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Adding beta version of a tool for searching the patient molecular
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Apr 10, 2023
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| package edu.utah.seq.pmr; | ||
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| import java.io.File; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.Iterator; | ||
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| import org.json.JSONArray; | ||
| import org.json.JSONObject; | ||
| import util.gen.IO; | ||
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| public class AvatarClinicalInfo { | ||
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| private HashMap<String, String> patient = new HashMap<String, String>(); | ||
| private HashMap<String, String> root = new HashMap<String, String>(); | ||
| private HashMap<String, String> tumorDna = new HashMap<String, String>(); | ||
| private HashMap<String, String> tumorRna = new HashMap<String, String>(); | ||
| private ArrayList<HashMap<String, String>> normalDna = new ArrayList<HashMap<String, String>>(); | ||
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| public static final String TUMOR_DNA_NAME = "TumorDNA"; | ||
| public static final String TUMOR_RNA_NAME = "TumorRNA"; | ||
| public static final String NORMAL_DNA_NAME = "NormalDNA"; | ||
| public static final String PATIENT_NAME = "Patient"; | ||
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| public AvatarClinicalInfo (File json) { | ||
| String jString = IO.loadFile(json, " ", true); | ||
| JSONObject mainJsonObject = new JSONObject(jString); | ||
| Iterator it = mainJsonObject.keys(); | ||
| while (it.hasNext()) { | ||
| String key = (String)it.next(); | ||
| if (key.equals(PATIENT_NAME)) loadHashMap(patient, mainJsonObject.getJSONObject(key)); | ||
| else if (key.equals(TUMOR_DNA_NAME)) loadHashMap(tumorDna, mainJsonObject.getJSONObject(key)); | ||
| else if (key.equals(TUMOR_RNA_NAME)) loadHashMap(tumorRna, mainJsonObject.getJSONObject(key)); | ||
| else if (key.equals(NORMAL_DNA_NAME)) { | ||
| JSONArray allNorm = mainJsonObject.getJSONArray(key); | ||
| int num = allNorm.length(); | ||
| for (int i=0; i< num; i++) { | ||
| JSONObject no = allNorm.getJSONObject(i); | ||
| HashMap<String, String> normal = new HashMap<String, String>(); | ||
| loadHashMap(normal, no); | ||
| normalDna.add(normal); | ||
| } | ||
| } | ||
| else { | ||
| root.put(key, mainJsonObject.get(key).toString()); | ||
| } | ||
| } | ||
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| } | ||
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| public String toString() { | ||
| StringBuilder sb = new StringBuilder(); | ||
| sb.append("Patient:\t"+ patient+"\n"); | ||
| sb.append("Root:\t"+ root+"\n"); | ||
| sb.append("TumorDNA:\t"+ tumorDna+"\n"); | ||
| sb.append("TumorRNA:\t"+ tumorRna+"\n"); | ||
| for (HashMap<String, String> n: normalDna) { | ||
| sb.append("NormalDNA:\t"+ n+"\n"); | ||
| } | ||
| return sb.toString(); | ||
| } | ||
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| private void loadHashMap(HashMap<String, String> hm, JSONObject j) { | ||
| Iterator it = j.keys(); | ||
| while (it.hasNext()) { | ||
| String key = (String)it.next(); | ||
| hm.put(key, j.getString(key)); | ||
| } | ||
| } | ||
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| public HashMap<String, String> getPatient() { | ||
| return patient; | ||
| } | ||
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| public HashMap<String, String> getRoot() { | ||
| return root; | ||
| } | ||
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| public HashMap<String, String> getTumorDna() { | ||
| return tumorDna; | ||
| } | ||
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| public HashMap<String, String> getTumorRna() { | ||
| return tumorRna; | ||
| } | ||
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| public ArrayList<HashMap<String, String>> getNormalDna() { | ||
| return normalDna; | ||
| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| package edu.utah.seq.pmr; | ||
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| import java.io.File; | ||
| import java.util.ArrayList; | ||
| import java.util.LinkedHashMap; | ||
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| import edu.utah.seq.vcf.json.TempusJsonSummary; | ||
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| public class Dataset { | ||
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| private String source; //Avatar, Tempus, Caris | ||
| private String datasetId; //A032049_SL419345_SL419548_SL420681, TL-20-B70ACE, TN21-123058_2022-01-27 | ||
| private ArrayList<String> partialPaths = new ArrayList<String>(); | ||
| private ArrayList<File> clinicalInfoFiles = null; | ||
| private AvatarClinicalInfo avatarClinicalInfo = null; //only for Avatar datasets | ||
| private TempusJsonSummary tempusJsonReportInfo = null; //only for Tempus datasets | ||
| private LinkedHashMap<String, String> carisClinicalInfo = null; //only for Caris datasets | ||
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| public Dataset(String source, String datasetId) { | ||
| this.source = source; | ||
| this.datasetId = datasetId; | ||
| } | ||
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| public String getSource() { | ||
| return source; | ||
| } | ||
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| public String getDatasetId() { | ||
| return datasetId; | ||
| } | ||
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| public ArrayList<String> getPartialPaths() { | ||
| return partialPaths; | ||
| } | ||
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| public ArrayList<File> getClinicalInfoFiles() { | ||
| return clinicalInfoFiles; | ||
| } | ||
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| public void setClinicalInfoFile(File clinicalInfo) { | ||
| if (clinicalInfoFiles == null) clinicalInfoFiles = new ArrayList<File>(); | ||
| clinicalInfoFiles.add(clinicalInfo); | ||
| } | ||
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| public AvatarClinicalInfo getAvatarClinicalInfo() { | ||
| return avatarClinicalInfo; | ||
| } | ||
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| public void setAvatarClinicalInfo(AvatarClinicalInfo avatarClinicalInfo) { | ||
| this.avatarClinicalInfo = avatarClinicalInfo; | ||
| } | ||
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| public TempusJsonSummary getTempusJsonReportInfo() { | ||
| return tempusJsonReportInfo; | ||
| } | ||
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| public void setTempusJsonReportInfo(TempusJsonSummary tempusJsonReportInfo) { | ||
| this.tempusJsonReportInfo = tempusJsonReportInfo; | ||
| } | ||
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| public void setCarisXmlReportInfo(LinkedHashMap<String, String> linkedHashMap) { | ||
| carisClinicalInfo = linkedHashMap; | ||
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| } | ||
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| public LinkedHashMap<String, String> getCarisClinicalInfo() { | ||
| return carisClinicalInfo; | ||
| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| package edu.utah.seq.pmr; | ||
| import java.util.HashMap; | ||
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| public class Patient { | ||
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| //fields | ||
| private String coreId = null; | ||
| private HashMap<String, Dataset> idDataSets = new HashMap<String, Dataset>(); | ||
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| public Patient(String coreId) { | ||
| this.coreId = coreId; | ||
| } | ||
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| public void addDataFile(String[] keys) { | ||
| //Patients AA2mF6Vy Avatar A032049_SL419345_SL419548_SL420681 ClinicalReport A032049_SL419345_SL419548_SL420681_IDTv1_SAR_F.json | ||
| // 0 1 2 3 4 5+ | ||
| String source = keys[2]; | ||
| String datasetId = keys[3]; | ||
| Dataset d = idDataSets.get(datasetId); | ||
| if (d == null) { | ||
| d = new Dataset(source, datasetId); | ||
| idDataSets.put(datasetId, d); | ||
| } | ||
| StringBuilder sb = new StringBuilder(keys[4]); | ||
| for (int i=5; i< keys.length; i++) { | ||
| sb.append("/"); | ||
| sb.append(keys[i]); | ||
| } | ||
| d.getPartialPaths().add(sb.toString()); | ||
| } | ||
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| public String getCoreId() { | ||
| return coreId; | ||
| } | ||
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| public HashMap<String, Dataset> getIdDataSets() { | ||
| return idDataSets; | ||
| } | ||
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| } |
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