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/NCIcaDSRFetcher.java b/importer/src/main/java/org/mskcc/cbio/importer/NCIcaDSRFetcher.java
deleted file mode 100644
index 2ec4b6c8816..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/NCIcaDSRFetcher.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-import org.mskcc.cbio.importer.model.NCIcaDSREntry;
-
-public interface NCIcaDSRFetcher
-{
- public NCIcaDSREntry fetchDSREntry(String cdiId);
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/PortalImporterTool.java b/importer/src/main/java/org/mskcc/cbio/importer/PortalImporterTool.java
deleted file mode 100644
index 9c6d53bccca..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/PortalImporterTool.java
+++ /dev/null
@@ -1,289 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-// imports
-import org.mskcc.cbio.portal.dao.DaoCancerStudy;
-import org.mskcc.cbio.portal.scripts.NormalizeExpressionLevels;
-
-import org.apache.commons.cli.*;
-
-import org.apache.commons.logging.*;
-import org.apache.log4j.PropertyConfigurator;
-
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.support.ClassPathXmlApplicationContext;
-
-import java.io.*;
-import java.util.Properties;
-
-/**
- * Class which provides command line admin capabilities
- * to the importer tool.
- */
-public class PortalImporterTool implements Runnable {
-
- private static final String HOME_DIR = "PORTAL_HOME";
- private static final Log LOG = LogFactory.getLog(PortalImporterTool.class);
- static {
- configureLogging();
- }
- private static final String contextFile = "classpath:applicationContext-portalImporterTool.xml";
- private static final ApplicationContext context = new ClassPathXmlApplicationContext(contextFile);
- private static final Options options = initializeOptions();
-
- private CommandLine commandLine;
-
- private static Options initializeOptions()
- {
-
- // create each option
- Option help = new Option("h", "Print this message.");
-
- Option annotateMAF = (OptionBuilder.withArgName("maf:output")
- .hasArgs(2)
- .withValueSeparator(':')
- .withDescription("Annotates the MAF file with additional information from mutationassessor.org and Oncotator." +
- "If output filename is not given, input filename will be used with a '.annotated' extension.")
- .create("a"));
-
- Option validateCancerStudy = (OptionBuilder.withArgName("dir")
- .hasArg()
- .withDescription("Validates cancer studies within the given cancer study directory.")
- .create("v"));
-
- Option normalizeDataFile = (OptionBuilder.withArgName("cna-file:expression-file:output-file:normal-sample-suffix")
- .hasArgs(4)
- .withValueSeparator(':')
- .withDescription("Given CNV & expression data for a set of samples, generate normalized expression values.")
- .create("n"));
-
- Option importCancerStudy = (OptionBuilder.withArgName("dir:skip:force")
- .hasArgs(3)
- .withValueSeparator(':')
- .withDescription("Import cancer study data into the database. " +
- "This command will traverse all subdirectories of cancer_study_directory " +
- "looking for cancer studies to import. If the skip argument is 't', " +
- "cancer studies will not be replaced. Set force to 't' to force a cancer study replacement.")
- .create("i"));
-
- Option deleteCancerStudy = (OptionBuilder.withArgName("cancer_study_id")
- .hasArg()
- .withDescription("Delete a cancer study matching the given cancer study id.")
- .create("d"));
-
-
- // create an options instance
- Options toReturn = new Options();
-
- // add options
- toReturn.addOption(help);
- toReturn.addOption(annotateMAF);
- toReturn.addOption(validateCancerStudy);
- toReturn.addOption(normalizeDataFile );
- toReturn.addOption(importCancerStudy);
- toReturn.addOption(deleteCancerStudy);
-
- // outta here
- return toReturn;
- }
-
- public void setCommandParameters(String[] args)
- {
- // create our parser
- CommandLineParser parser = new PosixParser();
-
- // parse
- try {
- commandLine = parser.parse(options, args);
- }
- catch (Exception e) {
- Admin.usage(new PrintWriter(System.out, true));
- }
- }
-
- public static void usage(PrintWriter writer)
- {
-
- HelpFormatter formatter = new HelpFormatter();
- formatter.printHelp(writer, 100,
- "PortalImporterTool", "", options,
- HelpFormatter.DEFAULT_LEFT_PAD,
- HelpFormatter.DEFAULT_DESC_PAD, "");
- }
-
- @Override
- public void run()
- {
- if (commandLine == null) return;
-
- try {
- if (commandLine.hasOption("h")) {
- Admin.usage(new PrintWriter(System.out, true));
- }
- else if (commandLine.hasOption("v")) {
- validateCancerStudy(commandLine.getOptionValue("v"));
- }
- else if (commandLine.hasOption("n")) {
- String[] values = commandLine.getOptionValues("n");
- normalizeExpressionLevels(values[0], values[1], values[2], values[3]);
- }
- else if (commandLine.hasOption("i")) {
- String[] values = commandLine.getOptionValues("i");
- importCancerStudy(values[0], (values.length >= 2) ? values[1] : "", (values.length == 3) ? values[2] : "");
- }
- else if (commandLine.hasOption("a")) {
- String[] values = commandLine.getOptionValues("a");
- annotateMAF(values[0], (values.length == 2) ? values[1] : values[0] + ".annotated");
- }
- else if (commandLine.hasOption("d")) {
- deleteCancerStudy(commandLine.getOptionValue("d"));
- }
- else {
- Admin.usage(new PrintWriter(System.out, true));
- }
- }
- catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- public static void main(String[] args) throws Exception
- {
- if (args.length == 0) {
- System.err.println("Missing args to PortalImporterTool.");
- PortalImporterTool.usage(new PrintWriter(System.err, true));
- return;
- }
-
- // process
- PortalImporterTool importer = new PortalImporterTool();
- try {
- importer.setCommandParameters(args);
- importer.run();
- }
- catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- private static void configureLogging()
- {
- String propertyFilename = "log4j.properties";
-
- try {
- String home = System.getenv(HOME_DIR);
- if (home != null) {
- propertyFilename = home + File.separator + "log4j.properties";
- InputStream fis = new FileInputStream(propertyFilename);
- Properties props = new Properties();
- props.load(fis);
- fis.close();
- PropertyConfigurator.configure(props);
- }
- }
- catch(IOException e) {
- System.err.println("Error loading: " + propertyFilename);
- }
- }
-
- private void validateCancerStudy(String cancerStudyDirectory) throws Exception
- {
- logMessage("validateCancerStudy(), cancer study directory: " + cancerStudyDirectory);
-
- Validator validator = (Validator)context.getBean("cancerStudyValidator");
- validator.validateCancerStudy(cancerStudyDirectory);
-
- logMessage("validateCancerStudy(), complete");
- }
-
- private void importCancerStudy(String cancerStudyDirectory, String skip, String force) throws Exception
- {
-
- logMessage("importCancerStudy(), cancer study directory: " + cancerStudyDirectory);
-
- boolean skipBool = getBoolean(skip);
- boolean forceBool = getBoolean(force);
- Importer importer = (Importer)context.getBean("cancerStudyImporter");
- importer.importCancerStudy(cancerStudyDirectory, skipBool, forceBool);
-
- logMessage("importCancerStudy(), complete");
- }
-
- private void annotateMAF(String inputFilename, String outputFilename) throws Exception {
-
- logMessage("annotateMAF(), mafFile: " + inputFilename);
-
- // sanity check
- File mafFile = new File(inputFilename);
- if (!mafFile.exists()) {
- throw new IllegalArgumentException("cannot find the give MAF: " + inputFilename);
- }
-
- // create fileUtils object
- FileUtils fileUtils = (FileUtils)context.getBean("fileUtils");
-
- // create output file
- File outputMAF =
- org.apache.commons.io.FileUtils.getFile(outputFilename);
-
- fileUtils.oncotateMAF(FileUtils.FILE_URL_PREFIX + mafFile.getCanonicalPath(),
- FileUtils.FILE_URL_PREFIX + outputMAF.getCanonicalPath());
-
- logMessage("annotateMAF(), complete");
- }
-
- private void normalizeExpressionLevels(String cnaFile, String expressionFile, String normalizedFile, String normalSampleSuffix) throws Exception
- {
- logMessage("normalizeExpressionLevels()");
- logMessage("cnaFile: " + cnaFile);
- logMessage("expressionFile: " + expressionFile);
- logMessage("outputFile: " + normalizedFile);
- logMessage("normalSampleSuffix: " + normalSampleSuffix);
-
- String[] args = { cnaFile, expressionFile, normalizedFile, normalSampleSuffix };
- NormalizeExpressionLevels.driver(args);
-
- logMessage("normalizeExpressionLevels(), complete");
- }
-
- private void deleteCancerStudy(String cancerStudyStableId) throws Exception
- {
- if (LOG.isInfoEnabled()) {
- LOG.info("deleteCancerStudy(), study id: " + cancerStudyStableId);
- }
- DaoCancerStudy.deleteCancerStudy(cancerStudyStableId);
- if (LOG.isInfoEnabled()) {
- LOG.info("deleteCancerStudy(), complete");
- }
- }
-
- private boolean getBoolean(String parameterValue)
- {
- return (parameterValue.equalsIgnoreCase("t")) ? Boolean.TRUE : Boolean.FALSE;
- }
-
- private void logMessage(String message)
- {
- if (LOG.isInfoEnabled()) {
- LOG.info(message);
- }
- System.err.println(message);
- }
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/SurvivalDataCalculator.java b/importer/src/main/java/org/mskcc/cbio/importer/SurvivalDataCalculator.java
deleted file mode 100644
index c33bb6f459e..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/SurvivalDataCalculator.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/** Copyright (c) 2013 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-import org.mskcc.cbio.importer.model.DataMatrix;
-import org.mskcc.cbio.importer.model.SurvivalStatus;
-
-import java.util.List;
-
-/**
- * Interface used to import portal data.
- */
-public interface SurvivalDataCalculator
-{
- /**
- * The list is in ascending (time) order,
- * i.e., patient matrix would come before follow-up matrices.
- */
- SurvivalStatus computeSurvivalData(List dataMatrices);
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/Validator.java b/importer/src/main/java/org/mskcc/cbio/importer/Validator.java
deleted file mode 100644
index 23bac529897..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/Validator.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer;
-
-/**
- * Interface used to validate cancer study import.
- */
-public interface Validator {
-
- /**
- * Validates all cancers studies fonud within the given directory.
- *
- * Validates:
- *
- * - meta_study.txt exists and is 'valid'
- * -- type of cancer is set
- * -- cancer study identifier is set
- * -- name is set
- * -- description is set
- *
- * - cancer_type.txt exists and is 'valid'
- * -- validates types of cancer id found in meta_study.txt
- *
- * - validates cancer study data:
- * -- for each metadata file found:
- * --- validates all properties are set
- * --- validates proper cancer study id
- * --- validates proper genetic alteration type
- * --- validates proper stable id (prefix matches cancer study id)
- * --- validates no duplicate stable ids
- * --- existence of staging file
- *
- * - validates case list directory exists and contains case lists
- * -- for each case list:
- * --- validates all properties are set
- * --- validates proper cancer study id
- * --- validates proper stable id (prefix matches cancer study id)
- * --- validates no duplicate stable ids
- *
- * @param cancerStudyDirectoryName
- */
- boolean validateCancerStudy(String cancerStudyDirectoryName) throws Exception;
-}
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/caseids/internal/CaseIDsImpl.java b/importer/src/main/java/org/mskcc/cbio/importer/caseids/internal/CaseIDsImpl.java
deleted file mode 100644
index 45b42f19015..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/caseids/internal/CaseIDsImpl.java
+++ /dev/null
@@ -1,179 +0,0 @@
-/** Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- * documentation provided hereunder is on an "as is" basis, and
- * Memorial Sloan-Kettering Cancer Center
- * has no obligations to provide maintenance, support,
- * updates, enhancements or modifications. In no event shall
- * Memorial Sloan-Kettering Cancer Center
- * be liable to any party for direct, indirect, special,
- * incidental or consequential damages, including lost profits, arising
- * out of the use of this software and its documentation, even if
- * Memorial Sloan-Kettering Cancer Center
- * has been advised of the possibility of such damage.
-*/
-
-// package
-package org.mskcc.cbio.importer.caseids.internal;
-
-// imports
-import org.mskcc.cbio.importer.*;
-import org.mskcc.cbio.importer.model.*;
-
-import org.mskcc.cbio.portal.dao.*;
-import org.mskcc.cbio.portal.model.*;
-
-import org.apache.commons.logging.*;
-
-import java.util.*;
-import java.util.regex.*;
-
-/**
- * Class which implements the CaseIDs interface.
- */
-public class CaseIDsImpl implements CaseIDs {
-
- private static final String SAMPLE_REGEX = "tcga-sample-pattern";
- private static final String PATIENT_REGEX = "tcga-patient-pattern";
- private static final String TRUCATED_PATIENT_REGEX = "tcga-truncated-patient-pattern";
- private static final String NON_TCGA_REGEX = "non-tcga-pattern";
-
- private static final List tcgaNormalTypes = initTCGANormalTypes();
- private static final List initTCGANormalTypes()
- {
- return Arrays.asList(new String[] { "10","11","12","13","14","15","16","17","18","19" });
- }
-
- // ref to our matchers
- private Pattern samplePattern;
- private Pattern patientPattern;
- private Pattern truncatedTCGAPatientPattern;
- private Pattern nonTCGAPattern;
-
- /**
- * Constructor.
- *
- * @param config Config
- */
- public CaseIDsImpl(Config config) {
-
- // get all the filters
- Collection caseIDFilters = config.getCaseIDFilterMetadata(Config.ALL);
-
- // sanity check
- if (caseIDFilters == null) {
- throw new IllegalArgumentException("cannot instantiate a proper collection of CaseIDFilterMetadata objects.");
- }
-
- // setup our matchers
- for (CaseIDFilterMetadata caseIDFilter : caseIDFilters) {
- if (caseIDFilter.getFilterName().equals(PATIENT_REGEX)) {
- patientPattern = Pattern.compile(caseIDFilter.getRegex());
- }
- else if (caseIDFilter.getFilterName().equals(TRUCATED_PATIENT_REGEX)) {
- truncatedTCGAPatientPattern = Pattern.compile(caseIDFilter.getRegex());
- }
- else if (caseIDFilter.getFilterName().equals(SAMPLE_REGEX)) {
- samplePattern = Pattern.compile(caseIDFilter.getRegex());
- }
- else if (caseIDFilter.getFilterName().equals(NON_TCGA_REGEX)) {
- nonTCGAPattern = Pattern.compile(caseIDFilter.getRegex());
- }
- }
- }
-
- @Override
- public boolean isSampleId(String caseId)
- {
- return isSampleId(0, caseId);
- }
-
- @Override
- public boolean isSampleId(int cancerStudyId, String caseId)
- {
- if (nonTCGAPattern.matcher(caseId).matches()) {
- Sample s = DaoSample.getSampleByCancerStudyAndSampleId(cancerStudyId, caseId);
- return (s != null);
- }
- else {
- caseId = clean(caseId);
- return (samplePattern.matcher(caseId).matches());
- }
- }
-
- @Override
- public boolean isNormalId(String caseId)
- {
- String cleanId = clean(caseId);
- Matcher matcher = samplePattern.matcher(cleanId);
- return (matcher.find()) ? tcgaNormalTypes.contains(matcher.group(2)) : false;
- }
-
- @Override
- public boolean isTruncatedTCGAPatientId(String caseId)
- {
- return truncatedTCGAPatientPattern.matcher(caseId).matches();
- }
-
- @Override
- public String getSampleId(String caseId)
- {
- return getSampleId(0, caseId);
- }
-
- @Override
- public String getSampleId(int cancerStudyId, String caseId)
- {
- if (nonTCGAPattern.matcher(caseId).matches()) {
- Sample s = DaoSample.getSampleByCancerStudyAndSampleId(cancerStudyId, caseId);
- return (s != null) ? s.getStableId() : caseId;
- }
- else {
- String cleanId = clean(caseId);
- Matcher matcher = samplePattern.matcher(cleanId);
- return (matcher.find()) ? matcher.group(1) : caseId;
- }
- }
-
- @Override
- public String getPatientId(String caseId)
- {
- return getPatientId(0, caseId);
- }
-
- @Override
- public String getPatientId(int cancerStudyId, String caseId)
- {
- if (nonTCGAPattern.matcher(caseId).matches()) {
- // data files should only have sample ids - get patient id via sample
- Sample s = DaoSample.getSampleByCancerStudyAndSampleId(cancerStudyId, caseId);
- if (s != null && s.getInternalPatientId() > 0) {
- Patient p = DaoPatient.getPatientById(s.getInternalPatientId());
- return (p != null) ? p.getStableId() : caseId;
- }
- else {
- return caseId;
- }
- }
- else {
- String cleanId = clean(caseId);
- Matcher matcher = patientPattern.matcher(cleanId);
- return (matcher.find()) ? matcher.group(1) : caseId;
- }
- }
-
- private String clean(String caseId)
- {
- if (caseId.contains("Tumor")) {
- return caseId.replace("Tumor", "01");
- }
- else if (caseId.contains("Normal")) {
- return caseId.replace("Normal", "11");
- }
- else {
- return caseId;
- }
- }
-}
\ No newline at end of file
diff --git a/importer/src/main/java/org/mskcc/cbio/importer/config/internal/GDataImpl.java b/importer/src/main/java/org/mskcc/cbio/importer/config/internal/GDataImpl.java
deleted file mode 100644
index 1ac06eed54c..00000000000
--- a/importer/src/main/java/org/mskcc/cbio/importer/config/internal/GDataImpl.java
+++ /dev/null
@@ -1,1148 +0,0 @@
-/**
- * Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center.
- *
- * This library is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
- * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
- * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
- * obligations to provide maintenance, support, updates, enhancements or
- * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
- * liable to any party for direct, indirect, special, incidental or
- * consequential damages, including lost profits, arising out of the use of this
- * software and its documentation, even if Memorial Sloan-Kettering Cancer
- * Center has been advised of the possibility of such damage.
- */
-// package
-package org.mskcc.cbio.importer.config.internal;
-
-// imports
-import org.mskcc.cbio.importer.Config;
-import org.mskcc.cbio.importer.model.*;
-import org.mskcc.cbio.importer.NCIcaDSRFetcher;
-import org.mskcc.cbio.importer.util.ClassLoader;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.google.common.base.Strings;
-import com.google.gdata.data.spreadsheet.*;
-import com.google.gdata.client.spreadsheet.*;
-import com.google.gdata.util.common.base.Preconditions;
-import com.google.common.collect.Lists;
-
-
-import java.util.*;
-import java.util.Calendar;
-import java.lang.reflect.Method;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-/**
- * Class which implements the Config interface using google docs as a backend.
- */
-class GDataImpl implements Config {
-
- // our logger
- private static Log LOG = LogFactory.getLog(GDataImpl.class);
-
- // google docs user
- private String gdataUser;
- // google docs password
- private String gdataPassword;
- // ref to spreadsheet client
- private SpreadsheetService spreadsheetService;
- private NCIcaDSRFetcher nciDSRFetcher;
-
- // for performance optimization - we try to limit the number of accesses to google
- ArrayList> cancerStudiesMatrix;
- ArrayList> caseIDFiltersMatrix;
- ArrayList> caseListMatrix;
- ArrayList> clinicalAttributesNamespaceMatrix;
- ArrayList> clinicalAttributesMatrix;
- ArrayList> datatypesMatrix;
- ArrayList> dataSourcesMatrix;
- ArrayList> portalsMatrix;
- ArrayList> referenceMatrix;
- ArrayList> oncotreeMatrix;
- ArrayList> oncotreePropertyMatrix;
- ArrayList> tcgaTumorTypesMatrix;
- ArrayList> foundationMatrix;
- ArrayList> icgcMatrix;
-
- // worksheet names we need for updates
- private String gdataSpreadsheet;
- private String oncotreeWorksheet;
- private String oncotreePropertyWorksheet;
- private String datatypesWorksheet;
- private String caseIDFiltersWorksheet;
- private String caseListWorksheet;
- private String clinicalAttributesNamespaceWorksheet;
- private String clinicalAttributesWorksheet;
- private String portalsWorksheet;
- private String referenceDataWorksheet;
- private String dataSourcesWorksheet;
- private String cancerStudiesWorksheet;
- private String foundationWorksheet;
- private String tcgaTumorTypesWorksheet;
- private String icgcWorksheet;
-
- private final String HTML_COLOR_NAME_ONCOTREE_PROP = "HTML_COLOR_NAME";
-
- /**
- * Constructor.
- *
- * Constructor args are passed viaw applicationContext. We do this so that all our
- * metadata objects can be retrieved during construction of this class. Which will
- * prevent us from having to access google more than once. Of course any changes to
- * the google docs will not be reflected in this class until its next instantiation.
- */
- public GDataImpl(String gdataUser, String gdataPassword, SpreadsheetService spreadsheetService,
- String gdataSpreadsheet,
- String oncotreeWorksheet, String oncotreePropertyWorksheet,
- String datatypesWorksheet,
- String caseIDFiltersWorksheet, String caseListWorksheet,
- String clinicalAttributesNamespaceWorksheet, String clinicalAttributesWorksheet,
- String portalsWorksheet, String referenceDataWorksheet, String dataSourcesWorksheet, String cancerStudiesWorksheet,
- String foundationWorksheet, String icgcWorksheet, String tcgaTumorTypesWorksheet, NCIcaDSRFetcher nciDSRFetcher)
- {
- // set members
- this.gdataUser = gdataUser;
- this.gdataPassword = gdataPassword;
- this.spreadsheetService = spreadsheetService;
- this.nciDSRFetcher = nciDSRFetcher;
-
- // save name(s) of worksheet we update later
- this.gdataSpreadsheet = gdataSpreadsheet;
- this.oncotreeWorksheet = oncotreeWorksheet;
- this.oncotreePropertyWorksheet = oncotreePropertyWorksheet;
- this.datatypesWorksheet = datatypesWorksheet;
- this.caseIDFiltersWorksheet = caseIDFiltersWorksheet;
- this.caseListWorksheet = caseListWorksheet;
- this.clinicalAttributesNamespaceWorksheet = clinicalAttributesNamespaceWorksheet;
- this.clinicalAttributesWorksheet = clinicalAttributesWorksheet;
- this.portalsWorksheet = portalsWorksheet;
- this.referenceDataWorksheet = referenceDataWorksheet;
- this.dataSourcesWorksheet = dataSourcesWorksheet;
- this.cancerStudiesWorksheet = cancerStudiesWorksheet;
- this.foundationWorksheet = foundationWorksheet;
- this.icgcWorksheet = icgcWorksheet;
- this.tcgaTumorTypesWorksheet = tcgaTumorTypesWorksheet;
- }
-
- /**
- * Function to get tumor types to download as String[]
- *
- * @return String[]
- */
- @Override
- public String[] getTumorTypesToDownload() {
-
- String toReturn = "";
- for (TCGATumorTypeMetadata tcgaTumorTypeMetadata : getTCGATumorTypeMetadata()) {
- toReturn += tcgaTumorTypeMetadata.getTCGACode() + ":";
- }
-
- // outta here
- return toReturn.split(":");
- }
-
- private Collection getTCGATumorTypeMetadata()
- {
- if (tcgaTumorTypesMatrix == null) {
- tcgaTumorTypesMatrix = getWorksheetData(gdataSpreadsheet, tcgaTumorTypesWorksheet);
- }
-
- return (Collection)getMetadataCollection(tcgaTumorTypesMatrix,
- "org.mskcc.cbio.importer.model.TCGATumorTypeMetadata");
- }
-
- public TCGATumorTypeMetadata getTCGATumorTypeMetadata(String oncotreeCode)
- {
- for (TCGATumorTypeMetadata md : getTCGATumorTypeMetadata()) {
- if (md.getOncoTreeCode().equals(oncotreeCode)) {
- return md;
- }
- }
- return null;
- }
-
- /**
- * Gets a TumorTypeMetadata object via tumorType.
- * If tumorType == Config.ALL, all are returned.
- *
- * @param tumortype String
- * @return TumorTypeMetadata
- */
- private String[] extractTumorTypeData(String dataCell) {
- String[] ret = new String[2];
- if (dataCell.contains("(") && dataCell.contains(")")) {
- String[] splitCell = dataCell.split("\\(");
- ret[0] = splitCell[0].trim();
- ret[1] = splitCell[1].split("\\)")[0];
- } else {
- // tissue
- ret[0] = dataCell;
- ret[1] = "";
- }
- return ret;
- }
-
- private TumorTypeMetadata parseTumorTypeMetadata(ArrayList line, int index, HashMap> propertyMap) {
- int newEntIndex = index;
- String newEnt = line.get(newEntIndex).trim();
- if (newEnt.isEmpty()) {
- return null;
- }
- String parentEnt = newEntIndex==0?"tissue":line.get(newEntIndex - 1).trim();
-
- String tissue = line.get(0);
- String color = propertyMap.get(tissue).get(HTML_COLOR_NAME_ONCOTREE_PROP);
- String[] newEntData = extractTumorTypeData(newEnt);
- String name = newEntData[0];
- String id = newEntData[1];
- if (id.isEmpty()) {
- id = name;
- }
- String[] parentEntData = extractTumorTypeData(parentEnt);
- String parent = parentEntData[1];
- if (parent.isEmpty()) {
- parent = parentEntData[0];
- }
- String clinicalTrialKeywords = name.toLowerCase();
- return new TumorTypeMetadata(id, name, color, parent, clinicalTrialKeywords, tissue);
- }
-
- @Override
- public Collection getTumorTypeMetadata(String tumorType) {
-
- Collection toReturn = new ArrayList();
-
- if (oncotreeMatrix == null) {
- oncotreeMatrix = getWorksheetData(gdataSpreadsheet, oncotreeWorksheet);
- }
- if (oncotreePropertyMatrix == null) {
- oncotreePropertyMatrix = getWorksheetData(gdataSpreadsheet, oncotreePropertyWorksheet);
- }
- HashMap> propertyMap = new HashMap<>();
- for (int i=1; i line = oncotreePropertyMatrix.get(i);
- String nodeName = line.get(0);
- String propertyName = line.get(1);
- String propertyValue = line.get(2);
- if (!propertyMap.containsKey(nodeName)) {
- propertyMap.put(nodeName, new HashMap());
- }
- propertyMap.get(nodeName).put(propertyName, propertyValue);
- }
-
- HashMap tumorTypes = new HashMap<>();
- int endOfData = 0;
- ArrayList line = oncotreeMatrix.get(0);
- for (; endOfData tumorTypeMetadatas = tumorTypes.values();
- // if user wants all, we're done
- if (tumorType.equals(Config.ALL)) {
- return tumorTypeMetadatas;
- }
-
- // iterate over all TumorTypeMetadata looking for match
- for (TumorTypeMetadata tumorTypeMetadata : tumorTypeMetadatas) {
- if (tumorTypeMetadata.getType().equals(tumorType)) {
- toReturn.add(tumorTypeMetadata);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Function to get datatypes to download as String[]
- *
- * @param dataSourcesMetadata DataSourcesMetadata
- * @return String[]
- * @throws Exception
- */
- @Override
- public String[] getDatatypesToDownload(DataSourcesMetadata dataSourcesMetadata) throws Exception {
-
- HashSet toReturn = new HashSet();
- for (DatatypeMetadata datatypeMetadata : getDatatypeMetadata(Config.ALL)) {
- if (datatypeMetadata.isDownloaded()) {
- Method downloadArchivesMethod = datatypeMetadata.getDownloadArchivesMethod(dataSourcesMetadata.getDataSource());
- toReturn.addAll((Set) downloadArchivesMethod.invoke(datatypeMetadata, null));
- }
- }
-
- // outta here
- return toReturn.toArray(new String[0]);
- }
-
- /**
- * Function to determine the datatype(s) of the datasource file (the file
- * that was fetched from a datasource).
- *
- * @param dataSourcesMetadata DataSourcesMetadata
- * @param filename String
- * @return Collection
- * @throws Exception
- */
- @Override
- public Collection getFileDatatype(DataSourcesMetadata dataSourcesMetadata, String filename) throws Exception {
-
- Collection toReturn = new ArrayList();
- for (DatatypeMetadata datatypeMetadata : getDatatypeMetadata(Config.ALL)) {
- Method downloadArchivesMethod = datatypeMetadata.getDownloadArchivesMethod(dataSourcesMetadata.getDataSource());
- for (String archive : (Set) downloadArchivesMethod.invoke(datatypeMetadata, null)) {
- if (filename.contains(archive)) {
- toReturn.add(datatypeMetadata);
- }
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets a DatatypeMetadata object for the given datatype name. If datatype
- * == Config.ALL, all are returned.
- *
- * @param datatype String
- * @return Collection
- */
- @Override
- public Collection getDatatypeMetadata(String datatype) {
-
- Collection toReturn = new ArrayList();
-
- if (LOG.isInfoEnabled()) {
- LOG.info("getDatatypeMetadata(): " + datatype);
- }
-
- if (datatypesMatrix == null) {
- datatypesMatrix = getWorksheetData(gdataSpreadsheet, datatypesWorksheet);
- }
-
- Collection datatypeMetadatas
- = (Collection) getMetadataCollection(datatypesMatrix,
- "org.mskcc.cbio.importer.model.DatatypeMetadata");
- // if user wants all, we're done
- if (datatype.equals(Config.ALL)) {
- return datatypeMetadatas;
- }
-
- for (DatatypeMetadata datatypeMetadata : datatypeMetadatas) {
- if (datatypeMetadata.getDatatype().equals(datatype)) {
- toReturn.add(datatypeMetadata);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets a collection of Datatype names for the given portal/cancer study.
- *
- * @param portalMetadata PortalMetadata
- * @param cancerStudyMetadata CancerStudyMetadata
- * @return Collection
- */
- @Override
- public Collection getDatatypeMetadata(PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata) {
-
- Collection toReturn = new ArrayList();
-
- if (LOG.isInfoEnabled()) {
- LOG.info("getDatatypeMetadata(): " + portalMetadata.getName() + ":" + cancerStudyMetadata.toString());
- }
-
- if (cancerStudiesMatrix == null) {
- cancerStudiesMatrix = getWorksheetData(gdataSpreadsheet, cancerStudiesWorksheet);
- }
-
- // get portal-column index in the cancer studies worksheet
- int portalColumnIndex = cancerStudiesMatrix.get(0).indexOf(portalMetadata.getName());
- if (portalColumnIndex == -1) {
- return toReturn;
- }
-
- // iterate over all studies in worksheet and find row whose first element is cancer study (path)
- for (ArrayList matrixRow : cancerStudiesMatrix) {
- if (matrixRow.get(0).equals(cancerStudyMetadata.getStudyPath())) {
- // the datatypes for the portal/cancer_study is the value of the cell
- String datatypesIndicator = matrixRow.get(portalColumnIndex);
- if (datatypesIndicator.equalsIgnoreCase(CancerStudyMetadata.CANCER_STUDY_IN_PORTAL_INDICATOR)) {
- // all datatypes are desired
- toReturn = getDatatypeMetadata(Config.ALL);
- } else {
- // a delimited list of datatypes have been requested
- toReturn = new ArrayList();
- for (String datatype : datatypesIndicator.split(DatatypeMetadata.DATATYPES_DELIMITER)) {
- Collection metaData = getDatatypeMetadata(datatype);
- if (!metaData.isEmpty()) {
- DatatypeMetadata datatypeMetadata = metaData.iterator().next();
- toReturn.add(datatypeMetadata);
- if (LOG.isInfoEnabled()) {
- LOG.info("Selecting data type" + datatypeMetadata.getDatatype());
- }
- }
- }
- }
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets a collection of CaseIDFilterMetadata.
- *
- * @param filterName String
- * @return Collection
- */
- @Override
- public Collection getCaseIDFilterMetadata(String filterName) {
-
- Collection toReturn = new ArrayList();
-
- if (caseIDFiltersMatrix == null) {
- caseIDFiltersMatrix = getWorksheetData(gdataSpreadsheet, caseIDFiltersWorksheet);
- }
-
- Collection caseIDFilterMetadatas
- = (Collection) getMetadataCollection(caseIDFiltersMatrix,
- "org.mskcc.cbio.importer.model.CaseIDFilterMetadata");
-
- // if user wants all, we're done
- if (filterName.equals(Config.ALL)) {
- return caseIDFilterMetadatas;
- }
-
- for (CaseIDFilterMetadata caseIDFilterMetadata : caseIDFilterMetadatas) {
- if (caseIDFilterMetadata.getFilterName().equals(filterName)) {
- toReturn.add(caseIDFilterMetadata);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets a collection of CaseListMetadata. If caseListFilename == Config.ALL,
- * all are returned.
- *
- * @param caseListFilename String
- * @return Collection
- */
- @Override
- public Collection getCaseListMetadata(String caseListFilename) {
-
- Collection toReturn = new ArrayList();
-
- if (caseListMatrix == null) {
- caseListMatrix = getWorksheetData(gdataSpreadsheet, caseListWorksheet);
- }
-
- Collection caseListMetadatas
- = (Collection) getMetadataCollection(caseListMatrix,
- "org.mskcc.cbio.importer.model.CaseListMetadata");
-
- // if user wants all, we're done
- if (caseListFilename.equals(Config.ALL)) {
- return caseListMetadatas;
- }
-
- for (CaseListMetadata caseListMetadata : caseListMetadatas) {
- if (caseListMetadata.getCaseListFilename().equals(caseListFilename)) {
- toReturn.add(caseListMetadata);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets a collection of ClinicalAttributesNamespace. If
- * clinicalAttributeNamespaceColumnHeader == Config.ALL, all are returned.
- *
- * @param clinicalAttributesNamespaceColumnHeader String
- * @return Collection
- */
- @Override
- public Collection getClinicalAttributesNamespace(String clinicalAttributesNamespaceColumnHeader) {
-
- Collection toReturn = new ArrayList();
-
- if (clinicalAttributesNamespaceMatrix == null) {
- clinicalAttributesNamespaceMatrix = getWorksheetData(gdataSpreadsheet, clinicalAttributesNamespaceWorksheet);
- }
-
- Collection clinicalAttributesNamespace
- = (Collection) getMetadataCollection(clinicalAttributesNamespaceMatrix,
- "org.mskcc.cbio.importer.model.ClinicalAttributesNamespace");
-
- // if user wants all, we're done
- if (clinicalAttributesNamespaceColumnHeader.equals(Config.ALL)) {
- return clinicalAttributesNamespace;
- }
-
- for (ClinicalAttributesNamespace clinicalAttributesNamespaceEntry : clinicalAttributesNamespace) {
- if (clinicalAttributesNamespaceEntry.getExternalColumnHeader().equals(clinicalAttributesNamespaceColumnHeader)) {
- toReturn.add(clinicalAttributesNamespaceEntry);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets a collection of ClinicalAttributesMetadata. If
- * clinicalAttributeColumnHeader == Config.ALL, all are returned.
- *
- * @param clinicalAttributesColumnHeader String
- * @return Collection
- */
- @Override
- public Collection getClinicalAttributesMetadata(String clinicalAttributesColumnHeader) {
-
- Collection toReturn = new ArrayList();
-
- if (clinicalAttributesMatrix == null) {
- clinicalAttributesMatrix = getWorksheetData(gdataSpreadsheet, clinicalAttributesWorksheet);
- }
-
- Collection clinicalAttributesMetadatas
- = (Collection) getMetadataCollection(clinicalAttributesMatrix,
- "org.mskcc.cbio.importer.model.ClinicalAttributesMetadata");
-
- // if user wants all, we're done
- if (clinicalAttributesColumnHeader.equals(Config.ALL)) {
- return clinicalAttributesMetadatas;
- }
-
- for (ClinicalAttributesMetadata clinicalAttributesMetadata : clinicalAttributesMetadatas) {
- if (clinicalAttributesMetadata.getNormalizedColumnHeader().equals(clinicalAttributesColumnHeader)) {
- toReturn.add(clinicalAttributesMetadata);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- @Override
- public Map getClinicalAttributesMetadata(Collection externalColumnHeaders) {
- Map toReturn = new HashMap();
-
- HashMap clinicalAttributesNamespace = makeClinicalAttributesNamespaceHashMap();
- for (String externalColumnHeader : externalColumnHeaders) {
- if (clinicalAttributesNamespace.containsKey(externalColumnHeader)) {
- ClinicalAttributesNamespace namespace = clinicalAttributesNamespace.get(externalColumnHeader);
- if (!namespace.getNormalizedColumnHeader().isEmpty()) {
- Collection metadata = getClinicalAttributesMetadata(namespace.getNormalizedColumnHeader());
- if (metadata.size() == 1) {
- toReturn.put(externalColumnHeader, metadata.iterator().next());
- }
- }
- }
- }
- return toReturn;
- }
-
- @Override
- public void importBCRClinicalAttributes(Collection bcrs) {
-
- HashMap clinicalAttributesNamespace = makeClinicalAttributesNamespaceHashMap();
-
- for (BCRDictEntry bcr : bcrs) {
- if (!clinicalAttributesNamespace.containsKey(bcr.id)) {
- updateWorksheet(gdataSpreadsheet, clinicalAttributesNamespaceWorksheet,
- true, null, null,
- ClinicalAttributesNamespace.getPropertiesMap(bcr,
- ClinicalAttributesNamespace.DATE_FORMAT.format(Calendar.getInstance().getTime())));
- }
- }
- }
-
- @Override
- public void flagMissingClinicalAttributes(String cancerStudy, String tumorType, Collection missingAttributeColumnHeaders) {
- BCRDictEntry bcr = new BCRDictEntry();
- HashMap clinicalAttributesNamespace = makeClinicalAttributesNamespaceHashMap();
-
- boolean updatedClinicalAttributes = false;
- for (String missingAttribute : missingAttributeColumnHeaders) {
- String[] parts = missingAttribute.split(ClinicalAttributesNamespace.CDE_DELIM);
- if (!clinicalAttributesNamespace.containsKey(parts[0])) {
- NCIcaDSREntry entry = (parts.length == 2 && parts[1].length() > 0)
- ? nciDSRFetcher.fetchDSREntry(parts[1]) : null;
- bcr.id = parts[0];
- bcr.displayName = (entry == null) ? "" : entry.preferredName;
- bcr.description = (entry == null) ? "" : entry.preferredDefinition;
- bcr.tumorType = tumorType;
- bcr.cancerStudy = cancerStudy;
- updateWorksheet(gdataSpreadsheet, clinicalAttributesNamespaceWorksheet,
- true, null, null,
- ClinicalAttributesNamespace.getPropertiesMap(bcr,
- ClinicalAttributesNamespace.DATE_FORMAT.format(Calendar.getInstance().getTime())));
- updatedClinicalAttributes = true;
- } else {
- ClinicalAttributesNamespace ns = clinicalAttributesNamespace.get(parts[0]);
- if (!ns.getCancerStudy().contains(cancerStudy)) {
- bcr.id = ns.getExternalColumnHeader();
- bcr.displayName = ns.getDisplayName();
- bcr.description = ns.getDescription();
- bcr.tumorType = (ns.getTumorType().contains(tumorType)) ? ns.getTumorType() : ns.getTumorType() + "," + tumorType;
- bcr.cancerStudy = ns.getCancerStudy() + "," + cancerStudy;
- updateWorksheet(gdataSpreadsheet, clinicalAttributesNamespaceWorksheet,
- false, ClinicalAttributesNamespace.WORKSHEET_UPDATE_COLUMN_KEY,
- ns.getExternalColumnHeader(),
- ClinicalAttributesNamespace.getPropertiesMap(bcr,
- ClinicalAttributesNamespace.DATE_FORMAT.format(Calendar.getInstance().getTime())));
- updatedClinicalAttributes = true;
- }
- }
- }
- if (updatedClinicalAttributes) {
- clinicalAttributesNamespaceMatrix = null;
- }
- }
-
- private HashMap makeClinicalAttributesNamespaceHashMap() {
- HashMap toReturn = new HashMap();
- for (ClinicalAttributesNamespace clinicalAttributeNamespace : getClinicalAttributesNamespace(Config.ALL)) {
- toReturn.put(clinicalAttributeNamespace.getExternalColumnHeader(), clinicalAttributeNamespace);
- }
-
- return toReturn;
- }
-
- /**
- * Gets a PortalMetadata object given a portal name.
- *
- * @param portalName String
- * @return Collection
- */
- @Override
- public Collection getPortalMetadata(String portalName) {
-
- Collection toReturn = new ArrayList();
-
- if (portalsMatrix == null) {
- portalsMatrix = getWorksheetData(gdataSpreadsheet, portalsWorksheet);
- }
-
- Collection portalMetadatas
- = (Collection) getMetadataCollection(portalsMatrix,
- "org.mskcc.cbio.importer.model.PortalMetadata");
-
- // if user wants all, we're done
- if (portalName.equals(Config.ALL)) {
- return portalMetadatas;
- }
-
- for (PortalMetadata portalMetadata : portalMetadatas) {
- if (portalMetadata.getName().equals(portalName)) {
- toReturn.add(portalMetadata);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets ReferenceMetadata for the given referenceType. If referenceType ==
- * Config.ALL, all are returned.
- *
- * @param referenceType String
- * @return Collection
- */
- @Override
- public Collection getReferenceMetadata(String referenceType) {
-
- Collection toReturn = new ArrayList();
-
- if (referenceMatrix == null) {
- referenceMatrix = getWorksheetData(gdataSpreadsheet, referenceDataWorksheet);
- }
-
- Collection referenceMetadatas
- = (Collection) getMetadataCollection(referenceMatrix,
- "org.mskcc.cbio.importer.model.ReferenceMetadata");
- // if user wants all, we're done
- if (referenceType.equals(Config.ALL)) {
- return referenceMetadatas;
- }
-
- // iterate over all ReferenceMetadata looking for match
- for (ReferenceMetadata referenceMetadata : referenceMetadatas) {
- if (referenceMetadata.getReferenceType().equals(referenceType)) {
- toReturn.add(referenceMetadata);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets DataSourcesMetadata for the given datasource. If dataSource ==
- * Config.ALL, all are returned.
- *
- * @param dataSource String
- * @return Collection
- */
- @Override
- public Collection getDataSourcesMetadata(String dataSource) {
-
- Collection toReturn = new ArrayList();
-
- if (dataSourcesMatrix == null) {
- dataSourcesMatrix = getWorksheetData(gdataSpreadsheet, dataSourcesWorksheet);
- }
-
- Collection dataSourceMetadatas
- = (Collection) getMetadataCollection(dataSourcesMatrix,
- "org.mskcc.cbio.importer.model.DataSourcesMetadata");
- // if user wants all, we're done
- if (dataSource.equals(Config.ALL)) {
- return dataSourceMetadatas;
- }
-
- // iterate over all DataSourcesMetadata looking for match
- for (DataSourcesMetadata dataSourceMetadata : dataSourceMetadatas) {
- if (dataSourceMetadata.getDataSource().equals(dataSource)) {
- toReturn.add(dataSourceMetadata);
- break;
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets all the cancer studies for a given portal.
- *
- * @param portalName String
- * @return Collection
- */
- @Override
- public Collection getCancerStudyMetadata(String portalName) {
-
- Collection toReturn = new ArrayList();
-
- if (cancerStudiesMatrix == null) {
- cancerStudiesMatrix = getWorksheetData(gdataSpreadsheet, cancerStudiesWorksheet);
- }
-
- // get portal-column index in the cancer studies worksheet
- int portalColumnIndex = cancerStudiesMatrix.get(0).indexOf(portalName);
- if (portalColumnIndex == -1) {
- return toReturn;
- }
-
- // iterate over all studies in worksheet and determine if
- // the value at the row and portal/column intersection is not empty
- // (we start at one, because row 0 is the column headers)
- for (int lc = 1; lc < cancerStudiesMatrix.size(); lc++) {
- ArrayList matrixRow = cancerStudiesMatrix.get(lc);
- String datatypesIndicator = matrixRow.get(portalColumnIndex);
- if (datatypesIndicator != null && datatypesIndicator.length() > 0) {
- CancerStudyMetadata cancerStudyMetadata
- = new CancerStudyMetadata(matrixRow.toArray(new String[0]));
- // get tumor type metadata
- Collection tumorTypeCollection = getTumorTypeMetadata(cancerStudyMetadata.getTumorType());
- if (!tumorTypeCollection.isEmpty()) {
- cancerStudyMetadata.setTumorTypeMetadata(tumorTypeCollection.iterator().next());
- }
- // add to return set
- toReturn.add(cancerStudyMetadata);
- }
- }
-
- // outta here
- return toReturn;
- }
-
- /**
- * Gets a CancerStudyMetadata for the given cancer study.
- *
- * @param cancerStudyName String - fully qualified path as entered on worksheet,
- * e.g.: prad/mskcc/foundation
- * @return CancerStudyMetadata or null if not found
- */
- @Override
- public CancerStudyMetadata getCancerStudyMetadataByName(String cancerStudyName) {
-
- Collection cancerStudyMetadatas = getAllCancerStudyMetadata();
-
- for (CancerStudyMetadata cancerStudyMetadata : cancerStudyMetadatas) {
- if (cancerStudyMetadata.getStudyPath().equals(cancerStudyName)) {
- // get tumor type metadata
- Collection tumorTypeCollection = getTumorTypeMetadata(cancerStudyMetadata.getTumorType());
- if (!tumorTypeCollection.isEmpty()) {
- cancerStudyMetadata.setTumorTypeMetadata(tumorTypeCollection.iterator().next());
- }
- return cancerStudyMetadata;
- }
- }
-
- return null;
- }
-
- @Override
- public Collection getAllCancerStudyMetadata()
- {
- if (cancerStudiesMatrix == null) {
- cancerStudiesMatrix = getWorksheetData(gdataSpreadsheet, cancerStudiesWorksheet);
- }
-
- Collection cancerStudyMetadatas
- = (Collection) getMetadataCollection(cancerStudiesMatrix,
- "org.mskcc.cbio.importer.model.CancerStudyMetadata");
-
- return cancerStudyMetadatas;
- }
-
- /*
- return a Collection of IcgcMetadata objects derived from
- the ICGC worksheet on the google spreadsheet
- */
- @Override
- public Collection getIcgcMetadata() {
- if (icgcMatrix == null) {
- icgcMatrix = getWorksheetData(gdataSpreadsheet, icgcWorksheet);
- }
-
-
- Collection
