edu.mayo.bsi.ngsportal.shared
Interface NGSPortalServiceAsync

public interface NGSPortalServiceAsync

The async counterpart of GreetingService.

Method Summary

void	addExternalUser(String firstName, String lastName, String id, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	addGroup(int connectionID, String name, String description, com.google.gwt.user.client.rpc.AsyncCallback<Integer> callback)
void	addKeyValuePair(int connectionID, int table, String name, String more, String key, String value, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	addNewRerun(int connectID, int projectID, String projectName, com.google.gwt.user.client.rpc.AsyncCallback<String> asyncCallback)
void	addNote(int connectionID, String note, String tableName, int rowID, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	addProject(int connectionID, String notes, boolean isReanalysis, int[] seqSampleIDs, Integer leadID, Integer specID, Integer piID, com.google.gwt.user.client.rpc.AsyncCallback<String> callback)
void	addToFamily(int connectionID, String family, String parentID, String rlimsID, String sampleParentID, String name, Boolean isMale, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	addUsersToGroup(int connectionID, int groupID, Map<String,Integer> users, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	addUsersToProject(int connectionID, Map<String,Boolean> users, int role, String project, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	checkAccessPrivilages(String string, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> asyncCallback)
void	deleteGroup(int connectionID, int groupID, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	deleteNote(int connectionID, String tableName, int rowID, Date noteDate, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	getAllSecondaryStatuses(com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> asyncCallback)
void	getAnalysisStatuses(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getAnalysisTypes(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getAnalyzedSamples(int connectionID, String runID, com.google.gwt.user.client.rpc.AsyncCallback<List<AnalysisInfo>> callback)
void	getApplicationTypes(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getApplicationTypes(String runID, String pi, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getApplicationTypesForSamples(int[] sampleIDs, com.google.gwt.user.client.rpc.AsyncCallback<Integer> callback)
void	getAvgCPUSecondsPerScript(SGEFilter filter, int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<SGEScriptSummary>> callback)
void	getAvgRun(SGEFilter filter, int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<SGEScriptSummary>> callback)
void	getCompletedRuns(int connectionID, String piName, String runID, com.google.gwt.user.client.rpc.AsyncCallback<List<RunData>> callback)
void	getConnection(com.google.gwt.user.client.rpc.AsyncCallback<ConnectionResponse> callback)
void	getContacts(int connectionID, int[] contactIDs, com.google.gwt.user.client.rpc.AsyncCallback<List<ContactInfo>> callback)
void	getCurrentPrimaryStatus(int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,PrimaryAnalysisBean>> callback)
void	getDefaultProjectName(String runName, String appType, String pi, boolean isReanalysis, com.google.gwt.user.client.rpc.AsyncCallback<String> callback) Get a default Secondary Project Reanalysis name from the server given the run, PI, and appType, then ask the user for the reanalysis name, given the default name
void	getErrorsPerRun(SGEFilter filter, int connectID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> asyncCallback)
void	getFileLocations(com.google.gwt.user.client.rpc.AsyncCallback<List<FileLocation>> callback)
void	getFlowcellsPerMonth(SGEFilter filter, int connectID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> asyncCallback)
void	getGroups(int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<GroupInfo>> callback)
void	getInstrumentHistory(int connectionID, String instrument, com.google.gwt.user.client.rpc.AsyncCallback<List<InstrumentInfo>> callback)
void	getInstrumentStatus(int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,String>> callback)
void	getISdetails(com.google.gwt.user.client.rpc.AsyncCallback<Map<String,String>> asyncCallback)
void	getMatchingRuns(int connectionID, String piName, String runID, String sample, String application, String rlimsProject, String rlimsID, Date startDate, Date endDate, boolean onlyAnalyzed, String projName, com.google.gwt.user.client.rpc.AsyncCallback<List<ResultInfo>> callback) Search the database for all the runs matching the criteria given, and return them
void	getNote(int connectionID, String tableName, int rowID, com.google.gwt.user.client.rpc.AsyncCallback<List<Note>> callback)
void	getPIForSamples(int[] sampleIDs, com.google.gwt.user.client.rpc.AsyncCallback<Integer> callback)
void	getPINames(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getPrimaryAnalysisStatuses(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getProjectNames(int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getProjects(int connectionID, int[] projIDs, com.google.gwt.user.client.rpc.AsyncCallback<List<ProjectInfo>> callback)
void	getProjects(int connectionID, String projectName, com.google.gwt.user.client.rpc.AsyncCallback<List<SecondaryProjectInfo>> callback)
void	getProjectsSummary(int connectID, String userName, Date fromDate, Date toDate, com.google.gwt.user.client.rpc.AsyncCallback<ProjectSummaryBuilder> asyncCallback)
void	getQCResults(int connectionID, String sampleName, String runID, com.google.gwt.user.client.rpc.AsyncCallback<List<QCResult>> callback)
void	getReadTypes(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getRetainedSamples(int connectionID, String piName, String runID, String sample, boolean isPrimary, com.google.gwt.user.client.rpc.AsyncCallback<List<ResultInfo>> callback)
void	getRLIMSIDs(int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getRLIMSProjectNames(int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getRoles(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getRunData(int connectionID, String piName, String runID, com.google.gwt.user.client.rpc.AsyncCallback<RunData> callback)
void	getRunIDs(int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getRunIDs(int connectionID, String pi, String appType, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getRunSecondaryAnalysisStatus(List<Integer> sampleids, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> asyncCallback)
void	getSampleNames(int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getSampleNames(int connectionID, String piName, String runID, com.google.gwt.user.client.rpc.AsyncCallback<List<SampleInfo>> callback)
void	getSamples(int connectionID, String piName, String runID, String appType, String projectName, com.google.gwt.user.client.rpc.AsyncCallback<List<SampleInfo>> callback)
void	getSamplesPerMonth(SGEFilter filter, int connectID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> asyncCallback)
void	getScriptInvocations(SGEFilter filter, int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<SGEScriptSummary>> callback)
void	getSecondaryAnalysisHistory(int connectID, int secondaryProjectID, com.google.gwt.user.client.rpc.AsyncCallback<List<SecondaryDetails>> asyncCallback)
void	getSecondaryAnalysisResults(int connectionID, Date finishedCutoff, com.google.gwt.user.client.rpc.AsyncCallback<List<Analysis2>> callback)
void	getSecondaryStatus(int connectID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,List<SecondaryAnalysisBean>>> asyncCallback)
void	getSGEFlowcellsPerMonth(SGEFilter filter, int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> callback)
void	getSumCPUSecondsPerScript(SGEFilter filter, int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<SGEScriptSummary>> callback)
void	getValidRLIMS(SGEFilter filter, int connectionID, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)
void	getValidRunTypes(int connectID, com.google.gwt.user.client.rpc.AsyncCallback<List<String>> asyncCallback)
void	getWallClockPerRun(SGEFilter filter, int connectID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Double>> asyncCallback)
void	getWallClockPerSample(SGEFilter filter, int connectID, com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Double>> asyncCallback)
void	grantProjectAccess(int connectionID, String project, String run, List<String> samples, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	grantUserAccess(int connectionID, Map<String,Boolean> users, int role, String run, List<String> samples, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	logIn(String userName, String password, int connectID, com.google.gwt.user.client.rpc.AsyncCallback<ConnectionResponse> callback)
void	logOut(String userName, String password, int searchID, com.google.gwt.user.client.rpc.AsyncCallback<Void> callback)
void	parseRunFile(String filePath, String user, String password, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	removeFromFamily(int connectionID, String family, String rlimsID, String parentID, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	removeProject(int connectionID, String projectName, com.google.gwt.user.client.rpc.AsyncCallback<Void> callback)
void	removeUsersFromGroup(int connectionID, int groupID, List<String> users, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	removeUsersFromProject(int connectionID, List<String> users, String project, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	retainSample(int connectionID, Date deleteDate, String piName, List<String> runIDs, String sample, String requestor, boolean isPrimary, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	revokeProjectAccess(int connectionID, String project, String run, List<String> samples, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	revokeUserAccess(int connectionID, List<String> users, String run, List<String> samples, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	saveBatched(int connectID, int projectID, String newnotes, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)
void	saveNotes(int connectID, int projectID, String runName, String pI, String application, String personnel, String newNotes, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback) Save Notes to the Database.
void	savePersonneltoDB(int connectID, int projectID, String newISAssignee, String oldISAssignee, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)
void	saveSecondaryAnalysisNotes(int connectID, int analysisID, String notes, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)
void	saveSecondaryAssignedDate(int connectID, int projectID, Date newValue, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)
void	saveSecondaryCompleteDate(int connectID, int projectID, Date object, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)
void	saveSecondaryDeliveryDate(int connectID, int projectID, Date newValue, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)
void	saveSecondaryStartDate(int connectID, int projectID, Date newValue, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)
void	sendEmailNotification(int connectID, String runName, String application, String pI, String userName, String notes, String newAssignee, String oldAssignee, int projectID, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback) Send an email to the new person assigned to a project, and the old person no longer assigned to a project
void	sendWeeklyReport(String lanID, int connectID, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> asyncCallback)
void	setIsBIC(int connectionID, boolean isBIC, int projectID, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback) Sets all the samples for a project to have their isBIC field either be true or false
void	setRunData(int connectionID, String piName, String runID, RunData theRun, List<SampleInfo> samples, int[] deletedIDs, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	updateAnalysis(String analysisPath, String uID, String password, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	updateGroup(int connectionID, int groupID, String name, String description, com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)
void	updateProject(int connectionID, String projectName, String notes, boolean isReanalysis, int[] seqSampleIDs, Integer leadID, Integer specID, Integer piID, com.google.gwt.user.client.rpc.AsyncCallback<Void> callback)
void	writedatatofile(int connectID, String exportdata, com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

Method Detail

getConnection

void getConnection(com.google.gwt.user.client.rpc.AsyncCallback<ConnectionResponse> callback)

logIn

void logIn(String userName,
           String password,
           int connectID,
           com.google.gwt.user.client.rpc.AsyncCallback<ConnectionResponse> callback)

logOut

void logOut(String userName,
            String password,
            int searchID,
            com.google.gwt.user.client.rpc.AsyncCallback<Void> callback)

getApplicationTypes

void getApplicationTypes(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getApplicationTypes

void getApplicationTypes(String runID,
                         String pi,
                         com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getApplicationTypesForSamples

void getApplicationTypesForSamples(int[] sampleIDs,
                                   com.google.gwt.user.client.rpc.AsyncCallback<Integer> callback)

getReadTypes

void getReadTypes(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getAnalysisTypes

void getAnalysisTypes(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getAnalysisStatuses

void getAnalysisStatuses(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getPrimaryAnalysisStatuses

void getPrimaryAnalysisStatuses(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getContacts

void getContacts(int connectionID,
                 int[] contactIDs,
                 com.google.gwt.user.client.rpc.AsyncCallback<List<ContactInfo>> callback)

getRoles

void getRoles(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getPINames

void getPINames(com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getPIForSamples

void getPIForSamples(int[] sampleIDs,
                     com.google.gwt.user.client.rpc.AsyncCallback<Integer> callback)

getRunIDs

void getRunIDs(int connectionID,
               com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getRunIDs

void getRunIDs(int connectionID,
               String pi,
               String appType,
               com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

parseRunFile

void parseRunFile(String filePath,
                  String user,
                  String password,
                  com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

getSecondaryAnalysisResults

void getSecondaryAnalysisResults(int connectionID,
                                 Date finishedCutoff,
                                 com.google.gwt.user.client.rpc.AsyncCallback<List<Analysis2>> callback)

getMatchingRuns

void getMatchingRuns(int connectionID,
                     String piName,
                     String runID,
                     String sample,
                     String application,
                     String rlimsProject,
                     String rlimsID,
                     Date startDate,
                     Date endDate,
                     boolean onlyAnalyzed,
                     String projName,
                     com.google.gwt.user.client.rpc.AsyncCallback<List<ResultInfo>> callback)

Search the database for all the runs matching the criteria given, and return them

Parameters:

connectionID - The id of the connection, so know what user has access to

piName - If not empty or null, the Last Name, First Name of the PI to look for

runID - If not empty or null, the single run ID to return

sample - If not empty or null, the name of the samples to return

application - If not empty or null, the type of application to search for

rlimsProject - If not empty or null, the RLIMS Project Name to search for

rlimsID - If not empty or null, the RLIMS ID to search for

startDate - If not null, lower bound on date range or allowed results

endDate - If not null, upper bound on date range or allowed results If startDate == endDate, will only return runs from that date.

onlyAnalyzed - If true, only find results where there's at least one secondary analysis available

projName - If not empty or null, the secondary project name to look for

callback - List of runs and samples that match the criteria, or an empty list if no matches

getRunData

void getRunData(int connectionID,
                String piName,
                String runID,
                com.google.gwt.user.client.rpc.AsyncCallback<RunData> callback)

setRunData

void setRunData(int connectionID,
                String piName,
                String runID,
                RunData theRun,
                List<SampleInfo> samples,
                int[] deletedIDs,
                com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

getSamples

void getSamples(int connectionID,
                String piName,
                String runID,
                String appType,
                String projectName,
                com.google.gwt.user.client.rpc.AsyncCallback<List<SampleInfo>> callback)

getRetainedSamples

void getRetainedSamples(int connectionID,
                        String piName,
                        String runID,
                        String sample,
                        boolean isPrimary,
                        com.google.gwt.user.client.rpc.AsyncCallback<List<ResultInfo>> callback)

retainSample

void retainSample(int connectionID,
                  Date deleteDate,
                  String piName,
                  List<String> runIDs,
                  String sample,
                  String requestor,
                  boolean isPrimary,
                  com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

getSampleNames

void getSampleNames(int connectionID,
                    String piName,
                    String runID,
                    com.google.gwt.user.client.rpc.AsyncCallback<List<SampleInfo>> callback)

getSampleNames

void getSampleNames(int connectionID,
                    com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getCompletedRuns

void getCompletedRuns(int connectionID,
                      String piName,
                      String runID,
                      com.google.gwt.user.client.rpc.AsyncCallback<List<RunData>> callback)

getQCResults

void getQCResults(int connectionID,
                  String sampleName,
                  String runID,
                  com.google.gwt.user.client.rpc.AsyncCallback<List<QCResult>> callback)

getAnalyzedSamples

void getAnalyzedSamples(int connectionID,
                        String runID,
                        com.google.gwt.user.client.rpc.AsyncCallback<List<AnalysisInfo>> callback)

addNote

void addNote(int connectionID,
             String note,
             String tableName,
             int rowID,
             com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

getNote

void getNote(int connectionID,
             String tableName,
             int rowID,
             com.google.gwt.user.client.rpc.AsyncCallback<List<Note>> callback)

deleteNote

void deleteNote(int connectionID,
                String tableName,
                int rowID,
                Date noteDate,
                com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

updateAnalysis

void updateAnalysis(String analysisPath,
                    String uID,
                    String password,
                    com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

getInstrumentStatus

void getInstrumentStatus(int connectionID,
                         com.google.gwt.user.client.rpc.AsyncCallback<Map<String,String>> callback)

getInstrumentHistory

void getInstrumentHistory(int connectionID,
                          String instrument,
                          com.google.gwt.user.client.rpc.AsyncCallback<List<InstrumentInfo>> callback)

addProject

void addProject(int connectionID,
                String notes,
                boolean isReanalysis,
                int[] seqSampleIDs,
                Integer leadID,
                Integer specID,
                Integer piID,
                com.google.gwt.user.client.rpc.AsyncCallback<String> callback)

updateProject

void updateProject(int connectionID,
                   String projectName,
                   String notes,
                   boolean isReanalysis,
                   int[] seqSampleIDs,
                   Integer leadID,
                   Integer specID,
                   Integer piID,
                   com.google.gwt.user.client.rpc.AsyncCallback<Void> callback)

getProjects

void getProjects(int connectionID,
                 String projectName,
                 com.google.gwt.user.client.rpc.AsyncCallback<List<SecondaryProjectInfo>> callback)

removeProject

void removeProject(int connectionID,
                   String projectName,
                   com.google.gwt.user.client.rpc.AsyncCallback<Void> callback)

getProjects

void getProjects(int connectionID,
                 int[] projIDs,
                 com.google.gwt.user.client.rpc.AsyncCallback<List<ProjectInfo>> callback)

getProjectNames

void getProjectNames(int connectionID,
                     com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getRLIMSProjectNames

void getRLIMSProjectNames(int connectionID,
                          com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getRLIMSIDs

void getRLIMSIDs(int connectionID,
                 com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getCurrentPrimaryStatus

void getCurrentPrimaryStatus(int connectionID,
                             com.google.gwt.user.client.rpc.AsyncCallback<Map<String,PrimaryAnalysisBean>> callback)

grantUserAccess

void grantUserAccess(int connectionID,
                     Map<String,Boolean> users,
                     int role,
                     String run,
                     List<String> samples,
                     com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

revokeUserAccess

void revokeUserAccess(int connectionID,
                      List<String> users,
                      String run,
                      List<String> samples,
                      com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

addExternalUser

void addExternalUser(String firstName,
                     String lastName,
                     String id,
                     com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

addUsersToProject

void addUsersToProject(int connectionID,
                       Map<String,Boolean> users,
                       int role,
                       String project,
                       com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

removeUsersFromProject

void removeUsersFromProject(int connectionID,
                            List<String> users,
                            String project,
                            com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

grantProjectAccess

void grantProjectAccess(int connectionID,
                        String project,
                        String run,
                        List<String> samples,
                        com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

revokeProjectAccess

void revokeProjectAccess(int connectionID,
                         String project,
                         String run,
                         List<String> samples,
                         com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

addGroup

void addGroup(int connectionID,
              String name,
              String description,
              com.google.gwt.user.client.rpc.AsyncCallback<Integer> callback)

updateGroup

void updateGroup(int connectionID,
                 int groupID,
                 String name,
                 String description,
                 com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

addUsersToGroup

void addUsersToGroup(int connectionID,
                     int groupID,
                     Map<String,Integer> users,
                     com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

removeUsersFromGroup

void removeUsersFromGroup(int connectionID,
                          int groupID,
                          List<String> users,
                          com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

deleteGroup

void deleteGroup(int connectionID,
                 int groupID,
                 com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

getGroups

void getGroups(int connectionID,
               com.google.gwt.user.client.rpc.AsyncCallback<List<GroupInfo>> callback)

addKeyValuePair

void addKeyValuePair(int connectionID,
                     int table,
                     String name,
                     String more,
                     String key,
                     String value,
                     com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

addToFamily

void addToFamily(int connectionID,
                 String family,
                 String parentID,
                 String rlimsID,
                 String sampleParentID,
                 String name,
                 Boolean isMale,
                 com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

removeFromFamily

void removeFromFamily(int connectionID,
                      String family,
                      String rlimsID,
                      String parentID,
                      com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

getFileLocations

void getFileLocations(com.google.gwt.user.client.rpc.AsyncCallback<List<FileLocation>> callback)

getSumCPUSecondsPerScript

void getSumCPUSecondsPerScript(SGEFilter filter,
                               int connectionID,
                               com.google.gwt.user.client.rpc.AsyncCallback<List<SGEScriptSummary>> callback)

getAvgCPUSecondsPerScript

void getAvgCPUSecondsPerScript(SGEFilter filter,
                               int connectionID,
                               com.google.gwt.user.client.rpc.AsyncCallback<List<SGEScriptSummary>> callback)

getScriptInvocations

void getScriptInvocations(SGEFilter filter,
                          int connectionID,
                          com.google.gwt.user.client.rpc.AsyncCallback<List<SGEScriptSummary>> callback)

getAvgRun

void getAvgRun(SGEFilter filter,
               int connectionID,
               com.google.gwt.user.client.rpc.AsyncCallback<List<SGEScriptSummary>> callback)

getValidRLIMS

void getValidRLIMS(SGEFilter filter,
                   int connectionID,
                   com.google.gwt.user.client.rpc.AsyncCallback<List<String>> callback)

getValidRunTypes

void getValidRunTypes(int connectID,
                      com.google.gwt.user.client.rpc.AsyncCallback<List<String>> asyncCallback)

getWallClockPerRun

void getWallClockPerRun(SGEFilter filter,
                        int connectID,
                        com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Double>> asyncCallback)

getWallClockPerSample

void getWallClockPerSample(SGEFilter filter,
                           int connectID,
                           com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Double>> asyncCallback)

getSamplesPerMonth

void getSamplesPerMonth(SGEFilter filter,
                        int connectID,
                        com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> asyncCallback)

getErrorsPerRun

void getErrorsPerRun(SGEFilter filter,
                     int connectID,
                     com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> asyncCallback)

getSecondaryStatus

void getSecondaryStatus(int connectID,
                        com.google.gwt.user.client.rpc.AsyncCallback<Map<String,List<SecondaryAnalysisBean>>> asyncCallback)

checkAccessPrivilages

void checkAccessPrivilages(String string,
                           com.google.gwt.user.client.rpc.AsyncCallback<Boolean> asyncCallback)

saveSecondaryStartDate

void saveSecondaryStartDate(int connectID,
                            int projectID,
                            Date newValue,
                            com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

saveSecondaryDeliveryDate

void saveSecondaryDeliveryDate(int connectID,
                               int projectID,
                               Date newValue,
                               com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

saveSecondaryCompleteDate

void saveSecondaryCompleteDate(int connectID,
                               int projectID,
                               Date object,
                               com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

sendEmailNotification

void sendEmailNotification(int connectID,
                           String runName,
                           String application,
                           String pI,
                           String userName,
                           String notes,
                           String newAssignee,
                           String oldAssignee,
                           int projectID,
                           com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

Send an email to the new person assigned to a project, and the old person no longer assigned to a project

Parameters:

connectID - The user's connection ID

runName - The name of the run

application - The type of analysis to be run

pI - The PI the work is being done for

userName - The LAN ID of the person assigning the work

notes - Any notes for the analysis

newAssignee - The person being assigned to run the analysis

oldAssignee - The previous person assigned to do the analysis, or null if no one

projectID - ID of the project, so can send along its name

asyncCallback - Gets nothing

saveNotes

void saveNotes(int connectID,
               int projectID,
               String runName,
               String pI,
               String application,
               String personnel,
               String newNotes,
               com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

Save Notes to the Database. Fails if user is neither an administrator or a member of the PI Support staff

Parameters:

connectID - The id of the connection, so know what user has access to

projectID - ID of the project we're adding notes about

runName - Name of the run we're adding notes about

pI - The PI the work is being done for

application - The type of analysis being run

personnel - LanID of the person doing the analysis

newNotes - New value of the notes field

asyncCallback - Gets nothing

getProjectsSummary

void getProjectsSummary(int connectID,
                        String userName,
                        Date fromDate,
                        Date toDate,
                        com.google.gwt.user.client.rpc.AsyncCallback<ProjectSummaryBuilder> asyncCallback)

saveSecondaryAssignedDate

void saveSecondaryAssignedDate(int connectID,
                               int projectID,
                               Date newValue,
                               com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

addNewRerun

void addNewRerun(int connectID,
                 int projectID,
                 String projectName,
                 com.google.gwt.user.client.rpc.AsyncCallback<String> asyncCallback)

writedatatofile

void writedatatofile(int connectID,
                     String exportdata,
                     com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

getSecondaryAnalysisHistory

void getSecondaryAnalysisHistory(int connectID,
                                 int secondaryProjectID,
                                 com.google.gwt.user.client.rpc.AsyncCallback<List<SecondaryDetails>> asyncCallback)

getFlowcellsPerMonth

void getFlowcellsPerMonth(SGEFilter filter,
                          int connectID,
                          com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> asyncCallback)

savePersonneltoDB

void savePersonneltoDB(int connectID,
                       int projectID,
                       String newISAssignee,
                       String oldISAssignee,
                       com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

saveSecondaryAnalysisNotes

void saveSecondaryAnalysisNotes(int connectID,
                                int analysisID,
                                String notes,
                                com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

getAllSecondaryStatuses

void getAllSecondaryStatuses(com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> asyncCallback)

getSGEFlowcellsPerMonth

void getSGEFlowcellsPerMonth(SGEFilter filter,
                             int connectionID,
                             com.google.gwt.user.client.rpc.AsyncCallback<Map<String,Integer>> callback)

getISdetails

void getISdetails(com.google.gwt.user.client.rpc.AsyncCallback<Map<String,String>> asyncCallback)

Parameters:

asyncCallback -

getDefaultProjectName

void getDefaultProjectName(String runName,
                           String appType,
                           String pi,
                           boolean isReanalysis,
                           com.google.gwt.user.client.rpc.AsyncCallback<String> callback)

Get a default Secondary Project Reanalysis name from the server given the run, PI, and appType, then ask the user for the reanalysis name, given the default name

Parameters:

runName - Name of the run of interest

appType - Application type

pi - Name of the PI

isReanalysis - True if it's a reanalysis, false otherwise

callback - A unique Project name that matches the specified characteristics

getRunSecondaryAnalysisStatus

void getRunSecondaryAnalysisStatus(List<Integer> sampleids,
                                   com.google.gwt.user.client.rpc.AsyncCallback<Boolean> asyncCallback)

saveBatched

void saveBatched(int connectID,
                 int projectID,
                 String newnotes,
                 com.google.gwt.user.client.rpc.AsyncCallback<Void> asyncCallback)

sendWeeklyReport

void sendWeeklyReport(String lanID,
                      int connectID,
                      com.google.gwt.user.client.rpc.AsyncCallback<Boolean> asyncCallback)

setIsBIC

void setIsBIC(int connectionID,
              boolean isBIC,
              int projectID,
              com.google.gwt.user.client.rpc.AsyncCallback<Boolean> callback)

Sets all the samples for a project to have their isBIC field either be true or false

Parameters:

connectionID - ID of the connection, used to retrieve the PortalConnection. Must match the session connection ID, if the session connection ID exists

isBIC - Value to set all the samples to

projectID - DB Row ID of the project holding the samples

callback - True if assigned the value, else false