edu.mayo.bsi.ngsportal.shared
Interface NGSPortalService

All Superinterfaces:

com.google.gwt.user.client.rpc.RemoteService

All Known Implementing Classes:

NGSPortalServiceImpl

@RemoteServiceRelativePath(value="NGSPortal")
public interface NGSPortalService
extends com.google.gwt.user.client.rpc.RemoteService

The client side stub for the RPC service.

Field Summary

static int	kAttachToGroup Specifies that the key : value pair is about a Group
static int	kAttachToProject Specifies that the key : value pair is about a Project
static int	kAttachToRun Specifies that the key : value pair is about a run
static int	kAttachToSample Specifies that the key : value pair is about a sample
static int	kAttachToSequencedSample Specifies that the key : value pair is about a sequenced sample
static int	kAttachToUser Specifies that the key : value pair is about a user
static int	kFirstLabUserRole The smallest role number that specifies a lab related user
static int	kIndexSeqLength Allowed length for a non-empty Index Sequence
static int	kLastLabUserRole The largest role number that specifies a lab related user
static int	kRoleAdmin
static int	kRoleCoPI
static int	kRoleInformaticsLead
static int	kRoleInformaticsPhdLead
static int	kRoleInformaticsSpecialist
static int	kRoleIt
static int	kRoleLabManager
static int	kRoleLabTech
static int	kRolePI
static int	kRoleProjCreator
static int	kRoleProjLead
static int	kRoleProjPI
static int	kRoleProjSpec
static int	kRoleResearcher
static int	kRoleSpa
static int	kRoleStatistician

Method Summary

boolean	addExternalUser(String firstName, String lastName, String id) Add an external user to the database
int	addGroup(int connectionID, String name, String description) Adds a new group
boolean	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	addNewRerun(int connectionID, int projectID, String projectName)
boolean	addNote(int connectionID, String note, String tableName, int rowID) Adds a note to the database
String	addProject(int connectionID, String notes, boolean isReanalysis, int[] seqSampleIDs, Integer leadID, Integer specID, Integer piID) Adds a new project.
boolean	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	addUsersToGroup(int connectionID, int groupID, Map<String,Integer> users) Add users to an existing group
boolean	addUsersToProject(int connectionID, Map<String,Boolean> users, int role, String project) Give one or more users' access to a project
boolean	checkAccessPrivilages(String string)
boolean	deleteGroup(int connectionID, int groupID) Delete an existing group
boolean	deleteNote(int connectionID, String tableName, int rowID, Date noteDate) Deletes a note from the database.
Map<String,Integer>	getAllSecondaryStatuses()
List<String>	getAnalysisStatuses() Get the names for each of the analysis statuses the database recognizes
List<String>	getAnalysisTypes() Get the names for each of the analysis types the database recognizes
List<AnalysisInfo>	getAnalyzedSamples(int connectionID, String theRun) Finds all the samples for a run that have had an analysis done
List<String>	getApplicationTypes() Get the Descriptions for each of the application types the database recognizes
List<String>	getApplicationTypes(String runID, String pi) Get the Descriptions for each of the application types the database recognizes, that occur with the specified PI and / or runID
int	getApplicationTypesForSamples(int[] sampleIDs) Gets the ID of the Application Type for more of the passed in samples than anyone else
List<SGEScriptSummary>	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>	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>	getCompletedRuns(int connectionID, String piName, String runID) Get all the completed runs
ConnectionResponse	getConnection() Ask the server for the information the client needs in order to send data to the server
List<ContactInfo>	getContacts(int connectionID, int[] contactIDs) Gets one or more contacts.
Map<String,PrimaryAnalysisBean>	getCurrentPrimaryStatus(int connectionID) Get the latest primary analysis statuses, from all the primary analysis results that have been updated in the last week
String	getDefaultProjectName(String runName, String appType, String pi, boolean isReanalysis) 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
Map<String,Integer>	getErrorsPerRun(SGEFilter filter, int connectionID) Returns a set of pairs of RunIDs - ScriptNames and error counts defined by the passed filter object.
List<FileLocation>	getFileLocations() Get a List of the available FileLocations that files might be saved in
Map<String,Integer>	getFlowcellsPerMonth(SGEFilter filter, int connectionID)
List<GroupInfo>	getGroups(int connectionID) Get the list of all the groups in the DB
List<InstrumentInfo>	getInstrumentHistory(int connectionID, String instrument) Get all the actions recorded for the given instrument
Map<String,String>	getInstrumentStatus(int connectionID) Query the Primary Analysis DB for the runs that have completed the given task, and when they did it
Map<String,String>	getISdetails() Get a map from LAN IDs to names for all the Informatics Specialists
List<ResultInfo>	getMatchingRuns(int connectionID, String piName, String runID, String sample, String application, String rlimsProject, String rlimsID, Date startDate, Date endDate, boolean onlyAnalyzed, String projName) Search the database for all the runs matching the criteria given, and return them
List<Note>	getNote(int connectionID, String tableName, int rowID) Get one or more notes from the database
int	getPIForSamples(int[] sampleIDs) Gets the ContactLinker ID of the Contact who is the PI for more of the passed in samples than anyone else
List<String>	getPINames() Get the names of all the PIs in the database
List<String>	getPrimaryAnalysisStatuses() Get the names for each of the Primary Analysis Statuses the database recognizes
List<String>	getProjectNames(int connectionID) Get the names of all the secondary analysis projects in the database that this user can see
List<ProjectInfo>	getProjects(int connectionID, int[] projIDs) Gets one or more projects.
List<SecondaryProjectInfo>	getProjects(int connectionID, String projectName) Get all the Secondary Projects created by this individual, or the single project projectName
ProjectSummaryBuilder	getProjectsSummary(int connectionID, String userName, Date fromDate, Date toDate)
List<QCResult>	getQCResults(int connectionID, String sampleName, String runID) Get all the information about the QCResults for a sample from a given run
List<String>	getReadTypes() Get the Descriptions for each of the read types the database recognizes
List<ResultInfo>	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>	getRLIMSIDs(int connectionID) Get all the RLIMS Sample "Sample IDs" in the database that this user can see
List<String>	getRLIMSProjectNames(int connectionID) Get all the RLIMS project names in the database that this user can see
List<String>	getRoles() Get all the Contact Roles in the database
RunData	getRunData(int connectionID, String piName, String runID) Get all the metadata from a given run, owned by a given PI
List<String>	getRunIDs(int connectionID) Get all the run IDs in the database this user can see
List<String>	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
boolean	getRunSecondaryAnalysisStatus(List<Integer> sampleIDs) Runs a SQL query to find if any of the Sequenced Samples in sampleIDs have a Secondary Analysis result of Delivered
List<String>	getSampleNames(int connectionID) Get the names of all the samples in the DB
List<SampleInfo>	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>	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>	getSamplesPerMonth(SGEFilter filter, int connectionID) Returns a set of pairs of months and unique samples defined by the passed filter object.
List<SGEScriptSummary>	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<SecondaryDetails>	getSecondaryAnalysisHistory(int connectionID, int secondaryProjectID)
List<Analysis2>	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>>	getSecondaryStatus(int connectionID)
Map<String,Integer>	getSGEFlowcellsPerMonth(SGEFilter filter, int connectionID)
List<SGEScriptSummary>	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>	getValidRLIMS(SGEFilter filter, int connectionID) Queries the portal database and returns a list of possible RunIDs falling within the provided SGEFilter
List<String>	getValidRunTypes(int connectionID) Returns a list of possible Run Types (eg., exome, whole_genome,...) available
Map<String,Double>	getWallClockPerRun(SGEFilter filter, int connectionID) Returns a set of pairs of WallClock times and RunIDs defined by the passed filter object.
Map<String,Double>	getWallClockPerSample(SGEFilter filter, int connectionID) Returns a set of pairs of WallClock times and SampleIDs defined by the passed filter object.
boolean	grantProjectAccess(int connectionID, String project, String run, List<String> samples) Routine to add samples to a project
boolean	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
ConnectionResponse	logIn(String userName, String password, int connectionID) Tell the server the lanID and Password (encrypted) of the person doing the querying, and get told by the server if the lan ID and password are valid
void	logOut(String userName, String password, int connectionID) Tell the server to forget about this user, and the user's current search
boolean	parseRunFile(String filePath, String user, String password) Parses the passed in file.
boolean	removeFromFamily(int connectionID, String family, String rlimsID, String parentID) Remove a sample from a family
void	removeProject(int connectionID, String projectName) Removes an existing project.
boolean	removeUsersFromGroup(int connectionID, int groupID, List<String> users) Remove users from a group
boolean	removeUsersFromProject(int connectionID, List<String> users, String project) Routine to remove one or more users' access to a project
boolean	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	revokeProjectAccess(int connectionID, String project, String run, List<String> samples) Routine to remove samples from a project
boolean	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	saveBatched(int connectionID, int projectID, String newnotes)
void	saveNotes(int connectionID, int projectID, String runName, String pI, String application, String personnel, String newNotes) Save Notes to the Database.
void	savePersonneltoDB(int connectionID, int projectID, String newISAssignee, String oldISAssignee)
void	saveSecondaryAnalysisNotes(int connectionID, int analysisID, String notes)
void	saveSecondaryAssignedDate(int connectionID, int projectID, Date newValue)
void	saveSecondaryCompleteDate(int connectionID, int projectID, Date date)
void	saveSecondaryDeliveryDate(int connectionID, int projectID, Date newValue)
void	saveSecondaryStartDate(int connectionID, int projectID, Date newValue)
void	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	sendWeeklyReport(String lanID, int connectionID)
boolean	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	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	updateAnalysis(String analysisPath, String uID, String password) Update the database with all the new analyses that have been added
boolean	updateGroup(int connectionID, int groupID, String name, String description) Updates information about an existing group
void	updateProject(int connectionID, String projectName, String notes, boolean isReanalysis, int[] seqSampleIDs, Integer leadID, Integer specID, Integer piID) Updates an existing project.
void	writedatatofile(int connectionID, String exportdata)

Field Detail

kIndexSeqLength

static final int kIndexSeqLength

Allowed length for a non-empty Index Sequence

See Also:

Constant Field Values

kAttachToSample

static final int kAttachToSample

Specifies that the key : value pair is about a sample

See Also:

Constant Field Values

kAttachToSequencedSample

static final int kAttachToSequencedSample

Specifies that the key : value pair is about a sequenced sample

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Constant Field Values

kAttachToRun

static final int kAttachToRun

Specifies that the key : value pair is about a run

See Also:

Constant Field Values

kAttachToUser

static final int kAttachToUser

Specifies that the key : value pair is about a user

See Also:

Constant Field Values

kAttachToGroup

static final int kAttachToGroup

Specifies that the key : value pair is about a Group

See Also:

Constant Field Values

kAttachToProject

static final int kAttachToProject

Specifies that the key : value pair is about a Project

See Also:

Constant Field Values

kRolePI

static final int kRolePI

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Constant Field Values

kRoleCoPI

static final int kRoleCoPI

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Constant Field Values

kRoleResearcher

static final int kRoleResearcher

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Constant Field Values

kRoleInformaticsPhdLead

static final int kRoleInformaticsPhdLead

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Constant Field Values

kRoleInformaticsLead

static final int kRoleInformaticsLead

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Constant Field Values

kRoleInformaticsSpecialist

static final int kRoleInformaticsSpecialist

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Constant Field Values

kRoleStatistician

static final int kRoleStatistician

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Constant Field Values

kRoleIt

static final int kRoleIt

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Constant Field Values

kRoleSpa

static final int kRoleSpa

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Constant Field Values

kRoleLabManager

static final int kRoleLabManager

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Constant Field Values

kRoleLabTech

static final int kRoleLabTech

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kRoleAdmin

static final int kRoleAdmin

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kRoleProjCreator

static final int kRoleProjCreator

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Constant Field Values

kRoleProjLead

static final int kRoleProjLead

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kRoleProjSpec

static final int kRoleProjSpec

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kRoleProjPI

static final int kRoleProjPI

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Constant Field Values

kFirstLabUserRole

static final int kFirstLabUserRole

The smallest role number that specifies a lab related user

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Constant Field Values

kLastLabUserRole

static final int kLastLabUserRole

The largest role number that specifies a lab related user

See Also:

Constant Field Values

Method Detail

getConnection

ConnectionResponse getConnection()

Ask the server for the information the client needs in order to send data to the server

Returns:

A ConnectionResponse object with the relevant information

logIn

ConnectionResponse logIn(String userName,
                         String password,
                         int connectionID)

Tell the server the lanID and Password (encrypted) of the person doing the querying, and get told by the server if the lan ID and password are valid

Parameters:

userName - User's lanID

password - User's password, encrypted to the server's specifications

connectionID - The unique ID of the connection, so server can track multiple connection at the same time.

Returns:

Updated ConnectionResponse if user logged in successfully, else null

logOut

void logOut(String userName,
            String password,
            int connectionID)

Tell the server to forget about this user, and the user's current search

Parameters:

userName - User's lanID

password - User's password, encrypted to the server's specifications

connectionID - The unique ID of the connection, so server can track multiple connection at the same time.

getApplicationTypes

List<String> getApplicationTypes()

Get the Descriptions for each of the application types the database recognizes

Returns:

List of Strings, one description per string

getApplicationTypes

List<String> getApplicationTypes(String runID,
                                 String pi)

Get the Descriptions for each of the application types the database recognizes, that occur with the specified PI and / or runID

Parameters:

runID - Name of the run of interest, or null if don't care

pi - LanID of the PI of interest, or null if don't care

Returns:

List of Strings, possibly empty (if PI doesn't have any samples in runID), never null

getApplicationTypesForSamples

int getApplicationTypesForSamples(int[] sampleIDs)

Gets the ID of the Application Type for more of the passed in samples than anyone else

Parameters:

sampleIDs - Array of SequencedSample IDs, must not be empty or null

Returns:

DB ID of the Application Type, or -1 if there was a problem

getReadTypes

List<String> getReadTypes()

Get the Descriptions for each of the read types the database recognizes

Returns:

List of Strings, one description per string

getAnalysisTypes

List<String> getAnalysisTypes()

Get the names for each of the analysis types the database recognizes

Returns:

List of Strings, one name per string

getAnalysisStatuses

List<String> getAnalysisStatuses()

Get the names for each of the analysis statuses the database recognizes

Returns:

List of Strings, one status per string

getFileLocations

List<FileLocation> getFileLocations()

Get a List of the available FileLocations that files might be saved in

Returns:

List of FileLocation objects, or null if there was a problem

getPrimaryAnalysisStatuses

List<String> getPrimaryAnalysisStatuses()

Get the names for each of the Primary Analysis Statuses the database recognizes

Returns:

List of Strings, one name per string

getCurrentPrimaryStatus

Map<String,PrimaryAnalysisBean> getCurrentPrimaryStatus(int connectionID)
                                                        throws ConnectionException

Get the latest primary analysis statuses, from all the primary analysis results that have been updated in the last week

Parameters:

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

Returns:

Map from run names to the latest primary analysis status information about that run

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getRoles

List<String> getRoles()

Get all the Contact Roles in the database

Returns:

List of Strings, one role ID per string

getPINames

List<String> getPINames()

Get the names of all the PIs in the database

Returns:

List of names, in the form Last Name, First Name

getPIForSamples

int getPIForSamples(int[] sampleIDs)

Gets the ContactLinker ID of the Contact who is the PI for more of the passed in samples than anyone else

Parameters:

sampleIDs - Array of SequencedSample IDs, must not be empty or null

Returns:

DB ID of the Contact, or -1 if there was a problem

getRunIDs

List<String> getRunIDs(int connectionID)
                       throws ConnectionException

Get all the run IDs in the database this user can see

Parameters:

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

Returns:

List of Strings, one run ID per string

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getRunIDs

List<String> getRunIDs(int connectionID,
                       String pi,
                       String appType)
                       throws ConnectionException

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

Parameters:

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

pi - LanID of the PI of interest, or null if don't care

appType - Description of the application type of interest, or null if don't care

Returns:

List of Strings, possibly empty (if PI doesn't have any samples in runID), never null

Throws:

ConnectionException

getMatchingRuns

List<ResultInfo> getMatchingRuns(int connectionID,
                                 String piName,
                                 String runID,
                                 String sample,
                                 String application,
                                 String rlimsProject,
                                 String rlimsID,
                                 Date startDate,
                                 Date endDate,
                                 boolean onlyAnalyzed,
                                 String projName)
                                 throws Exception

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 Run RLIMS BatchID 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

Returns:

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

Throws:

Exception

getRunData

RunData getRunData(int connectionID,
                   String piName,
                   String runID)
                   throws ConnectionException

Get all the metadata from a given run, owned by a given PI

Parameters:

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

piName - The Last Name, First Name of the PI to look for, empty or null if don't care

runID - The run ID we're interested in

Returns:

RunData object with the metadata, or null if no run was found

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getRetainedSamples

List<ResultInfo> getRetainedSamples(int connectionID,
                                    String piName,
                                    String runID,
                                    String sample,
                                    boolean isPrimary)
                                    throws ConnectionException

Get all the runs and samples that have data files that are currently marked for non-deletion

Parameters:

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

piName - The Last Name, First Name of the PI to look for, or null if not restricting on that

runID - The run ID we're interested in, null or empty if not restricting on that

sample - Name of the sample we're searching for

isPrimary - True if want to know about primary analysis files, false if want to know about secondary analysis files

Returns:

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

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

retainSample

boolean retainSample(int connectionID,
                     Date deleteDate,
                     String piName,
                     List<String> runIDs,
                     String sample,
                     String requestor,
                     boolean isPrimary)
                     throws ConnectionException

Mark a sample or set of samples as needing their data files to be retained

Parameters:

connectionID - The id of the connection, so know that user has write access

deleteDate - New deletion date for the sample(s)

piName - The Last Name, First Name of the PI who owns the samples, or null if not restricting on that

runIDs - The run IDs we're interested in, list must not be null or empty

sample - Name of the sample we're updating, null for all samples on that run

requestor - Person making the update request. If user is not an "all access" user, this is ignored, and the user's name is used

isPrimary - True if want to retain primary analysis files, false if want to retain secondary analysis files

Returns:

True if added successfully, else false if there was a problem

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

setRunData

boolean setRunData(int connectionID,
                   String piName,
                   String runID,
                   RunData theRun,
                   List<SampleInfo> samples,
                   int[] deletedIDs)
                   throws ConnectionException

Update all the metadata for a given run, owned by a given PI, and for its samples

Parameters:

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

piName - The Last Name, First Name of the PI to look for

runID - The run ID we're interested in

theRun - The updated run metadata, or null if no change to that data

samples - The changed samples for the this run - PI pair

deletedIDs - Array of the ids of Samples that were deleted, null if none were deleted

Returns:

True if changed things successfully, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getSamples

List<SampleInfo> getSamples(int connectionID,
                            String piName,
                            String runID,
                            String appType,
                            String projectName)
                            throws ConnectionException

Get all the information about all the samples from a given run, owned by a given PI

Parameters:

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

piName - The Last Name, First Name of the PI to look for

runID - The run ID we're interested in. One of this and projID can NOT be blank

appType - If not empty or null, The type of application to return

projectName - The name of the project we're interested in. One of this and runID can NOT be blank

Returns:

List of SampleInfo, possibly empty but never null

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

addExternalUser

boolean addExternalUser(String firstName,
                        String lastName,
                        String id)

Add an external user to the database

Parameters:

firstName - The new user's first name

lastName - The new user's last name

id - The new user's unique ID. Cannot match any id in the DB, or any Mayo LAN ID

Returns:

True if the id was unique, and were able to add the user to the DB, else false

grantUserAccess

boolean grantUserAccess(int connectionID,
                        Map<String,Boolean> users,
                        int role,
                        String run,
                        List<String> samples)
                        throws ConnectionException

Routine to give users access to samples that the caller has access to

Parameters:

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

users - Map of the users being granted access to whether they're internal or not. For internal users, the String should be the user's lanID. For external, it needs to be a unique last name, first name

role - The role the Users are being given for these samples

run - The name of the run they're being granted access to

samples - List of samples from the run that the users are being granted access to, null or empty to grant access to all the samples of that run

Returns:

True if changed things successfully, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

revokeUserAccess

boolean revokeUserAccess(int connectionID,
                         List<String> users,
                         String run,
                         List<String> samples)
                         throws ConnectionException

Routine to remove users' access to samples that the caller has PI access to, or where the caller has all sample access.

Parameters:

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

users - List of the users losing access

run - The name of the run they're losing access to

samples - List of samples from the run that the users are losing access to, null or empty to revoke access to all the samples of that run

Returns:

True if changed things successfully, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

addUsersToProject

boolean addUsersToProject(int connectionID,
                          Map<String,Boolean> users,
                          int role,
                          String project)
                          throws ConnectionException

Give one or more users' access to a project

Parameters:

connectionID - The id of the person doing the add, must be part of Bioinformatics Staff

users - Map of the users being granted access to whether they're internal or not. For internal users, the String should be the user's lanID. For external, it needs to be a unique last name, first name

role - The role the Users are being given for this project

project - Name of the project the users are being added to

Returns:

True if changed things successfully, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

removeUsersFromProject

boolean removeUsersFromProject(int connectionID,
                               List<String> users,
                               String project)
                               throws ConnectionException

Routine to remove one or more users' access to a project

Parameters:

connectionID - The id of the person doing the add, must be part of Bioinformatics Staff

users - List of the users losing access

project - The name of the project they're losing access to

Returns:

True if changed things successfully, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

grantProjectAccess

boolean grantProjectAccess(int connectionID,
                           String project,
                           String run,
                           List<String> samples)
                           throws ConnectionException

Routine to add samples to a project

Parameters:

connectionID - The id of the person doing the add, must be part of Bioinformatics Staff

project - Name of the project getting access to the samples

run - The name of the run they're being granted access to

samples - List of samples from the run that are being added to the project, null or empty to grant access to all the samples of that run

Returns:

True if changed things successfully, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

revokeProjectAccess

boolean revokeProjectAccess(int connectionID,
                            String project,
                            String run,
                            List<String> samples)
                            throws ConnectionException

Routine to remove samples from a project

Parameters:

connectionID - The id of the person doing the remove, must be part of Bioinformatics Staff

project - Name of the project losing access to the samples

run - The name of the run the project is losing access to

samples - List of samples from the run that the project is losing access to, null or empty to revoke access to all the samples of that run

Returns:

True if changed things successfully, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getSampleNames

List<SampleInfo> getSampleNames(int connectionID,
                                String piName,
                                String runID)
                                throws ConnectionException

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

Parameters:

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

piName - The Last Name, First Name of the PI to look for, empty or null if don't care

runID - The run ID we're interested in, empty or null if don't care

Returns:

List of SampleInfo, possibly empty but never null, with only the sample name, sample id, sampleRLIMSID, and species filled in

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getSampleNames

List<String> getSampleNames(int connectionID)
                            throws ConnectionException

Get the names of all the samples in the DB

Parameters:

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

Returns:

List of String, possibly empty but never null, holding the sample name

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getCompletedRuns

List<RunData> getCompletedRuns(int connectionID,
                               String piName,
                               String runID)
                               throws ConnectionException

Get all the completed runs

Parameters:

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

piName - The Last Name, First Name of the PI to look for, empty or null if don't care

runID - The run ID we're interested in, empty or null if want all completed runs

Returns:

List of the runs, could be empty. Null if there was a problem

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getQCResults

List<QCResult> getQCResults(int connectionID,
                            String sampleName,
                            String runID)
                            throws ConnectionException

Get all the information about the QCResults for a sample from a given run

Parameters:

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

sampleName - The name of the Sample to look for

runID - The run ID we're interested in

Returns:

List of QCResult, possibly empty but never null

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getSecondaryAnalysisResults

List<Analysis2> getSecondaryAnalysisResults(int connectionID,
                                            Date finishedCutoff)
                                            throws ConnectionException

Get all the information about the Secondary Analysis results for a sample from a given run

Parameters:

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

finishedCutoff - The cutoff date for finished runs (i.e. only report on finished runs that finished at or after this date). Defaults to one week ago if is null

Returns:

List of Analysis2, possibly empty but never null

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

parseRunFile

boolean parseRunFile(String filePath,
                     String user,
                     String password)

Parses the passed in file. If it's a directory, parses all the .xml files in that directory, or in any of its sub-directories. Ignores any runs already in the DB.

Parameters:

filePath - XML file or directory to use

user - user ID to give to the DB, in order to get write permission

password - password to give to the DB, in order to get write permission

Returns:

True if everything was successful, else false

getAnalyzedSamples

List<AnalysisInfo> getAnalyzedSamples(int connectionID,
                                      String theRun)
                                      throws ConnectionException

Finds all the samples for a run that have had an analysis done

Parameters:

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

theRun - The run whose samples we're looking at

Returns:

List of the samples. As this can only be called when one or more of the run's samples has been analyzed, the list should never be empty

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

addNote

boolean addNote(int connectionID,
                String note,
                String tableName,
                int rowID)
                throws ConnectionException

Adds a note to the database

Parameters:

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

note - The Note

tableName - Name of the table the note's about

rowID - The id of the item in the table the note is about

Returns:

True if added the note, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getNote

List<Note> getNote(int connectionID,
                   String tableName,
                   int rowID)
                   throws ConnectionException

Get one or more notes from the database

Parameters:

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

tableName - Name of the table we're looking for notes for, null or empty string to get notes for all tables

rowID - The row id of the item in the table that we're looking for notes for, or kInvalidID to get the notes for all the items for table tableName

Returns:

List of notes that match the criteria (which might be empty) or null if there was a non-connection problem

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

deleteNote

boolean deleteNote(int connectionID,
                   String tableName,
                   int rowID,
                   Date noteDate)
                   throws ConnectionException

Deletes a note from the database.

Parameters:

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

tableName - Name of the table we're looking for notes for, null or empty string to get notes for all tables

rowID - The row id of the item in the table that we're looking for notes for, or kInvalidID to get the notes for all the items for table tableName

noteDate - The date of the note

Returns:

True if deleted the note, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

updateAnalysis

boolean updateAnalysis(String analysisPath,
                       String uID,
                       String password)

Update the database with all the new analyses that have been added

Parameters:

analysisPath - The path to where the analysis results are located

uID - The user ID to use when modifying the database

password - The password to use when modifying the database

Returns:

True if added successfully, else false

getInstrumentStatus

Map<String,String> getInstrumentStatus(int connectionID)
                                       throws ConnectionException

Query the Primary Analysis DB for the runs that have completed the given task, and when they did it

Parameters:

connectionID - The user's connection ID

Returns:

Map of runs and their dates, or null if there was a problem

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getInstrumentHistory

List<InstrumentInfo> getInstrumentHistory(int connectionID,
                                          String instrument)
                                          throws ConnectionException

Get all the actions recorded for the given instrument

Parameters:

connectionID - The user's connection ID

instrument - The name of the instrument to look up

Returns:

List of the Instrument's history, in sorted order, or null if there was a problem

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

addGroup

int addGroup(int connectionID,
             String name,
             String description)
             throws ConnectionException

Adds a new group

Parameters:

connectionID - The user's connection ID

name - Name of the new group. Must be unique

description - The group description

Returns:

ID of the new group, or -1 if there was a problem

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

updateGroup

boolean updateGroup(int connectionID,
                    int groupID,
                    String name,
                    String description)
                    throws ConnectionException

Updates information about an existing group

Parameters:

connectionID - The user's connection ID

groupID - The DB ID for the group

name - The group name

description - The group description

Returns:

True if successfully updated the group, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

deleteGroup

boolean deleteGroup(int connectionID,
                    int groupID)
                    throws ConnectionException

Delete an existing group

Parameters:

connectionID - The user's connection ID

groupID - The DB ID for the group

Returns:

True if successfully deleted the group, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

addUsersToGroup

boolean addUsersToGroup(int connectionID,
                        int groupID,
                        Map<String,Integer> users)
                        throws ConnectionException

Add users to an existing group

Parameters:

connectionID - The user's connection ID

groupID - The DB ID for the group

users - Map holding the users' lanIDs and roles

Returns:

True if successfully updated the group, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

removeUsersFromGroup

boolean removeUsersFromGroup(int connectionID,
                             int groupID,
                             List<String> users)
                             throws ConnectionException

Remove users from a group

Parameters:

connectionID - The user's connection ID

groupID - The DB ID for the group

users - List holding the lanIDs of the users being removed from the group

Returns:

True if successfully updated the group, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

getGroups

List<GroupInfo> getGroups(int connectionID)
                          throws ConnectionException

Get the list of all the groups in the DB

Parameters:

connectionID - The user's connection ID

Returns:

List of all the Groups in the DB

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

addKeyValuePair

boolean addKeyValuePair(int connectionID,
                        int table,
                        String name,
                        String more,
                        String key,
                        String value)
                        throws ConnectionException

Add a Key : Value pair about a specified item to the DB

Parameters:

connectionID - The user's connection ID. Must be part of Informatics staff

table - Specifier for which table to attach the data to

name - Unique specifier for the table of interest

more - Additional data to create a unique specifier for the table of interest, or null if don't need it

key - Key of the key : Value pair to add

value - Value of the key : Value pair to add

Returns:

True if added the Key: Value pair to the DB, false if there was a problem

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

addToFamily

boolean addToFamily(int connectionID,
                    String family,
                    String parentID,
                    String rlimsID,
                    String sampleParentID,
                    String name,
                    Boolean isMale)
                    throws ConnectionException

Add a sample to a family, creating the family if necessary.

Parameters:

connectionID - The user's connection ID. Must be part of Informatics staff

family - The name of the family, each family has a unique name

parentID - The RLIMS ID of a sample belonging to a parent who is part of this family. The method will fail if the sample ID is not null and the sample doesn't exist, or if the sample is not part of the family

rlimsID - The RLIMS Family ID of the sample being added to the family

sampleParentID - The RLIMS Parent ID of the sample being added to the family

name - Name of the sample being added to the family, can be null or empty

isMale - True if male, false if female, null if not known

Returns:

True if added the sample to the family, false if there was a problem

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

removeFromFamily

boolean removeFromFamily(int connectionID,
                         String family,
                         String rlimsID,
                         String parentID)
                         throws ConnectionException

Remove a sample from a family

Parameters:

connectionID - The user's connection ID. Must be part of Informatics staff

family - The name of the family, each family has a unique name

rlimsID - The RLIMS family ID of the sample being removed from the family

parentID - The RLIMS parent ID of the sample being removed from the family

Returns:

True sample was part of the family, and isn't any more, false if there was a problem, or if the sample was not part of the family to begin with

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID

addProject

String addProject(int connectionID,
                  String notes,
                  boolean isReanalysis,
                  int[] seqSampleIDs,
                  Integer leadID,
                  Integer specID,
                  Integer piID)
                  throws ConnectionException

Adds a new project.

Parameters:

connectionID - The user's connection ID

notes - The project notes.

isReanalysis - Is this a reanalysis project.

seqSampleIDs - One or more sequenced sample IDs assigned to the project.

leadID - Contact user ID for the informatics lead, or null if none

specID - Contact user ID for the informatics specialist, or null if none

piID - Contact user ID for the PI, or null if none

Returns:

Name of the new project.

Throws:

ConnectionException

updateProject

void updateProject(int connectionID,
                   String projectName,
                   String notes,
                   boolean isReanalysis,
                   int[] seqSampleIDs,
                   Integer leadID,
                   Integer specID,
                   Integer piID)
                   throws ConnectionException

Updates an existing project.

Parameters:

connectionID - The user's connection ID

projectName - Name of project to update.

notes - The project notes.

isReanalysis - Is this a reanalysis project.

seqSampleIDs - One or more sequenced sample IDs assigned to the project.

leadID - Contact user ID for the informatics lead

specID - Contact user ID for the informatics specialist

piID - Contact user ID for the PI

Throws:

ConnectionException

getProjects

List<SecondaryProjectInfo> getProjects(int connectionID,
                                       String projectName)
                                       throws ConnectionException

Get all the Secondary Projects created by this individual, or the single project projectName

Parameters:

connectionID - The user's connection ID

projectName - If not null, the name of the single project to get. Only will get if the user created the project, or has canEditAll authorization

Returns:

List of Secondary projects, or null if there was a problem

Throws:

ConnectionException

removeProject

void removeProject(int connectionID,
                   String projectName)
                   throws ConnectionException

Removes an existing project.

Parameters:

connectionID - The user's connection ID

projectName - Name of project to remove.

Throws:

ConnectionException

getProjects

List<ProjectInfo> getProjects(int connectionID,
                              int[] projIDs)
                              throws ConnectionException

Gets one or more projects.

Parameters:

connectionID - The user's connection ID

projIDs - ID(s) of the projects to fetch. If empty or null, all projects are returned.

Returns:

List of projects, or null if there was a problem

Throws:

ConnectionException

getProjectNames

List<String> getProjectNames(int connectionID)
                             throws ConnectionException

Get the names of all the secondary analysis projects in the database that this user can see

Parameters:

connectionID - The user's connection ID

Returns:

List of names

Throws:

ConnectionException

getRLIMSProjectNames

List<String> getRLIMSProjectNames(int connectionID)
                                  throws ConnectionException

Get all the RLIMS project names in the database that this user can see

Parameters:

connectionID - The user's connection ID

Returns:

List of names

Throws:

ConnectionException

getRLIMSIDs

List<String> getRLIMSIDs(int connectionID)
                         throws ConnectionException

Get all the RLIMS Sample "Sample IDs" in the database that this user can see

Parameters:

connectionID - The user's connection ID

Returns:

List of names

Throws:

ConnectionException

getContacts

List<ContactInfo> getContacts(int connectionID,
                              int[] contactIDs)
                              throws ConnectionException

Gets one or more contacts.

Parameters:

connectionID - The user's connection ID

contactIDs - ID(s) of the contacts to fetch. If empty or null, all contacts are returned.

Returns:

List of contacts, or null if there was a problem

Throws:

ConnectionException

getProjectsSummary

ProjectSummaryBuilder getProjectsSummary(int connectionID,
                                         String userName,
                                         Date fromDate,
                                         Date toDate)
                                         throws ConnectionException

Throws:

ConnectionException

getDefaultProjectName

String getDefaultProjectName(String runName,
                             String appType,
                             String pi,
                             boolean isReanalysis)

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

Returns:

A unique Project name that matches the specified characteristics

getSumCPUSecondsPerScript

List<SGEScriptSummary> getSumCPUSecondsPerScript(SGEFilter filter,
                                                 int connectionID)
                                                 throws ConnectionException

Queries the portal database and returns a list of SGEScriptSummary containing the sum of cpuseconds consumed by the scripts defined by the provided SGEFilter

Parameters:

filter - An SGEFilter (null gives no filtering)

connectionID - The user's connection ID.

Returns:

List List of scripts and their total cpu seconds or null if not authorized or no data

Throws:

ConnectionException

getAvgCPUSecondsPerScript

List<SGEScriptSummary> getAvgCPUSecondsPerScript(SGEFilter filter,
                                                 int connectionID)
                                                 throws ConnectionException

Queries the portal database and returns a list of SGEScriptSummary containing the average of cpuseconds consumed by the scripts defined by the provided SGEFilter

Parameters:

filter - An SGEFilter (null gives no filtering)

connectionID - The user's connection ID.

Returns:

List List of scripts and their average cpu seconds or null if not authorized or no data

Throws:

ConnectionException

getScriptInvocations

List<SGEScriptSummary> getScriptInvocations(SGEFilter filter,
                                            int connectionID)
                                            throws ConnectionException

Queries the portal database and returns a list of SGEScriptSummary containing the total script invocations in the runs defined by the provided SGEFilter

Parameters:

filter - An SGEFilter (null gives no filtering)

connectionID - The user's connection ID.

Returns:

List List of scripts and the number of executions or null if not authorized or no data

Throws:

ConnectionException

getAvgRun

List<SGEScriptSummary> getAvgRun(SGEFilter filter,
                                 int connectionID)
                                 throws ConnectionException

Queries the portal database and returns a list of SGEScriptSummary containing the sum of cpuseconds consumed by the scripts defined by the provided SGEFilter

Parameters:

filter - An SGEFilter (null gives no filtering)

connectionID - The user's connection ID.

Returns:

List List of scripts and their total cpu seconds or null if not authorized or no data

Throws:

ConnectionException

getValidRLIMS

List<String> getValidRLIMS(SGEFilter filter,
                           int connectionID)
                           throws ConnectionException

Queries the portal database and returns a list of possible RunIDs falling within the provided SGEFilter

Parameters:

filter - An SGEFilter (null gives no filtering)

connectionID - The user's connection ID.

Returns:

List List of RunIDs or null if none available

Throws:

ConnectionException

getValidRunTypes

List<String> getValidRunTypes(int connectionID)
                              throws ConnectionException

Returns a list of possible Run Types (eg., exome, whole_genome,...) available

Parameters:

connectionID - The user's connection ID.

Returns:

List of run types

Throws:

ConnectionException

getWallClockPerRun

Map<String,Double> getWallClockPerRun(SGEFilter filter,
                                      int connectionID)
                                      throws ConnectionException

Returns a set of pairs of WallClock times and RunIDs defined by the passed filter object.

Parameters:

filter - An SGEFilter (null gives no filtering)

connectionID - The user's connection ID.

Returns:

Map or null if no data available

Throws:

ConnectionException

getWallClockPerSample

Map<String,Double> getWallClockPerSample(SGEFilter filter,
                                         int connectionID)
                                         throws ConnectionException

Returns a set of pairs of WallClock times and SampleIDs defined by the passed filter object.

Parameters:

filter - An SGEFilter (null gives no filtering)

connectionID - The user's connection ID.

Returns:

Map or null if no data available

Throws:

ConnectionException

getSamplesPerMonth

Map<String,Integer> getSamplesPerMonth(SGEFilter filter,
                                       int connectionID)
                                       throws ConnectionException

Returns a set of pairs of months and unique samples defined by the passed filter object.

Parameters:

filter - An SGEFilter(null gives no filtering)

connectionID - The user's connection ID.

Returns:

Map or null if no data available

Throws:

ConnectionException

getErrorsPerRun

Map<String,Integer> getErrorsPerRun(SGEFilter filter,
                                    int connectionID)
                                    throws ConnectionException

Returns a set of pairs of RunIDs - ScriptNames and error counts defined by the passed filter object.

Parameters:

filter - An SGEFilter(null gives no filtering)

connectionID - The user's connection ID.

Returns:

Map or null if no data available

Throws:

ConnectionException

getSecondaryStatus

Map<String,List<SecondaryAnalysisBean>> getSecondaryStatus(int connectionID)
                                                           throws ConnectionException

Throws:

ConnectionException

sendEmailNotification

void sendEmailNotification(int connectionID,
                           String runName,
                           String application,
                           String pI,
                           String assignerLanID,
                           String notes,
                           String newAssignee,
                           String oldAssignee,
                           int projectID)
                           throws ConnectionException

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

Parameters:

connectionID - 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

assignerLanID - 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

Throws:

ConnectionException

checkAccessPrivilages

boolean checkAccessPrivilages(String string)

saveSecondaryStartDate

void saveSecondaryStartDate(int connectionID,
                            int projectID,
                            Date newValue)
                            throws ConnectionException

Throws:

ConnectionException

saveSecondaryDeliveryDate

void saveSecondaryDeliveryDate(int connectionID,
                               int projectID,
                               Date newValue)
                               throws ConnectionException

Throws:

ConnectionException

saveSecondaryCompleteDate

void saveSecondaryCompleteDate(int connectionID,
                               int projectID,
                               Date date)
                               throws ConnectionException

Throws:

ConnectionException

saveNotes

void saveNotes(int connectionID,
               int projectID,
               String runName,
               String pI,
               String application,
               String personnel,
               String newNotes)
               throws ConnectionException

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

Parameters:

connectionID - 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

Throws:

ConnectionException

saveSecondaryAssignedDate

void saveSecondaryAssignedDate(int connectionID,
                               int projectID,
                               Date newValue)
                               throws ConnectionException

Throws:

ConnectionException

addNewRerun

String addNewRerun(int connectionID,
                   int projectID,
                   String projectName)
                   throws ConnectionException

Throws:

ConnectionException

writedatatofile

void writedatatofile(int connectionID,
                     String exportdata)
                     throws IOException

Throws:

IOException

getSecondaryAnalysisHistory

List<SecondaryDetails> getSecondaryAnalysisHistory(int connectionID,
                                                   int secondaryProjectID)

getFlowcellsPerMonth

Map<String,Integer> getFlowcellsPerMonth(SGEFilter filter,
                                         int connectionID)

savePersonneltoDB

void savePersonneltoDB(int connectionID,
                       int projectID,
                       String newISAssignee,
                       String oldISAssignee)
                       throws ConnectionException

Throws:

ConnectionException

saveSecondaryAnalysisNotes

void saveSecondaryAnalysisNotes(int connectionID,
                                int analysisID,
                                String notes)
                                throws ConnectionException

Throws:

ConnectionException

getAllSecondaryStatuses

Map<String,Integer> getAllSecondaryStatuses()

getSGEFlowcellsPerMonth

Map<String,Integer> getSGEFlowcellsPerMonth(SGEFilter filter,
                                            int connectionID)
                                            throws ConnectionException

Throws:

ConnectionException

getISdetails

Map<String,String> getISdetails()

Get a map from LAN IDs to names for all the Informatics Specialists

Returns:

Map from Lan IDs to Names in the form "[last name], [first name]", or empty map if couldn't load it

getRunSecondaryAnalysisStatus

boolean getRunSecondaryAnalysisStatus(List<Integer> sampleIDs)

Runs a SQL query to find if any of the Sequenced Samples in sampleIDs have a Secondary Analysis result of Delivered

Parameters:

sampleIDs - List of IDs to look for, must not be empty or null

Returns:

True if any have been delivered, false otherwise

saveBatched

void saveBatched(int connectionID,
                 int projectID,
                 String newnotes)
                 throws ConnectionException

Throws:

ConnectionException

sendWeeklyReport

boolean sendWeeklyReport(String lanID,
                         int connectionID)
                         throws ConnectionException

Throws:

ConnectionException

setIsBIC

boolean setIsBIC(int connectionID,
                 boolean isBIC,
                 int projectID)
                 throws ConnectionException

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

Returns:

True if assigned the value, else false

Throws:

ConnectionException - If the connectionID is not valid, or if it doesn't match the session connection ID