|
||||||||||
| PREV NEXT | FRAMES NO FRAMES | |||||||||
| Packages that use ConnectionException | |
|---|---|
| edu.mayo.bsi.ngsportal.server | |
| edu.mayo.bsi.ngsportal.shared | |
| Uses of ConnectionException in edu.mayo.bsi.ngsportal.server |
|---|
| Methods in edu.mayo.bsi.ngsportal.server that throw ConnectionException | |
|---|---|
int |
NGSPortalServiceImpl.addGroup(int connectionID,
String name,
String description)
Adds a new group |
boolean |
NGSPortalServiceImpl.addKeyValuePair(int connectionID,
int table,
String name,
String more,
String key,
String value)
Add a Key : Value pair about a specified item to the DB |
String |
NGSPortalServiceImpl.addNewRerun(int connectID,
int projectID,
String projectName)
|
boolean |
NGSPortalServiceImpl.addNote(int connectionID,
String note,
String tableName,
int rowID)
Adds a note to the database |
String |
NGSPortalServiceImpl.addProject(int connectionID,
String notes,
boolean isReanalysis,
int[] seqSampleIDs,
Integer leadID,
Integer specID,
Integer piID)
|
boolean |
NGSPortalServiceImpl.addSampleAnalysis(int connectionID,
int groupID,
String appName,
double version,
String status,
Date analysisDate,
boolean complete,
boolean failed)
Add a Secondary analysis to the DB, setting up all the relevant information |
boolean |
NGSPortalServiceImpl.addToFamily(int connectionID,
String family,
String parentID,
String rlimsID,
String sampleParentID,
String name,
Boolean isMale)
Add a sample to a family, creating the family if necessary. |
boolean |
NGSPortalServiceImpl.addUsersToGroup(int connectionID,
int groupID,
Map<String,Integer> users)
Add users to an existing group |
boolean |
NGSPortalServiceImpl.addUsersToProject(int connectionID,
Map<String,Boolean> users,
int role,
String project)
Give one or more users' access to a project |
int |
NGSPortalServiceImpl.createAnalysisGroup(int connectionID,
String analysisName,
String runName,
String flowCell,
String index,
int[] lanes)
Add an Analysis Group to the DB, setting up all the relevant information |
boolean |
NGSPortalServiceImpl.deleteGroup(int connectionID,
int groupID)
Delete an existing group, and all related information |
boolean |
NGSPortalServiceImpl.deleteNote(int connectionID,
String tableName,
int rowID,
Date noteDate)
|
List<AnalysisInfo> |
NGSPortalServiceImpl.getAnalyzedSamples(int connectionID,
String theRun)
|
List<SGEScriptSummary> |
NGSPortalServiceImpl.getAvgCPUSecondsPerScript(SGEFilter filter,
int connectionID)
|
List<SGEScriptSummary> |
NGSPortalServiceImpl.getAvgRun(SGEFilter filter,
int connectionID)
|
List<RunData> |
NGSPortalServiceImpl.getCompletedRuns(int connectionID,
String piName,
String runID)
Get all the completed runs |
List<ContactInfo> |
NGSPortalServiceImpl.getContacts(int connectionID,
int[] contactIDs)
|
Map<String,PrimaryAnalysisBean> |
NGSPortalServiceImpl.getCurrentPrimaryStatus(int connectionID)
Get the latest primary analysis statuses, from all the primary analysis results that have been updated in the last week |
Map<String,Integer> |
NGSPortalServiceImpl.getErrorsPerRun(SGEFilter filter,
int connectionID)
|
List<GroupInfo> |
NGSPortalServiceImpl.getGroups(int connectionID)
Get the list of all the groups in the DB |
List<InstrumentInfo> |
NGSPortalServiceImpl.getInstrumentHistory(int connectionID,
String instrument)
Get all the actions recorded for the given instrument |
Map<String,String> |
NGSPortalServiceImpl.getInstrumentStatus(int connectionID)
Query the Primary Analysis DB for the runs that have completed the given task, and when they did it |
List<ResultInfo> |
NGSPortalServiceImpl.getMatchingRuns(int connectionID,
String piName,
String runID,
String sample,
String application,
String rlimsProject,
String rlimsID,
Date startDate,
Date endDate,
boolean onlyAnalyzed,
String projName)
|
List<Note> |
NGSPortalServiceImpl.getNote(int connectionID,
String tableName,
int rowID)
Get one or more notes from the database |
List<String> |
NGSPortalServiceImpl.getPrimaryProjectNames(int connectionID)
Get the names of all the projects in the database |
List<String> |
NGSPortalServiceImpl.getProjectNames(int connectionID)
|
List<ProjectInfo> |
NGSPortalServiceImpl.getProjects(int connectionID,
int[] projIDs)
|
List<SecondaryProjectInfo> |
NGSPortalServiceImpl.getProjects(int connectionID,
String projectName)
|
ProjectSummaryBuilder |
NGSPortalServiceImpl.getProjectsSummary(int connectionID,
String userLanID,
Date fromDate,
Date toDate)
|
List<QCResult> |
NGSPortalServiceImpl.getQCResults(int connectionID,
String sampleName,
String runID)
Get all the information about the QCResults for a sample from a given run |
List<ReportData> |
NGSPortalServiceImpl.getReport(int connectionID,
String piName,
String instrument,
int appType,
Date minStartDate,
Date maxStartDate,
Date minEndDate,
Date maxEndDate)
Get a report on the runs specified by the following criteria |
List<ResultInfo> |
NGSPortalServiceImpl.getRetainedSamples(int connectionID,
String piName,
String runID,
String sample,
boolean isPrimary)
Get all the runs and samples that have data files that are currently marked for non-deletion |
List<String> |
NGSPortalServiceImpl.getRLIMSIDs(int connectionID)
Get all the RLIMS Sample "Sample IDs" in the database that this user can see |
List<String> |
NGSPortalServiceImpl.getRLIMSProjectNames(int connectionID)
Get all the RLIMS project names in the database that this user can see |
RunData |
NGSPortalServiceImpl.getRunData(int connectionID,
String piName,
String runID)
Get all the metadata from a given run, owned by a given PI |
List<String> |
NGSPortalServiceImpl.getRunIDs(int connectionID)
|
List<String> |
NGSPortalServiceImpl.getRunIDs(int connectionID,
String pi,
String appType)
|
List<String> |
NGSPortalServiceImpl.getSampleNames(int connectionID)
Get the names of all the samples in the DB |
List<SampleInfo> |
NGSPortalServiceImpl.getSampleNames(int connectionID,
String piName,
String runID)
Get all the information about all the samples from a given run, owned by a given PI |
List<SampleInfo> |
NGSPortalServiceImpl.getSamples(int connectionID,
String piName,
String runID,
String appType,
String projectName)
Get all the information about all the samples from a given run, owned by a given PI |
Map<String,Integer> |
NGSPortalServiceImpl.getSamplesPerMonth(SGEFilter filter,
int connectionID)
|
List<SGEScriptSummary> |
NGSPortalServiceImpl.getScriptInvocations(SGEFilter filter,
int connectionID)
|
List<Analysis2> |
NGSPortalServiceImpl.getSecondaryAnalysisResults(int connectionID,
Date finishedCutoff)
Get all the information about the Secondary Analysis results for a sample from a given run |
Map<String,List<SecondaryAnalysisBean>> |
NGSPortalServiceImpl.getSecondaryStatus(int connectID)
SQL query and result set to Return current Secondary Analysis status |
Map<String,Integer> |
NGSPortalServiceImpl.getSGEFlowcellsPerMonth(SGEFilter filter,
int connectionID)
|
List<SGEScriptSummary> |
NGSPortalServiceImpl.getSumCPUSecondsPerScript(SGEFilter filter,
int connectionID)
|
List<String> |
NGSPortalServiceImpl.getValidRLIMS(SGEFilter filter,
int connectionID)
|
List<String> |
NGSPortalServiceImpl.getValidRunTypes(int connectionID)
|
Map<String,Double> |
NGSPortalServiceImpl.getWallClockPerRun(SGEFilter filter,
int connectionID)
|
Map<String,Double> |
NGSPortalServiceImpl.getWallClockPerSample(SGEFilter filter,
int connectionID)
|
boolean |
NGSPortalServiceImpl.grantProjectAccess(int connectionID,
String project,
String run,
List<String> samples)
Routine to add samples to a project |
boolean |
NGSPortalServiceImpl.grantUserAccess(int connectionID,
Map<String,Boolean> users,
int role,
String run,
List<String> samples)
Routine to give users access to samples that the caller has access to |
boolean |
NGSPortalServiceImpl.removeFromFamily(int connectionID,
String family,
String rlimsID,
String parentID)
Remove a sample from a family |
void |
NGSPortalServiceImpl.removeProject(int connectionID,
int projID)
Code to delete a Patrick style Project |
void |
NGSPortalServiceImpl.removeProject(int connectionID,
String projectName)
|
boolean |
NGSPortalServiceImpl.removeUsersFromGroup(int connectionID,
int groupID,
List<String> users)
Remove users from a group |
boolean |
NGSPortalServiceImpl.removeUsersFromProject(int connectionID,
List<String> users,
String project)
Routine to remove one or more users' access to a project |
boolean |
NGSPortalServiceImpl.retainSample(int connectionID,
Date deleteDate,
String piName,
List<String> runIDs,
String sample,
String requestor,
boolean isPrimary)
Mark a sample or set of samples as needing their data files to be retained |
boolean |
NGSPortalServiceImpl.revokeProjectAccess(int connectionID,
String project,
String run,
List<String> samples)
Routine to remove samples from a project |
boolean |
NGSPortalServiceImpl.revokeUserAccess(int connectionID,
List<String> users,
String run,
List<String> samples)
Routine to remove users' access to samples that the caller has PI access to, or where the caller has all sample access. |
void |
NGSPortalServiceImpl.saveBatched(int connectID,
int projectID,
String value)
Saves the batched value |
void |
NGSPortalServiceImpl.saveNotes(int connectID,
int projectID,
String runName,
String pI,
String application,
String personnel,
String newNotes)
Save Notes to the Database. |
void |
NGSPortalServiceImpl.savePersonneltoDB(int connectID,
int projectID,
String newISAssignee,
String oldISAssignee)
|
void |
NGSPortalServiceImpl.saveSecondaryAnalysisNotes(int connectID,
int analysisID,
String notes)
Replace the notes for a secondary analysis. |
void |
NGSPortalServiceImpl.saveSecondaryAssignedDate(int connectID,
int projectID,
Date newValue)
|
void |
NGSPortalServiceImpl.saveSecondaryCompleteDate(int connectID,
int projectID,
Date date)
Saves the secondary Complete Date. |
void |
NGSPortalServiceImpl.saveSecondaryDeliveryDate(int connectID,
int projectID,
Date date)
Saves the Secondary Delivery Date |
void |
NGSPortalServiceImpl.saveSecondaryStartDate(int connectID,
int projectID,
Date date)
Saves the Secondary Start Date |
void |
NGSPortalServiceImpl.sendEmailNotification(int connectID,
String runName,
String application,
String pi,
String assignerLanID,
String notes,
String newAssignee,
String oldAssignee,
int projectID)
Saves the Assigned Date and Personnel to the DB |
boolean |
NGSPortalServiceImpl.sendWeeklyReport(String userlanID,
int connectionID)
Generate an EMail Weekly Report |
boolean |
NGSPortalServiceImpl.setIsBIC(int connectionID,
boolean isBIC,
int projectID)
Sets all the samples for a project to have their isBIC field either be true or false |
boolean |
NGSPortalServiceImpl.setRunData(int connectionID,
String piName,
String runID,
RunData theRun,
List<SampleInfo> samples,
int[] deletedIDs)
Update all the metadata for a given run, owned by a given PI |
void |
ProjectTest.testAddProject()
Add a project to the DB |
void |
ProjectTest.testAddProjectSQLInject()
Add a project to the DB |
void |
ProjectTest.testGetProjects()
|
void |
ProjectTest.testRemoveProject()
|
void |
ProjectTest.testUpdateProject()
Update a project in the DB |
boolean |
NGSPortalServiceImpl.updateGroup(int connectionID,
int groupID,
String name,
String description)
Updates information about an existing group |
void |
NGSPortalServiceImpl.updateProject(int connectionID,
String projectName,
String notes,
boolean isReanalysis,
int[] seqSampleIDs,
Integer leadID,
Integer specID,
Integer piID)
|
| Uses of ConnectionException in edu.mayo.bsi.ngsportal.shared |
|---|
| Methods in edu.mayo.bsi.ngsportal.shared that throw ConnectionException | |
|---|---|
int |
NGSPortalService.addGroup(int connectionID,
String name,
String description)
Adds a new group |
boolean |
NGSPortalService.addKeyValuePair(int connectionID,
int table,
String name,
String more,
String key,
String value)
Add a Key : Value pair about a specified item to the DB |
String |
NGSPortalService.addNewRerun(int connectionID,
int projectID,
String projectName)
|
boolean |
NGSPortalService.addNote(int connectionID,
String note,
String tableName,
int rowID)
Adds a note to the database |
String |
NGSPortalService.addProject(int connectionID,
String notes,
boolean isReanalysis,
int[] seqSampleIDs,
Integer leadID,
Integer specID,
Integer piID)
Adds a new project. |
boolean |
NGSPortalService.addToFamily(int connectionID,
String family,
String parentID,
String rlimsID,
String sampleParentID,
String name,
Boolean isMale)
Add a sample to a family, creating the family if necessary. |
boolean |
NGSPortalService.addUsersToGroup(int connectionID,
int groupID,
Map<String,Integer> users)
Add users to an existing group |
boolean |
NGSPortalService.addUsersToProject(int connectionID,
Map<String,Boolean> users,
int role,
String project)
Give one or more users' access to a project |
boolean |
NGSPortalService.deleteGroup(int connectionID,
int groupID)
Delete an existing group |
boolean |
NGSPortalService.deleteNote(int connectionID,
String tableName,
int rowID,
Date noteDate)
Deletes a note from the database. |
List<AnalysisInfo> |
NGSPortalService.getAnalyzedSamples(int connectionID,
String theRun)
Finds all the samples for a run that have had an analysis done |
List<SGEScriptSummary> |
NGSPortalService.getAvgCPUSecondsPerScript(SGEFilter filter,
int connectionID)
Queries the portal database and returns a list of SGEScriptSummary containing the average of cpuseconds consumed by the scripts defined by the provided SGEFilter |
List<SGEScriptSummary> |
NGSPortalService.getAvgRun(SGEFilter filter,
int connectionID)
Queries the portal database and returns a list of SGEScriptSummary containing the sum of cpuseconds consumed by the scripts defined by the provided SGEFilter |
List<RunData> |
NGSPortalService.getCompletedRuns(int connectionID,
String piName,
String runID)
Get all the completed runs |
List<ContactInfo> |
NGSPortalService.getContacts(int connectionID,
int[] contactIDs)
Gets one or more contacts. |
Map<String,PrimaryAnalysisBean> |
NGSPortalService.getCurrentPrimaryStatus(int connectionID)
Get the latest primary analysis statuses, from all the primary analysis results that have been updated in the last week |
Map<String,Integer> |
NGSPortalService.getErrorsPerRun(SGEFilter filter,
int connectionID)
Returns a set of pairs of RunIDs - ScriptNames and error counts defined by the passed filter object. |
List<GroupInfo> |
NGSPortalService.getGroups(int connectionID)
Get the list of all the groups in the DB |
List<InstrumentInfo> |
NGSPortalService.getInstrumentHistory(int connectionID,
String instrument)
Get all the actions recorded for the given instrument |
Map<String,String> |
NGSPortalService.getInstrumentStatus(int connectionID)
Query the Primary Analysis DB for the runs that have completed the given task, and when they did it |
List<Note> |
NGSPortalService.getNote(int connectionID,
String tableName,
int rowID)
Get one or more notes from the database |
List<String> |
NGSPortalService.getProjectNames(int connectionID)
Get the names of all the secondary analysis projects in the database that this user can see |
List<ProjectInfo> |
NGSPortalService.getProjects(int connectionID,
int[] projIDs)
Gets one or more projects. |
List<SecondaryProjectInfo> |
NGSPortalService.getProjects(int connectionID,
String projectName)
Get all the Secondary Projects created by this individual, or the single project projectName |
ProjectSummaryBuilder |
NGSPortalService.getProjectsSummary(int connectionID,
String userName,
Date fromDate,
Date toDate)
|
List<QCResult> |
NGSPortalService.getQCResults(int connectionID,
String sampleName,
String runID)
Get all the information about the QCResults for a sample from a given run |
List<ResultInfo> |
NGSPortalService.getRetainedSamples(int connectionID,
String piName,
String runID,
String sample,
boolean isPrimary)
Get all the runs and samples that have data files that are currently marked for non-deletion |
List<String> |
NGSPortalService.getRLIMSIDs(int connectionID)
Get all the RLIMS Sample "Sample IDs" in the database that this user can see |
List<String> |
NGSPortalService.getRLIMSProjectNames(int connectionID)
Get all the RLIMS project names in the database that this user can see |
RunData |
NGSPortalService.getRunData(int connectionID,
String piName,
String runID)
Get all the metadata from a given run, owned by a given PI |
List<String> |
NGSPortalService.getRunIDs(int connectionID)
Get all the run IDs in the database this user can see |
List<String> |
NGSPortalService.getRunIDs(int connectionID,
String pi,
String appType)
Get all the run IDs in the database this user can see, that have at least one sample that has the specified PI and / or application type |
List<String> |
NGSPortalService.getSampleNames(int connectionID)
Get the names of all the samples in the DB |
List<SampleInfo> |
NGSPortalService.getSampleNames(int connectionID,
String piName,
String runID)
Get the name, RLIMS ID, and DB ID of all the samples in the DB, or only those samples associated with a given Run, PI, or both |
List<SampleInfo> |
NGSPortalService.getSamples(int connectionID,
String piName,
String runID,
String appType,
String projectName)
Get all the information about all the samples from a given run, owned by a given PI |
Map<String,Integer> |
NGSPortalService.getSamplesPerMonth(SGEFilter filter,
int connectionID)
Returns a set of pairs of months and unique samples defined by the passed filter object. |
List<SGEScriptSummary> |
NGSPortalService.getScriptInvocations(SGEFilter filter,
int connectionID)
Queries the portal database and returns a list of SGEScriptSummary containing the total script invocations in the runs defined by the provided SGEFilter |
List<Analysis2> |
NGSPortalService.getSecondaryAnalysisResults(int connectionID,
Date finishedCutoff)
Get all the information about the Secondary Analysis results for a sample from a given run |
Map<String,List<SecondaryAnalysisBean>> |
NGSPortalService.getSecondaryStatus(int connectionID)
|
Map<String,Integer> |
NGSPortalService.getSGEFlowcellsPerMonth(SGEFilter filter,
int connectionID)
|
List<SGEScriptSummary> |
NGSPortalService.getSumCPUSecondsPerScript(SGEFilter filter,
int connectionID)
Queries the portal database and returns a list of SGEScriptSummary containing the sum of cpuseconds consumed by the scripts defined by the provided SGEFilter |
List<String> |
NGSPortalService.getValidRLIMS(SGEFilter filter,
int connectionID)
Queries the portal database and returns a list of possible RunIDs falling within the provided SGEFilter |
List<String> |
NGSPortalService.getValidRunTypes(int connectionID)
Returns a list of possible Run Types (eg., exome, whole_genome,...) available |
Map<String,Double> |
NGSPortalService.getWallClockPerRun(SGEFilter filter,
int connectionID)
Returns a set of pairs of WallClock times and RunIDs defined by the passed filter object. |
Map<String,Double> |
NGSPortalService.getWallClockPerSample(SGEFilter filter,
int connectionID)
Returns a set of pairs of WallClock times and SampleIDs defined by the passed filter object. |
boolean |
NGSPortalService.grantProjectAccess(int connectionID,
String project,
String run,
List<String> samples)
Routine to add samples to a project |
boolean |
NGSPortalService.grantUserAccess(int connectionID,
Map<String,Boolean> users,
int role,
String run,
List<String> samples)
Routine to give users access to samples that the caller has access to |
boolean |
NGSPortalService.removeFromFamily(int connectionID,
String family,
String rlimsID,
String parentID)
Remove a sample from a family |
void |
NGSPortalService.removeProject(int connectionID,
String projectName)
Removes an existing project. |
boolean |
NGSPortalService.removeUsersFromGroup(int connectionID,
int groupID,
List<String> users)
Remove users from a group |
boolean |
NGSPortalService.removeUsersFromProject(int connectionID,
List<String> users,
String project)
Routine to remove one or more users' access to a project |
boolean |
NGSPortalService.retainSample(int connectionID,
Date deleteDate,
String piName,
List<String> runIDs,
String sample,
String requestor,
boolean isPrimary)
Mark a sample or set of samples as needing their data files to be retained |
boolean |
NGSPortalService.revokeProjectAccess(int connectionID,
String project,
String run,
List<String> samples)
Routine to remove samples from a project |
boolean |
NGSPortalService.revokeUserAccess(int connectionID,
List<String> users,
String run,
List<String> samples)
Routine to remove users' access to samples that the caller has PI access to, or where the caller has all sample access. |
void |
NGSPortalService.saveBatched(int connectionID,
int projectID,
String newnotes)
|
void |
NGSPortalService.saveNotes(int connectionID,
int projectID,
String runName,
String pI,
String application,
String personnel,
String newNotes)
Save Notes to the Database. |
void |
NGSPortalService.savePersonneltoDB(int connectionID,
int projectID,
String newISAssignee,
String oldISAssignee)
|
void |
NGSPortalService.saveSecondaryAnalysisNotes(int connectionID,
int analysisID,
String notes)
|
void |
NGSPortalService.saveSecondaryAssignedDate(int connectionID,
int projectID,
Date newValue)
|
void |
NGSPortalService.saveSecondaryCompleteDate(int connectionID,
int projectID,
Date date)
|
void |
NGSPortalService.saveSecondaryDeliveryDate(int connectionID,
int projectID,
Date newValue)
|
void |
NGSPortalService.saveSecondaryStartDate(int connectionID,
int projectID,
Date newValue)
|
void |
NGSPortalService.sendEmailNotification(int connectionID,
String runName,
String application,
String pI,
String assignerLanID,
String notes,
String newAssignee,
String oldAssignee,
int projectID)
Send an email to the new person assigned to a project, and the old person no longer assigned to a project |
boolean |
NGSPortalService.sendWeeklyReport(String lanID,
int connectionID)
|
boolean |
NGSPortalService.setIsBIC(int connectionID,
boolean isBIC,
int projectID)
Sets all the samples for a project to have their isBIC field either be true or false |
boolean |
NGSPortalService.setRunData(int connectionID,
String piName,
String runID,
RunData theRun,
List<SampleInfo> samples,
int[] deletedIDs)
Update all the metadata for a given run, owned by a given PI, and for its samples |
boolean |
NGSPortalService.updateGroup(int connectionID,
int groupID,
String name,
String description)
Updates information about an existing group |
void |
NGSPortalService.updateProject(int connectionID,
String projectName,
String notes,
boolean isReanalysis,
int[] seqSampleIDs,
Integer leadID,
Integer specID,
Integer piID)
Updates an existing project. |
|
||||||||||
| PREV NEXT | FRAMES NO FRAMES | |||||||||