Java tutorial
/* * OpenClinica is distributed under the * GNU Lesser General Public License (GNU LGPL). * For details see: http://www.openclinica.org/license * copyright 2003-2005 Akaza Research */ package org.akaza.openclinica.dao.managestudy; import java.sql.Types; import java.util.ArrayList; import java.util.Collection; import java.util.Date; import java.util.HashMap; import java.util.Iterator; import java.util.Locale; import javax.sql.DataSource; /** * <P> * StudyDAO.java, the data access object that users will access the database for * study objects, tbh. * * @author thickerson * * */ import org.akaza.openclinica.bean.core.EntityBean; import org.akaza.openclinica.bean.core.Status; import org.akaza.openclinica.bean.managestudy.StudyBean; import org.akaza.openclinica.bean.managestudy.StudyType; import org.akaza.openclinica.dao.core.AuditableEntityDAO; import org.akaza.openclinica.dao.core.CoreResources; import org.akaza.openclinica.dao.core.DAODigester; import org.akaza.openclinica.dao.core.SQLFactory; import org.akaza.openclinica.dao.core.TypeNames; import org.akaza.openclinica.domain.datamap.StudyEnvEnum; import org.apache.commons.lang.StringUtils; public class StudyDAO<K extends String, V extends ArrayList> extends AuditableEntityDAO { // private DataSource ds; // private DAODigester digester; public StudyDAO(DataSource ds) { super(ds); } public StudyDAO(DataSource ds, DAODigester digester) { super(ds); this.digester = digester; } // This constructor sets up the Locale for JUnit tests; see the locale // member variable in EntityDAO, and its initializeI18nStrings() method public StudyDAO(DataSource ds, DAODigester digester, Locale locale) { this(ds, digester); this.locale = locale; } @Override protected void setDigesterName() { digesterName = SQLFactory.getInstance().DAO_STUDY; } @Override public void setTypesExpected() { this.unsetTypeExpected(); this.setTypeExpected(1, TypeNames.INT);// sid this.setTypeExpected(2, TypeNames.INT);// parent id this.setTypeExpected(3, TypeNames.STRING);// ident this.setTypeExpected(4, TypeNames.STRING);// second ident this.setTypeExpected(5, TypeNames.STRING);// name this.setTypeExpected(6, TypeNames.STRING);// summary this.setTypeExpected(7, TypeNames.DATE);// start this.setTypeExpected(8, TypeNames.DATE);// end this.setTypeExpected(9, TypeNames.DATE);// create this.setTypeExpected(10, TypeNames.DATE);// update this.setTypeExpected(11, TypeNames.INT);// owner this.setTypeExpected(12, TypeNames.INT);// updater this.setTypeExpected(13, TypeNames.INT);// type id this.setTypeExpected(14, TypeNames.INT);// status this.setTypeExpected(15, TypeNames.STRING);// pi this.setTypeExpected(16, TypeNames.STRING);// fname this.setTypeExpected(17, TypeNames.STRING);// fcity this.setTypeExpected(18, TypeNames.STRING);// fstate this.setTypeExpected(19, TypeNames.STRING);// fzip this.setTypeExpected(20, TypeNames.STRING);// country this.setTypeExpected(21, TypeNames.STRING);// frs this.setTypeExpected(22, TypeNames.STRING);// fcn this.setTypeExpected(23, TypeNames.STRING);// fcdegree this.setTypeExpected(24, TypeNames.STRING);// fcphone this.setTypeExpected(25, TypeNames.STRING);// fcemail this.setTypeExpected(26, TypeNames.STRING);// prottype this.setTypeExpected(27, TypeNames.STRING);// protdesc this.setTypeExpected(28, TypeNames.DATE);// pdateverif this.setTypeExpected(29, TypeNames.STRING);// phase this.setTypeExpected(30, TypeNames.INT);// expectotenroll this.setTypeExpected(31, TypeNames.STRING);// sponsor this.setTypeExpected(32, TypeNames.STRING);// collab this.setTypeExpected(33, TypeNames.STRING);// medline this.setTypeExpected(34, TypeNames.STRING);// url this.setTypeExpected(35, TypeNames.STRING);// url-desc this.setTypeExpected(36, TypeNames.STRING);// conds this.setTypeExpected(37, TypeNames.STRING);// keyw this.setTypeExpected(38, TypeNames.STRING);// eligible this.setTypeExpected(39, TypeNames.STRING);// gender, no char avail. this.setTypeExpected(40, TypeNames.STRING);// agemax this.setTypeExpected(41, TypeNames.STRING);// agemin this.setTypeExpected(42, TypeNames.BOOL);// healthy volunteer this.setTypeExpected(43, TypeNames.STRING);// purpose this.setTypeExpected(44, TypeNames.STRING);// allocation this.setTypeExpected(45, TypeNames.STRING);// masking this.setTypeExpected(46, TypeNames.STRING);// control this.setTypeExpected(47, TypeNames.STRING);// assignment this.setTypeExpected(48, TypeNames.STRING);// endpoint this.setTypeExpected(49, TypeNames.STRING);// interv this.setTypeExpected(50, TypeNames.STRING);// duration this.setTypeExpected(51, TypeNames.STRING);// selection this.setTypeExpected(52, TypeNames.STRING);// timing this.setTypeExpected(53, TypeNames.STRING);// official_title this.setTypeExpected(54, TypeNames.BOOL);// results_reference this.setTypeExpected(55, TypeNames.STRING);// oc oid this.setTypeExpected(56, TypeNames.INT); this.setTypeExpected(57, TypeNames.STRING);// schema name this.setTypeExpected(58, TypeNames.STRING);// studyEnvSiteUuid this.setTypeExpected(59, TypeNames.STRING);// env type this.setTypeExpected(60, TypeNames.STRING);// study env uuid this.setTypeExpected(61, TypeNames.BOOL);// published this.setTypeExpected(62, TypeNames.INT);// file path } /** * <b>update </b>, the method that returns an updated study bean after it * updates the database. Note that we can use the three stages from our * creation use case. * * @return sb an updated study bean. */ public EntityBean update(EntityBean eb) { StudyBean sb = (StudyBean) eb; sb = this.updateStepOne(sb); sb = this.createStepTwo(sb); sb = this.createStepThree(sb); sb = this.createStepFour(sb); return sb; } /** * <P> * updateStepOne, the update method for the database. This method takes the * place of createStepOne, since it runs an update and assumes you already * have a primary key in the study bean object. * * @param sb * the study bean which will be updated. * @return sb the study bean after it is updated with this phase. */ public StudyBean updateStepOne(StudyBean sb) { HashMap variables = new HashMap(); HashMap nullVars = new HashMap(); if (sb.getParentStudyId() == 0) { nullVars.put(new Integer(1), new Integer(Types.INTEGER)); variables.put(new Integer(1), null); } else { variables.put(new Integer(1), new Integer(sb.getParentStudyId())); } variables.put(new Integer(2), sb.getName()); variables.put(new Integer(3), sb.getOfficialTitle()); variables.put(new Integer(4), sb.getIdentifier()); variables.put(new Integer(5), sb.getSecondaryIdentifier()); variables.put(new Integer(6), sb.getSummary()); variables.put(new Integer(7), sb.getPrincipalInvestigator()); if (sb.getDatePlannedStart() == null) { nullVars.put(new Integer(8), new Integer(Types.DATE)); variables.put(new Integer(8), null); } else { variables.put(new Integer(8), sb.getDatePlannedStart()); } if (sb.getDatePlannedEnd() == null) { nullVars.put(new Integer(9), new Integer(Types.DATE)); variables.put(new Integer(9), null); } else { variables.put(new Integer(9), sb.getDatePlannedEnd()); } variables.put(new Integer(10), sb.getFacilityName()); variables.put(new Integer(11), sb.getFacilityCity()); variables.put(new Integer(12), sb.getFacilityState()); variables.put(new Integer(13), sb.getFacilityZip()); variables.put(new Integer(14), sb.getFacilityCountry()); variables.put(new Integer(15), sb.getFacilityRecruitmentStatus()); variables.put(new Integer(16), sb.getFacilityContactName()); variables.put(new Integer(17), sb.getFacilityContactDegree()); variables.put(new Integer(18), sb.getFacilityContactPhone()); variables.put(new Integer(19), sb.getFacilityContactEmail()); variables.put(new Integer(20), new Integer(sb.getStatus().getId()));// status // id // variables.put(new Integer(19), sb.getStatus())//need to get a // function // to get the id // variables.put(new Integer(19), sb.getCreatedDate()); variables.put(new Integer(21), new Integer(sb.getUpdaterId()));// owner // id if (sb.getUpdatedDate() == null) { nullVars.put(new Integer(22), new Integer(Types.DATE)); variables.put(new Integer(22), null); } else { variables.put(new Integer(22), sb.getUpdatedDate()); } variables.put(new Integer(23), new Integer(sb.getOldStatus().getId()));// study id // variables.put(new Integer(22), new Integer(1)); // stop gap measure for owner and updater id variables.put(new Integer(24), new Integer(sb.getId()));// study id this.execute(digester.getQuery("updateStepOne"), variables, nullVars); return sb; } /** * <b>create </b>, the method that creates a study in the database. * <P> * note: create is split up into four custom functions, per the use case; we * are creating the standard create function here which calls all four * functions at once, but the seperate functions may be required in the * control servlets. * * @return eb the created entity bean. */ public EntityBean create(EntityBean eb) { StudyBean sb = (StudyBean) eb; sb = this.createStepOne(sb); // in the above step, we will have created a primary key, // and in the next steps, we update the study bean // in phases sb = this.createStepTwo(sb); sb = this.createStepThree(sb); sb = this.createStepFour(sb); return sb; } /** * <P> * findNextKey, a method to return a simple int from the database. * * @return int, which is the next primary key for creating a study. */ public int findNextKey() { this.unsetTypeExpected(); Integer keyInt = new Integer(0); this.setTypeExpected(1, TypeNames.INT); ArrayList alist = this.select(digester.getQuery("findNextKey")); Iterator it = alist.iterator(); if (it.hasNext()) { HashMap key = (HashMap) it.next(); keyInt = (Integer) key.get("key"); } return keyInt.intValue(); } /** * <P> * createStepOne, per the 'Detailed use case for administer system document * v1.0rc1' document. We insert the study in this method, and then update * the same study in the next three steps. * <P> * The next three steps, by the way, can then be used to update studies as * well. * * @param sb * Study bean about to be created. * @return same study bean with a primary key in the ID field. */ public StudyBean createStepOne(StudyBean sb) { HashMap variables = new HashMap(); HashMap nullVars = new HashMap(); sb.setId(this.findNextKey()); variables.put(new Integer(1), new Integer(sb.getId())); if (sb.getParentStudyId() == 0) { nullVars.put(new Integer(2), new Integer(Types.INTEGER)); variables.put(new Integer(2), null); } else { variables.put(new Integer(2), new Integer(sb.getParentStudyId())); } variables.put(new Integer(3), sb.getName()); variables.put(new Integer(4), sb.getOfficialTitle()); variables.put(new Integer(5), sb.getIdentifier()); variables.put(new Integer(6), sb.getSecondaryIdentifier()); variables.put(new Integer(7), sb.getSummary()); variables.put(new Integer(8), sb.getPrincipalInvestigator()); if (sb.getDatePlannedStart() == null) { nullVars.put(new Integer(9), new Integer(Types.DATE)); variables.put(new Integer(9), null); } else { variables.put(new Integer(9), sb.getDatePlannedStart()); } if (sb.getDatePlannedEnd() == null) { nullVars.put(new Integer(10), new Integer(Types.DATE)); variables.put(new Integer(10), null); } else { variables.put(new Integer(10), sb.getDatePlannedEnd()); } variables.put(new Integer(11), sb.getFacilityName()); variables.put(new Integer(12), sb.getFacilityCity()); variables.put(new Integer(13), sb.getFacilityState()); variables.put(new Integer(14), sb.getFacilityZip()); variables.put(new Integer(15), sb.getFacilityCountry()); variables.put(new Integer(16), sb.getFacilityRecruitmentStatusKey()); variables.put(new Integer(17), sb.getFacilityContactName()); variables.put(new Integer(18), sb.getFacilityContactDegree()); variables.put(new Integer(19), sb.getFacilityContactPhone()); variables.put(new Integer(20), sb.getFacilityContactEmail()); variables.put(new Integer(21), new Integer(sb.getStatus().getId())); // variables.put(new Integer(19), sb.getStatus())//need to get a // function // to get the id variables.put(new Integer(22), new java.util.Date()); variables.put(new Integer(23), new Integer(sb.getOwnerId())); variables.put(new Integer(24), getValidOid(sb)); variables.put(new Integer(25), sb.getEnvType().toString()); // replace this with the owner id this.execute(digester.getQuery("createStepOne"), variables, nullVars); return sb; } // we are generating and creating the valid oid at step one, tbh private String getOid(StudyBean sb) { String oid; try { oid = sb.getOid() != null ? sb.getOid() : sb.getOidGenerator().generateOid(sb.getIdentifier()); return oid; } catch (Exception e) { throw new RuntimeException("CANNOT GENERATE OID"); } } private String getValidOid(StudyBean sb) { String oid = getOid(sb); logger.info("*** " + oid); String oidPreRandomization = oid; while (findByOid(oid) != null) { oid = sb.getOidGenerator().randomizeOid(oidPreRandomization); } logger.info("returning the following oid: " + oid); return oid; } public StudyBean findByOid(String oid) { StudyBean sb = null; this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), oid); ArrayList alist = this.select(digester.getQuery("findByOid"), variables); Iterator it = alist.iterator(); if (it.hasNext()) { sb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); return sb; } else { logger.info("returning null from find by oid..."); return null; } } public StudyBean findByPublicOid(String oid) { StudyBean sb = null; this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), oid); ArrayList alist = this.select(digester.getQuery("findByPublicOid"), variables); Iterator it = alist.iterator(); if (it.hasNext()) { sb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); return sb; } else { logger.info("returning null from find by oid..."); return null; } } public StudyBean findByPublicPK(int id) { StudyBean sb = null; this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), id); ArrayList alist = this.select(digester.getQuery("findByPublicPK"), variables); Iterator it = alist.iterator(); if (it.hasNext()) { sb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); return sb; } else { logger.info("returning null from find by oid..."); return null; } } public StudyBean findByUniqueIdentifier(String oid) { StudyBean sb = null; this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), oid); ArrayList alist = this.select(digester.getQuery("findByUniqueIdentifier"), variables); Iterator it = alist.iterator(); if (it.hasNext()) { sb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); return sb; } else { logger.info("returning null from find by Unique Identifier..."); return null; } } public StudyBean findByStudyEnvUuid(String uuid) { StudyBean sb = null; this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), uuid); variables.put(new Integer(2), uuid); ArrayList alist = this.select(digester.getQuery("findByStudyEnvUuid"), variables); Iterator it = alist.iterator(); if (it.hasNext()) { sb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); return sb; } else { logger.info("returning null from find by Study Env Uuid..."); return null; } } public StudyBean findSiteByUniqueIdentifier(String parentUniqueIdentifier, String siteUniqueIdentifier) { StudyBean sb = null; this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), parentUniqueIdentifier); variables.put(new Integer(2), siteUniqueIdentifier); ArrayList alist = this.select(digester.getQuery("findSiteByUniqueIdentifier"), variables); Iterator it = alist.iterator(); if (it.hasNext()) { sb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); return sb; } else { logger.info("returning null from find by Unique Identifier..."); return null; } } public StudyBean createStepTwo(StudyBean sb) { // UPDATE STUDY SET TYPE_ID=?, PROTOCOL_TYPE=?,PROTOCOL_DESCRIPTION=?, // PROTOCOL_DATE_VERIFICATION=?, PHASE=?, EXPECTED_TOTAL_ENROLLMENT=?, // SPONSOR=?, COLLABORATORS=?, MEDLINE_IDENTIFIER=?, URL=?, // URL_DESCRIPTION=?, CONDITIONS=?, KEYWORDS=?, ELIGIBILITY=?, // GENDER=?, AGE_MAX=?, AGE_MIN=?, HEALTHY_VOLUNTEER_ACCEPTED=? // WHERE STUDY_ID=? HashMap variables = new HashMap(); HashMap nullVars = new HashMap(); variables.put(new Integer(1), new Integer(sb.getType().getId())); variables.put(new Integer(2), sb.getProtocolTypeKey()); variables.put(new Integer(3), sb.getProtocolDescription()); if (sb.getProtocolDateVerification() == null) { nullVars.put(new Integer(4), new Integer(Types.DATE)); variables.put(new Integer(4), null); } else { variables.put(new Integer(4), sb.getProtocolDateVerification()); } variables.put(new Integer(5), sb.getPhaseKey()); variables.put(new Integer(6), new Integer(sb.getExpectedTotalEnrollment())); variables.put(new Integer(7), sb.getSponsor()); variables.put(new Integer(8), sb.getCollaborators()); variables.put(new Integer(9), sb.getMedlineIdentifier()); variables.put(new Integer(10), new Boolean(sb.isResultsReference())); variables.put(new Integer(11), sb.getUrl()); variables.put(new Integer(12), sb.getUrlDescription()); variables.put(new Integer(13), sb.getConditions()); variables.put(new Integer(14), sb.getKeywords()); variables.put(new Integer(15), sb.getEligibility()); variables.put(new Integer(16), sb.getGenderKey()); variables.put(new Integer(17), sb.getAgeMax()); variables.put(new Integer(18), sb.getAgeMin()); variables.put(new Integer(19), new Boolean(sb.getHealthyVolunteerAccepted())); variables.put(new Integer(20), sb.getSchemaName()); if (sb.getStudyEnvUuid() == null) { nullVars.put(new Integer(21), new Integer(TypeNames.STRING)); variables.put(new Integer(21), null); } else { variables.put(new Integer(21), sb.getStudyEnvUuid()); } variables.put(new Integer(22), sb.getStudyEnvSiteUuid()); variables.put(new Integer(23), sb.isPublished()); variables.put(new Integer(24), sb.getFilePath()); variables.put(new Integer(25), new Integer(sb.getId())); this.execute(digester.getQuery("createStepTwo"), variables, nullVars); return sb; } public StudyBean createStepThree(StudyBean sb) { HashMap variables = new HashMap(); variables.put(new Integer(1), sb.getPurposeKey()); variables.put(new Integer(2), sb.getAllocationKey()); variables.put(new Integer(3), sb.getMaskingKey()); variables.put(new Integer(4), sb.getControlKey()); variables.put(new Integer(5), sb.getAssignmentKey()); variables.put(new Integer(6), sb.getEndpointKey()); variables.put(new Integer(7), sb.getInterventionsKey()); variables.put(new Integer(8), new Integer(sb.getId())); this.execute(digester.getQuery("createStepThree"), variables); return sb; } public StudyBean createStepFour(StudyBean sb) { HashMap variables = new HashMap(); variables.put(new Integer(1), sb.getDurationKey()); variables.put(new Integer(2), sb.getSelectionKey()); variables.put(new Integer(3), sb.getTimingKey()); variables.put(new Integer(4), new Integer(sb.getId())); this.execute(digester.getQuery("createStepFour"), variables); return sb; } /* * public HashMap fillVariables(StudyBean sb) { HashMap variables = new * HashMap(); variables.put(new Integer(1),new * Integer(sb.getParentStudyId())); variables.put(new * Integer(2),sb.getLabel()); return variables; } */ /** * <p> * getEntityFromHashMap, the method that gets the object from the database * query. */ public Object getEntityFromHashMap(HashMap hm) { StudyBean eb = new StudyBean(); // first set all the strings eb.setIdentifier((String) hm.get("unique_identifier")); eb.setName((String) hm.get("name")); eb.setSummary((String) hm.get("summary")); eb.setSecondaryIdentifier((String) hm.get("secondary_identifier")); eb.setPrincipalInvestigator((String) hm.get("principal_investigator")); eb.setFacilityName((String) hm.get("facility_name")); eb.setFacilityCity((String) hm.get("facility_city")); eb.setFacilityState((String) hm.get("facility_state")); eb.setFacilityZip((String) hm.get("facility_zip")); eb.setFacilityCountry((String) hm.get("facility_country")); eb.setFacilityRecruitmentStatus((String) hm.get("facility_recruitment_status")); eb.setFacilityContactName((String) hm.get("facility_contact_name")); eb.setFacilityContactDegree((String) hm.get("facility_contact_degree")); eb.setFacilityContactPhone((String) hm.get("facility_contact_phone")); eb.setFacilityContactEmail((String) hm.get("facility_contact_email")); eb.setProtocolType((String) hm.get("protocol_type")); eb.setProtocolDescription((String) hm.get("protocol_description")); eb.setPhase((String) hm.get("phase")); eb.setSponsor((String) hm.get("sponsor")); eb.setCollaborators((String) hm.get("collaborators")); eb.setMedlineIdentifier((String) hm.get("medline_identifier")); eb.setUrl((String) hm.get("url")); eb.setUrlDescription((String) hm.get("url_description")); eb.setConditions((String) hm.get("conditions")); eb.setKeywords((String) hm.get("keywords")); eb.setEligibility((String) hm.get("eligibility")); String gender = (String) hm.get("gender"); // char[] genderarr = gender.toCharArray(); // Character gender = (Character)hm.get("gender"); // eb.setGender(gender.charValue());//CHAR? eb.setGender(gender); // throws null pointer exception? eb.setAgeMax((String) hm.get("age_max")); eb.setAgeMin((String) hm.get("age_min")); eb.setPurpose((String) hm.get("purpose")); eb.setAllocation((String) hm.get("allocation")); eb.setMasking((String) hm.get("masking")); eb.setControl((String) hm.get("control")); eb.setAssignment((String) hm.get("assignment")); eb.setEndpoint((String) hm.get("endpoint")); eb.setInterventions((String) hm.get("interventions")); eb.setDuration((String) hm.get("duration")); eb.setSelection((String) hm.get("selection")); eb.setTiming((String) hm.get("timing")); eb.setOfficialTitle((String) hm.get("official_title")); eb.setHealthyVolunteerAccepted(((Boolean) hm.get("healthy_volunteer_accepted")).booleanValue()); eb.setResultsReference(((Boolean) hm.get("results_reference")).booleanValue()); // eb.setUsingDOB(((Boolean)hm.get("collect_dob")).booleanValue()); // eb.setDiscrepancyManagement(((Boolean)hm.get("discrepancy_management") // ).booleanValue()); // next set all the ints/dates Integer studyId = (Integer) hm.get("study_id"); eb.setId(studyId.intValue()); Integer parentStudyId = (Integer) hm.get("parent_study_id"); if (parentStudyId == null) { eb.setParentStudyId(0); } else { eb.setParentStudyId(parentStudyId.intValue()); } Integer ownerId = (Integer) hm.get("owner_id"); eb.setOwnerId(ownerId.intValue()); Integer updateId = (Integer) hm.get("update_id"); eb.setUpdaterId(updateId.intValue()); Integer typeId = (Integer) hm.get("type_id"); eb.setType(StudyType.get(typeId.intValue())); Integer statusId = (Integer) hm.get("status_id"); eb.setStatus(Status.get(statusId.intValue())); Integer expecTotalEnrollment = (Integer) hm.get("expected_total_enrollment"); eb.setExpectedTotalEnrollment(expecTotalEnrollment.intValue()); Date dateCreated = (Date) hm.get("date_created"); Date dateUpdated = (Date) hm.get("date_updated"); Date datePlannedStart = (Date) hm.get("date_planned_start"); Date datePlannedEnd = (Date) hm.get("date_planned_end"); Date dateProtocolVerification = (Date) hm.get("protocol_date_verification"); eb.setCreatedDate(dateCreated); eb.setUpdatedDate(dateUpdated); eb.setDatePlannedStart(datePlannedStart); eb.setDatePlannedEnd(datePlannedEnd); eb.setProtocolDateVerification(dateProtocolVerification);// added by // jxu eb.setStatus(Status.get(statusId.intValue())); eb.setOid((String) hm.get("oc_oid")); Integer oldStatusId = (Integer) hm.get("old_status_id"); eb.setOldStatus(Status.get(oldStatusId)); eb.setSchemaName((String) hm.get("schema_name")); String envTypeStr = (String) hm.get("env_type"); if (StringUtils.isNotEmpty(envTypeStr)) eb.setEnvType(StudyEnvEnum.valueOf(envTypeStr.toUpperCase())); eb.setStudyEnvSiteUuid((String) hm.get("study_env_site_uuid")); eb.setStudyEnvUuid((String) hm.get("study_env_uuid")); eb.setPublished(((Boolean) hm.get("published")).booleanValue()); eb.setFilePath((Integer) hm.get("file_path")); return eb; } public Collection findAllByUser(String username) { this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), username); ArrayList alist = this.select(digester.getQuery("findAllByUser"), variables); ArrayList al = new ArrayList(); Iterator it = alist.iterator(); while (it.hasNext()) { StudyBean eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); al.add(eb); } return al; } public ArrayList<Integer> getStudyIdsByCRF(int crfId) { this.unsetTypeExpected(); this.setTypeExpected(1, TypeNames.INT); HashMap<Integer, Integer> variables = new HashMap<Integer, Integer>(); variables.put(1, crfId); ArrayList alist = this.select(digester.getQuery("getStudyIdsByCRF"), variables); ArrayList<Integer> al = new ArrayList<Integer>(); Iterator it = alist.iterator(); while (it.hasNext()) { HashMap h = (HashMap) it.next(); al.add((Integer) h.get("study_id")); } return al; } // YW 10-18-2007 public Collection findAllByUserNotRemoved(String username) { this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), username); ArrayList alist = this.select(digester.getQuery("findAllByUserNotRemoved"), variables); ArrayList al = new ArrayList(); Iterator it = alist.iterator(); while (it.hasNext()) { StudyBean eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); al.add(eb); } return al; } public ArrayList findAllByStatus(Status status) { this.unsetTypeExpected(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), new Integer(status.getId())); String sql = digester.getQuery("findAllByStatus"); ArrayList alist = this.select(sql, variables); ArrayList al = new ArrayList(); Iterator it = alist.iterator(); while (it.hasNext()) { StudyBean eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); al.add(eb); } return al; } public Collection findAll() { return findAllByLimit(false); } public Collection findAllByLimit(boolean isLimited) { this.setTypesExpected(); String sql = null; // Updated for ORACLE and PGSQL compatibility if (isLimited) { if (CoreResources.getDBName().equals("oracle")) { sql = digester.getQuery("findAll") + " where ROWNUM <=5"; } else { sql = digester.getQuery("findAll") + " limit 5"; } } else { sql = digester.getQuery("findAll"); } ArrayList alist = this.select(sql); ArrayList al = new ArrayList(); Iterator it = alist.iterator(); while (it.hasNext()) { StudyBean eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); al.add(eb); } return al; } public Collection findAllParents() { this.setTypesExpected(); String sql = digester.getQuery("findAllParents"); ArrayList alist = this.select(sql); ArrayList al = new ArrayList(); Iterator it = alist.iterator(); while (it.hasNext()) { StudyBean eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); al.add(eb); } return al; } /** * isAParent(), finds out whether or not a study is a parent. * * @return a boolean */ public boolean isAParent(int studyId) { boolean ret = false; Collection col = findAllByParent(studyId); if (col != null && col.size() > 0) { ret = true; } return ret; } public Collection findAllByParent(int parentStudyId) { return findAllByParentAndLimit(parentStudyId, false); } public Collection findAllByParentAndLimit(int parentStudyId, boolean isLimited) { this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), new Integer(parentStudyId)); ArrayList alist = null; if (isLimited) { alist = this.select(digester.getQuery("findAllByParentLimit5"), variables); } else { alist = this.select(digester.getQuery("findAllByParent"), variables); } ArrayList al = new ArrayList(); Iterator it = alist.iterator(); while (it.hasNext()) { StudyBean eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); al.add(eb); } return al; } public Collection findAll(int studyId) { this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), new Integer(studyId)); variables.put(new Integer(2), new Integer(studyId)); ArrayList alist = null; alist = this.select(digester.getQuery("findAllByStudyId"), variables); ArrayList al = new ArrayList(); Iterator it = alist.iterator(); while (it.hasNext()) { StudyBean eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); al.add(eb); } return al; } public Collection findAll(String strOrderByColumn, boolean blnAscendingSort, String strSearchPhrase) { ArrayList al = new ArrayList(); return al; } public EntityBean findByPK(int ID) { StudyBean eb = new StudyBean(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), new Integer(ID)); String sql = digester.getQuery("findByPK"); ArrayList alist = this.select(sql, variables); Iterator it = alist.iterator(); if (it.hasNext()) { eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); } return eb; } /* * added 02/2008, tbh */ public EntityBean findByName(String name) { StudyBean eb = new StudyBean(); this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), name); String sql = digester.getQuery("findByName"); ArrayList alist = this.select(sql, variables); Iterator it = alist.iterator(); if (it.hasNext()) { eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); } return eb; } /** * deleteTestOnly, used only to clean up after unit testing * * @param name */ public void deleteTestOnly(String name) { HashMap variables = new HashMap(); variables.put(new Integer(1), name); this.execute(digester.getQuery("deleteTestOnly"), variables); } public Collection findAllByPermission(Object objCurrentUser, int intActionType, String strOrderByColumn, boolean blnAscendingSort, String strSearchPhrase) { ArrayList al = new ArrayList(); return al; } public Collection findAllByPermission(Object objCurrentUser, int intActionType) { ArrayList al = new ArrayList(); return al; } /** * Only for use by getChildrenByParentIds * * @param answer * @param parentId * @param child * @return */ private HashMap addChildToParent(HashMap answer, int parentId, StudyBean child) { Integer key = new Integer(parentId); ArrayList children = (ArrayList) answer.get(key); if (children == null) { children = new ArrayList(); } children.add(child); answer.put(key, children); return answer; } /** * @param allStudies * The result of findAll(). * @return A HashMap where the keys are Integers whose intValue are studyIds * and the values are ArrayLists; each element of the ArrayList is a * StudyBean representing a child of the study whose id is the key * <p> * e.g., if A has children B and C, then this will return a HashMap * h where h.get(A.getId()) returns an ArrayList whose elements are * B and C */ public HashMap getChildrenByParentIds(ArrayList allStudies) { HashMap answer = new HashMap(); if (allStudies == null) { return answer; } for (int i = 0; i < allStudies.size(); i++) { StudyBean study = (StudyBean) allStudies.get(i); int parentStudyId = study.getParentStudyId(); if (parentStudyId > 0) { // study is a child answer = addChildToParent(answer, parentStudyId, study); } } return answer; } public Collection<Integer> findAllSiteIdsByStudy(StudyBean study) { this.unsetTypeExpected(); this.setTypeExpected(1, TypeNames.INT);// sid HashMap<Integer, Integer> variables = new HashMap<Integer, Integer>(); variables.put(new Integer(1), new Integer(study.getId())); variables.put(new Integer(2), new Integer(study.getId())); ArrayList alist = this.select(digester.getQuery("findAllSiteIdsByStudy"), variables); ArrayList<Integer> al = new ArrayList<Integer>(); Iterator it = alist.iterator(); while (it.hasNext()) { HashMap h = (HashMap) it.next(); al.add((Integer) h.get("study_id")); } return al; } public Collection<Integer> findOlnySiteIdsByStudy(StudyBean study) { this.unsetTypeExpected(); this.setTypeExpected(1, TypeNames.INT);// sid HashMap<Integer, Integer> variables = new HashMap<Integer, Integer>(); variables.put(new Integer(1), new Integer(study.getId())); ArrayList alist = this.select(digester.getQuery("findOlnySiteIdsByStudy"), variables); ArrayList<Integer> al = new ArrayList<Integer>(); Iterator it = alist.iterator(); while (it.hasNext()) { HashMap h = (HashMap) it.next(); al.add((Integer) h.get("study_id")); } return al; } public StudyBean updateSitesStatus(StudyBean sb) { HashMap variables = new HashMap(); HashMap nullVars = new HashMap(); variables.put(new Integer(1), sb.getStatus().getId()); variables.put(new Integer(2), sb.getOldStatus().getId()); variables.put(new Integer(3), sb.getId()); this.execute(digester.getQuery("updateSitesStatus"), variables, nullVars); return sb; } public StudyBean updateStudyStatus(StudyBean sb) { HashMap variables = new HashMap(); HashMap nullVars = new HashMap(); variables.put(new Integer(1), sb.getStatus().getId()); variables.put(new Integer(2), sb.getOldStatus().getId()); variables.put(new Integer(3), sb.getId()); this.execute(digester.getQuery("updateStudyStatus"), variables, nullVars); return sb; } public StudyBean findByStudySubjectId(int studySubjectId) { StudyBean sb = new StudyBean(); HashMap variables = new HashMap(); this.setTypesExpected(); variables.put(new Integer(1), studySubjectId); // >> tbh // String sql = digester.getQuery("findByStudySubjectId"); // ArrayList alist = this.select(sql, variables); // Iterator it = alist.iterator(); // if (it.hasNext()) { // sb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); // } // was not returning anything? ArrayList alist = this.select(digester.getQuery("findByStudySubjectId"), variables); Iterator it = alist.iterator(); if (it.hasNext()) { sb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); } return sb; } public Collection findAllByParentStudyIdOrderedByIdAsc(int parentStudyId) { this.setTypesExpected(); HashMap variables = new HashMap(); variables.put(new Integer(1), new Integer(parentStudyId)); variables.put(new Integer(2), new Integer(parentStudyId)); ArrayList alist = this.select(digester.getQuery("findAllByParentStudyIdOrderedByIdAsc"), variables); ArrayList al = new ArrayList(); Iterator it = alist.iterator(); while (it.hasNext()) { StudyBean eb = (StudyBean) this.getEntityFromHashMap((HashMap) it.next()); al.add(eb); } return al; } public StudyBean getPublicStudy(String ocId) { StudyBean study = findByPublicOid(ocId); return study; } }