edu.iastate.metnet.interfaces
Interface MyPaper

All Superinterfaces:

javax.ejb.EJBObject, java.rmi.Remote

public interface MyPaper
extends javax.ejb.EJBObject

Remote interface for MyPaper.

Version:

${version}

Author:

XDoclet

Method Summary

void	approveCandidate(java.util.Vector blockidlist) approve the candidate maybe we need lock the table to prevent any concurrent approve procedure???
void	attachPathway(java.lang.Integer interactionID, java.lang.Integer pathwayID) attach the interaciton to the pathway
void	attachPathwayToClass(java.lang.Integer classId, java.util.Collection pbidList) add pathway to selected category
void	batchDelete(java.util.Vector vector) batch delete
void	batchInsert(java.util.Vector vector) batch insert
void	batchUpdate(java.util.Vector vector) batch update
java.util.Collection	changeSoybeanOR() change the duplicate soybean probes in the network to the OR relation except for those exising OR relation, use flattern OR relation.
java.lang.Integer	checkOrCreateLatestHistory(java.lang.Integer blockId, java.lang.String username) since things are complicated to create all initial history in advance, we move this step to the action on the normal blockunit operation
void	checkOrInsertAbbreviation(java.lang.Integer blockid, java.lang.String abbreviation) insert the abbreviation for the blockunit
void	checkOrInsertComment(java.lang.Integer blockid, java.util.Vector commentList) check or insert comment
java.lang.Integer	checkOrInsertEntity(java.lang.String name, java.lang.String entityType, java.lang.String organism, java.lang.String source, java.lang.String username) check if the entity exists, if not, create a new one
void	checkOrInsertEntitySynonym(java.lang.Integer entityid, java.util.Vector synonymList) insert the synonym list for the entity
void	checkOrInsertEntitywithcontext(java.lang.Integer blockid, java.lang.Integer entityid) fix the entitywithcontext at background
java.lang.Integer	checkOrInsertPathway(java.util.Collection ibidList, java.lang.String pathwayName, java.lang.String username, java.lang.String organism) check or create a pathway based on the interaction list
void	checkOrInsertReference(java.lang.Integer blockid, java.util.Vector refereceList) check or insert reference
void	checkOrInsertSynonym(java.lang.Integer blockid, java.util.Vector synonymList) check or insert the synonym
java.lang.Integer	checkOrInsertTransInteraction(java.lang.Integer sourceBlockid, java.lang.Integer targetBlockid, java.lang.String interactionType, java.lang.String name, java.lang.String location, java.lang.String organism, java.lang.String username) create an transport, translation or transcription interaction and return the blockid of the interaction.
void	copyCategory(java.lang.Integer newParentClassId, java.lang.Integer oldParentClassId, java.lang.Integer childClassId) copy the category to the new position
java.lang.Integer	copyPathway(java.util.Collection pbidList, java.lang.String name, java.lang.String organism, java.lang.String username, java.lang.String source) This funciton copy the pathway specified by the blockid to a new pathway belongs to the specified organism.
void	createAgrisNetwork() create the AGRIS regulatory network pathways.
void	createAgrisPathway() create the pathway for AGRIS data, must after the network is created and expanded
java.lang.Integer	createBasicPathway(Blockunit blockunit, java.lang.String username) create pathway without the structure
void	createCategory(java.lang.Integer classId, java.lang.String name, java.lang.String username) create new category
void	createInitialHistory() create initial history for all blockunits in the database
void	createSoybeanLocus() create the soybean locus
void	deleteAbbreviation(java.lang.Integer blockid, java.lang.String abbreviation) delete the abbreviation for the blockunit and potential entity, if the abbreviation exists in the entity's table, move the abbreviation to all other blockunit' synonym table
void	deleteAbbreviationRule(java.lang.String shortterm, java.lang.String longterm) delete the abbreviation rule
void	deleteBlockunit(java.lang.Integer blockid, java.lang.String username, int callLevel) delete a blockunit
void	deleteCategory(java.lang.Integer classId) delete one category from the database
void	deleteComment(java.lang.Integer blockid, CommentObject commentObject) delete the comment from the blockunit
void	deleteReference(java.lang.Integer blockid, ReferenceObject referenceObject) delete the reference from the blockunit
void	deleteSynonym(java.lang.Integer blockid, java.lang.String synonym) delete the synonym for the blockunit and potential entity, if the synonym exists in the entity's table, move the synonym to all other blockunit'
void	detachPathway(java.lang.Integer ibid, java.lang.Integer pbid, java.lang.String username) detach the interaction from the pathway
void	detachPathwayFromClass(java.lang.Integer classId, java.util.Collection pbidList) detach the pathway from the class
void	extendLocusInPathway(java.lang.Integer pathwayid, java.lang.String username) extend all monomers in the pathway to the gene level, add translation and transcription if necessary
void	findOrInsertAbbreviationRule(java.lang.String shortterm, java.lang.String longterm) find or insert the abbreviation rule
java.util.Vector	findUser(User userObject) search by example
org.apache.commons.collections.keyvalue.MultiKey	fullCheckOrInsertEntitywithlocation(java.lang.String name, java.lang.String entityType, java.lang.String location, java.lang.String organism, java.lang.String source, java.lang.String username, java.lang.String aracycId) full insert blockunit and entity and entitywithcontext, since the data can be from expert data or aracyc, so source and username are parameters also
void	generateHistory(java.lang.Integer blockId) generate the history and the version graph record.
void	generateHistory(java.lang.Integer blockId, java.lang.Integer recordOldId, java.lang.String username) generate the history and the version graph record
void	generateSoybeanNetwork() generate soybean network from arabidopsis network
void	generateSynonyms() generate the synonyms
int	getCounter() a test of state in stateless session bean
void	insertBlockunitConfidence(int blockid, int locationConfidence, int functionConfidence) insert new confidence
void	mergeBlockunit(Blockunit blockunitOld, Blockunit blockunitNew, boolean replace, java.lang.String username) merge the two blockunits in the database.
void	moreSoybeanAnnotation() create more soybean annotation
void	moreSoybeanPathwayCategory() fill the category for soybean pathway
void	moveCategory(java.lang.Integer newParentClassId, java.lang.Integer oldParentClassId, java.lang.Integer childClassId) move the category to the new position
java.lang.Integer	moveInteractionHistory(Blockunit blockunit, java.lang.String username) move the current interaction to the history
java.lang.Integer	moveLiveEntityHistory(Blockunit blockunit) move the current live entity to the history
java.lang.Integer	movePathwayHistory(Blockunit blockunit, java.lang.String username) move the current pathway to the history
void	notifyPathwayStructureChange(java.util.Collection pbidList, java.lang.String username) change the pathway structure history.
java.util.Collection	permitOrganismList(java.lang.String username) get all organism that the user allowed to edit
java.lang.Integer	realizePathwayHistory(java.lang.Integer pbid, java.lang.Integer prid, java.lang.String pathwayName, java.lang.String username) concrete one history of the pathway into the database so we can use it for comparison or other purposed like a normal pathway
void	remoteDelete(java.lang.Object object) remote delete a database object
java.io.Serializable	remoteInsert(java.lang.Object object) remote insert a database object
void	remoteInsert(java.lang.Object object, java.io.Serializable serializable) remote insert a database object
void	remoteUpdate(java.lang.Object object) remote update a database object
void	remoteUpdate(java.lang.Object oldRecord, java.lang.Object newRecord) remote update a database object which has a natural key by itself
void	removeChebiLink(EntityOntology entityOntology) remove the entityontology
void	removeGroup(java.lang.Integer groupid) remove the selected group
void	renameCategory(java.lang.Integer classId, java.lang.String name) rename the category
void	saveGraph(java.lang.Integer pbid, MetnetPathway metnetPathway, org._3pq.jgrapht.DirectedGraph network, java.util.Map dataMap, org.apache.commons.collections.map.MultiKeyMap coeffMap, java.lang.String sessionUsername, java.lang.String sessionOrganism, boolean isAracycUpdate) save graph to the database.
java.lang.Integer	saveInteractionDeletionHistory(java.lang.Integer blockId, java.lang.String username) save the deletion history, who delete it and when it is deleted, we can use null name to determine this is a saved deletion history
java.lang.Integer	saveLiveEntityDeletionHistory(java.lang.Integer blockId, java.lang.String username) save the deletion history
void	saveNetwork4All() save all compilation in the database.
java.lang.Integer	savePathwayDeletionHistory(java.lang.Integer blockId, java.lang.String username) move the current pathway to the history.
Blockunit	undeleteBlockunit(java.lang.Integer blockId, java.lang.String username) undelete one history
void	updateAbbreviationrules(java.util.Vector rulevec) update the rules changed by users
void	updateBlockunitConfidence(int blockid, int locationConfidence, int functionConfidence) update existing confidence
void	updateMembers(java.lang.Integer groupid, java.util.Vector memberList) update the member list

Methods inherited from interface javax.ejb.EJBObject

getEJBHome, getHandle, getPrimaryKey, isIdentical, remove

Method Detail

getCounter

int getCounter()
               throws java.rmi.RemoteException

a test of state in stateless session bean

Returns:

the counter

Throws:

java.rmi.RemoteException

approveCandidate

void approveCandidate(java.util.Vector blockidlist)
                      throws java.rmi.RemoteException

approve the candidate maybe we need lock the table to prevent any concurrent approve procedure???

Parameters:

blockidlist - the id list of the candidates

Throws:

EJBException - Throw if the instance could not perform the function requested by the container because of an system-level error

java.rmi.RemoteException

generateSynonyms

void generateSynonyms()
                      throws java.rmi.RemoteException

generate the synonyms

Throws:

EJBException - Throw if the instance could not perform the function requested by the container because of an system-level error

java.rmi.RemoteException

updateAbbreviationrules

void updateAbbreviationrules(java.util.Vector rulevec)
                             throws java.rmi.RemoteException

update the rules changed by users

Throws:

java.rmi.RemoteException

mergeBlockunit

void mergeBlockunit(Blockunit blockunitOld,
                    Blockunit blockunitNew,
                    boolean replace,
                    java.lang.String username)
                    throws java.rmi.RemoteException

merge the two blockunits in the database.

Parameters:

blockunitOld - the old blockunit

blockunitNew - the new blockunit

replace - if true, all old blockunits in the database are replaced by the new blockunit. if false, old blockunit information are not deleted, only the interaction parts are replaced while the old information is merged to new blockunit information set

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

deleteBlockunit

void deleteBlockunit(java.lang.Integer blockid,
                     java.lang.String username,
                     int callLevel)
                     throws java.rmi.RemoteException

delete a blockunit

Parameters:

blockid - the blockid of the blockunit

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

attachPathway

void attachPathway(java.lang.Integer interactionID,
                   java.lang.Integer pathwayID)
                   throws java.rmi.RemoteException

attach the interaciton to the pathway

Parameters:

interactionID - the blokid of the interaction

pathwayID - the blockid of the pathway

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

detachPathway

void detachPathway(java.lang.Integer ibid,
                   java.lang.Integer pbid,
                   java.lang.String username)
                   throws java.rmi.RemoteException

detach the interaction from the pathway

Parameters:

ibid - the blockid of the interaction

pbid - the blockid of the pathway

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

remoteInsert

java.io.Serializable remoteInsert(java.lang.Object object)
                                  throws java.rmi.RemoteException

remote insert a database object

Parameters:

object - the DAO

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

remoteInsert

void remoteInsert(java.lang.Object object,
                  java.io.Serializable serializable)
                  throws java.rmi.RemoteException

remote insert a database object

Parameters:

object - the DAO

serializable - the id of the object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

batchInsert

void batchInsert(java.util.Vector vector)
                 throws java.rmi.RemoteException

batch insert

Parameters:

vector - the list of object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

remoteUpdate

void remoteUpdate(java.lang.Object object)
                  throws java.rmi.RemoteException

remote update a database object

Parameters:

object - the DAO

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

remoteUpdate

void remoteUpdate(java.lang.Object oldRecord,
                  java.lang.Object newRecord)
                  throws java.rmi.RemoteException

remote update a database object which has a natural key by itself

Parameters:

oldRecord - the old DAO

newRecord - the new DAO

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

remoteDelete

void remoteDelete(java.lang.Object object)
                  throws java.rmi.RemoteException

remote delete a database object

Parameters:

object - the DAO

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

batchDelete

void batchDelete(java.util.Vector vector)
                 throws java.rmi.RemoteException

batch delete

Parameters:

vector - list of the object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

batchUpdate

void batchUpdate(java.util.Vector vector)
                 throws java.rmi.RemoteException

batch update

Parameters:

vector - list of the object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

checkOrInsertEntitywithcontext

void checkOrInsertEntitywithcontext(java.lang.Integer blockid,
                                    java.lang.Integer entityid)
                                    throws java.rmi.RemoteException

fix the entitywithcontext at background

Parameters:

blockid - the blockid of the blockunit

entityid - the entityid of the entity

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

fullCheckOrInsertEntitywithlocation

org.apache.commons.collections.keyvalue.MultiKey fullCheckOrInsertEntitywithlocation(java.lang.String name,
                                                                                     java.lang.String entityType,
                                                                                     java.lang.String location,
                                                                                     java.lang.String organism,
                                                                                     java.lang.String source,
                                                                                     java.lang.String username,
                                                                                     java.lang.String aracycId)
                                                                                     throws java.rmi.RemoteException

full insert blockunit and entity and entitywithcontext, since the data can be from expert data or aracyc, so source and username are parameters also

Parameters:

name - name of the entitywithlocation

entityType - entity type of the entitywithlocation

location - location of the entitywithlocation

organism - organism of the entitywithlocation

source - source of the data

username - username of the data source

Returns:

blockid, entityid and insertion flag of the live entity

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

checkOrInsertSynonym

void checkOrInsertSynonym(java.lang.Integer blockid,
                          java.util.Vector synonymList)
                          throws java.rmi.RemoteException

check or insert the synonym

Parameters:

blockid - the id of the blockunit

synonymList - the synonym list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

checkOrInsertAbbreviation

void checkOrInsertAbbreviation(java.lang.Integer blockid,
                               java.lang.String abbreviation)
                               throws java.rmi.RemoteException

insert the abbreviation for the blockunit

Parameters:

blockid - the id of the blockunit

synonymList - the synonym list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

deleteSynonym

void deleteSynonym(java.lang.Integer blockid,
                   java.lang.String synonym)
                   throws java.rmi.RemoteException

delete the synonym for the blockunit and potential entity, if the synonym exists in the entity's table, move the synonym to all other blockunit'

Parameters:

blockid - id of the blockunit

synonym - the synonym of the blockunit to be removed

Throws:

java.rmi.RemoteException

deleteAbbreviation

void deleteAbbreviation(java.lang.Integer blockid,
                        java.lang.String abbreviation)
                        throws java.rmi.RemoteException

delete the abbreviation for the blockunit and potential entity, if the abbreviation exists in the entity's table, move the abbreviation to all other blockunit' synonym table

Parameters:

blockid - id of the blockunit

abbreviation - the abbreviation of the blockunit

Throws:

java.rmi.RemoteException

checkOrInsertReference

void checkOrInsertReference(java.lang.Integer blockid,
                            java.util.Vector refereceList)
                            throws java.rmi.RemoteException

check or insert reference

Parameters:

blockid - blockid of the blockunit

refereceList - the list of reference object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

checkOrInsertComment

void checkOrInsertComment(java.lang.Integer blockid,
                          java.util.Vector commentList)
                          throws java.rmi.RemoteException

check or insert comment

Parameters:

blockid - id of the blockunit

commentList - the list of comment object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

deleteReference

void deleteReference(java.lang.Integer blockid,
                     ReferenceObject referenceObject)
                     throws java.rmi.RemoteException

delete the reference from the blockunit

Parameters:

blockid - the id of the blockunit

referenceObject - the reference object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

deleteComment

void deleteComment(java.lang.Integer blockid,
                   CommentObject commentObject)
                   throws java.rmi.RemoteException

delete the comment from the blockunit

Parameters:

blockid - the id of hte blockunit

commentObject - the comment object

Throws:

EJBException - any remote call exeption

java.rmi.RemoteException

checkOrInsertEntitySynonym

void checkOrInsertEntitySynonym(java.lang.Integer entityid,
                                java.util.Vector synonymList)
                                throws java.rmi.RemoteException

insert the synonym list for the entity

Parameters:

entityid - the id of the entity

synonymList - the synonym list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

removeChebiLink

void removeChebiLink(EntityOntology entityOntology)
                     throws java.rmi.RemoteException

remove the entityontology

Parameters:

entityOntology - the entityonlogy not contain the serial id

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

removeGroup

void removeGroup(java.lang.Integer groupid)
                 throws java.rmi.RemoteException

remove the selected group

Parameters:

groupid - the id of the group

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

updateMembers

void updateMembers(java.lang.Integer groupid,
                   java.util.Vector memberList)
                   throws java.rmi.RemoteException

update the member list

Parameters:

groupid - the id of the group

memberList - member list only contain the username key

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

checkOrInsertEntity

java.lang.Integer checkOrInsertEntity(java.lang.String name,
                                      java.lang.String entityType,
                                      java.lang.String organism,
                                      java.lang.String source,
                                      java.lang.String username)
                                      throws java.rmi.RemoteException

check if the entity exists, if not, create a new one

Parameters:

name - entity name

entityType - entity type like gene, rna or polypeptide

organism - entity organism like human, mouse or arabidopsis

source - source of the data

username - username of the data owner

Returns:

the entity id

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

extendLocusInPathway

void extendLocusInPathway(java.lang.Integer pathwayid,
                          java.lang.String username)
                          throws java.rmi.RemoteException

extend all monomers in the pathway to the gene level, add translation and transcription if necessary

Parameters:

pathwayid - the blockid of pathway

username - user name since new interaction may be created

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

deleteAbbreviationRule

void deleteAbbreviationRule(java.lang.String shortterm,
                            java.lang.String longterm)
                            throws java.rmi.RemoteException

delete the abbreviation rule

Parameters:

shortterm - short term

longterm - long term

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findOrInsertAbbreviationRule

void findOrInsertAbbreviationRule(java.lang.String shortterm,
                                  java.lang.String longterm)
                                  throws java.rmi.RemoteException

find or insert the abbreviation rule

Parameters:

shortterm - short term

longterm - long term

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

insertBlockunitConfidence

void insertBlockunitConfidence(int blockid,
                               int locationConfidence,
                               int functionConfidence)
                               throws java.rmi.RemoteException

insert new confidence

Parameters:

blockid - the blockid of the blockunit

locationConfidence - confidence of the location

functionConfidence - confidence of the function

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

updateBlockunitConfidence

void updateBlockunitConfidence(int blockid,
                               int locationConfidence,
                               int functionConfidence)
                               throws java.rmi.RemoteException

update existing confidence

Parameters:

blockid - the blockid of the blockunit

locationConfidence - confidence of the location

functionConfidence - confidence of the function

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

moveLiveEntityHistory

java.lang.Integer moveLiveEntityHistory(Blockunit blockunit)
                                        throws java.rmi.RemoteException

move the current live entity to the history

Parameters:

blockId - the block id of the live entity

Returns:

the history record Id

Throws:

EJBException - any remote exception

java.rmi.RemoteException

moveInteractionHistory

java.lang.Integer moveInteractionHistory(Blockunit blockunit,
                                         java.lang.String username)
                                         throws java.rmi.RemoteException

move the current interaction to the history

Parameters:

blockunit - the block id of the interaction

username - session username

Returns:

the history record Id

Throws:

EJBException - any remote exception

java.rmi.RemoteException

movePathwayHistory

java.lang.Integer movePathwayHistory(Blockunit blockunit,
                                     java.lang.String username)
                                     throws java.rmi.RemoteException

move the current pathway to the history

Parameters:

blockId - the block id of the pathway

username - session username

Returns:

the history record Id

Throws:

EJBException - any remote exception

java.rmi.RemoteException

generateHistory

void generateHistory(java.lang.Integer blockId,
                     java.lang.Integer recordOldId,
                     java.lang.String username)
                     throws java.rmi.RemoteException

generate the history and the version graph record

Parameters:

blockId - the blockid which has just been updated

recordNewId - new record id

recordOldId - old record id

username - session username

Throws:

EJBException - any remote exception

java.rmi.RemoteException

createInitialHistory

void createInitialHistory()
                          throws java.rmi.RemoteException

create initial history for all blockunits in the database

Parameters:

username - session username

Throws:

EJBException - any remote exception

java.rmi.RemoteException

checkOrCreateLatestHistory

java.lang.Integer checkOrCreateLatestHistory(java.lang.Integer blockId,
                                             java.lang.String username)
                                             throws java.rmi.RemoteException

since things are complicated to create all initial history in advance, we move this step to the action on the normal blockunit operation

Parameters:

blockId - the blockid of the blockunit

username - session username

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

generateHistory

void generateHistory(java.lang.Integer blockId)
                     throws java.rmi.RemoteException

generate the history and the version graph record. By default use the latest two

Parameters:

blockId - the blockid which has just been updated

Throws:

EJBException - any remote exception

java.rmi.RemoteException

notifyPathwayStructureChange

void notifyPathwayStructureChange(java.util.Collection pbidList,
                                  java.lang.String username)
                                  throws java.rmi.RemoteException

change the pathway structure history. If nothing is changed in the structure, then skip this

Parameters:

pbidList - the blockid list of the pathway

username - session username

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

createAgrisNetwork

void createAgrisNetwork()
                        throws java.rmi.RemoteException

create the AGRIS regulatory network pathways. each pathway contains one locus and its neighbors.

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

checkOrInsertTransInteraction

java.lang.Integer checkOrInsertTransInteraction(java.lang.Integer sourceBlockid,
                                                java.lang.Integer targetBlockid,
                                                java.lang.String interactionType,
                                                java.lang.String name,
                                                java.lang.String location,
                                                java.lang.String organism,
                                                java.lang.String username)
                                                throws java.rmi.RemoteException

create an transport, translation or transcription interaction and return the blockid of the interaction.

Parameters:

sourceBlockid - the blockid of the blockunit in the source location

targetBlockid - the blockid of the blockunit in the target location

interactionType - the interaction type, only be trasnportation, transcription, or translation

name - the name of the interaction, used for insertion only

location - the location of the interaction, used for insertion only

organism - the organism of the interaction, used for insertion only

username - user name since new interaction may be created

Returns:

the blockid of the trans-interaction

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

checkOrInsertPathway

java.lang.Integer checkOrInsertPathway(java.util.Collection ibidList,
                                       java.lang.String pathwayName,
                                       java.lang.String username,
                                       java.lang.String organism)
                                       throws java.rmi.RemoteException

check or create a pathway based on the interaction list

Parameters:

ibidList - the blockid list of interaction

pathwayName - the name of the pathway if it needs creation

username - the user who input the pathway

Returns:

the block id of the pathway

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

createAgrisPathway

void createAgrisPathway()
                        throws java.rmi.RemoteException

create the pathway for AGRIS data, must after the network is created and expanded

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

saveInteractionDeletionHistory

java.lang.Integer saveInteractionDeletionHistory(java.lang.Integer blockId,
                                                 java.lang.String username)
                                                 throws java.rmi.RemoteException

save the deletion history, who delete it and when it is deleted, we can use null name to determine this is a saved deletion history

Parameters:

blockId - the block id of the interaction

username - session username

Returns:

the history record Id

Throws:

EJBException - any remote exception

java.rmi.RemoteException

saveLiveEntityDeletionHistory

java.lang.Integer saveLiveEntityDeletionHistory(java.lang.Integer blockId,
                                                java.lang.String username)
                                                throws java.rmi.RemoteException

save the deletion history

Parameters:

blockId - the block id of the live entity

Returns:

the history record Id

Throws:

EJBException - any remote exception

java.rmi.RemoteException

savePathwayDeletionHistory

java.lang.Integer savePathwayDeletionHistory(java.lang.Integer blockId,
                                             java.lang.String username)
                                             throws java.rmi.RemoteException

move the current pathway to the history.

Parameters:

blockunit - the blockunit instance of the pathway

username - session username

Returns:

the history record Id

Throws:

EJBException - any remote exception

java.rmi.RemoteException

undeleteBlockunit

Blockunit undeleteBlockunit(java.lang.Integer blockId,
                            java.lang.String username)
                            throws java.rmi.RemoteException

undelete one history

Parameters:

blockId - the block id of the blockunit to be undeleted

Returns:

the block id of the undeleted stuff

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

realizePathwayHistory

java.lang.Integer realizePathwayHistory(java.lang.Integer pbid,
                                        java.lang.Integer prid,
                                        java.lang.String pathwayName,
                                        java.lang.String username)
                                        throws java.rmi.RemoteException

concrete one history of the pathway into the database so we can use it for comparison or other purposed like a normal pathway

Parameters:

pbid - the blockid of the pathway

prid - the record id of the history

pathwayName - new pathway name

username - session username

Returns:

the blockid of the new pathway

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

saveNetwork4All

void saveNetwork4All()
                     throws java.rmi.RemoteException

save all compilation in the database. this must be called after any changes in the data structure of matching network

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

moveCategory

void moveCategory(java.lang.Integer newParentClassId,
                  java.lang.Integer oldParentClassId,
                  java.lang.Integer childClassId)
                  throws java.rmi.RemoteException

move the category to the new position

Parameters:

newParentClassId - the new parent category

oldParentClassId - the old parent category

childClassId - the child category

Throws:

EJBException - remote call exception

java.rmi.RemoteException

copyCategory

void copyCategory(java.lang.Integer newParentClassId,
                  java.lang.Integer oldParentClassId,
                  java.lang.Integer childClassId)
                  throws java.rmi.RemoteException

copy the category to the new position

Parameters:

newParentClassId - the new parent category

oldParentClassId - the old parent category

childClassId - the child category

Throws:

EJBException - remote call exception

java.rmi.RemoteException

renameCategory

void renameCategory(java.lang.Integer classId,
                    java.lang.String name)
                    throws java.rmi.RemoteException

rename the category

Parameters:

classId - the class id of the category

name - the new name of the category

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

detachPathwayFromClass

void detachPathwayFromClass(java.lang.Integer classId,
                            java.util.Collection pbidList)
                            throws java.rmi.RemoteException

detach the pathway from the class

Parameters:

classId - the class id of the class

pbidList - the pathway blockid list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

deleteCategory

void deleteCategory(java.lang.Integer classId)
                    throws java.rmi.RemoteException

delete one category from the database

Parameters:

classId - the class id of the category

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

createCategory

void createCategory(java.lang.Integer classId,
                    java.lang.String name,
                    java.lang.String username)
                    throws java.rmi.RemoteException

create new category

Parameters:

classId - the class id of current category

name - the new category name

username - the user who provides the data

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

attachPathwayToClass

void attachPathwayToClass(java.lang.Integer classId,
                          java.util.Collection pbidList)
                          throws java.rmi.RemoteException

add pathway to selected category

Parameters:

classId - the class id of the selected category

pbidList - the pathway blockid list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

copyPathway

java.lang.Integer copyPathway(java.util.Collection pbidList,
                              java.lang.String name,
                              java.lang.String organism,
                              java.lang.String username,
                              java.lang.String source)
                              throws java.rmi.RemoteException

This funciton copy the pathway specified by the blockid to a new pathway belongs to the specified organism. By default, the organism is not identical so we only copy all metabolite only interactions

Parameters:

pbid - the blockid of the pathway

name - new pathway name

organism - the new organism, normally should be different with the old organism of the pathway

username - user name

source - data source

Returns:

the new blockid of the pathway

Throws:

java.rmi.RemoteException

createSoybeanLocus

void createSoybeanLocus()
                        throws java.rmi.RemoteException

create the soybean locus

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

generateSoybeanNetwork

void generateSoybeanNetwork()
                            throws java.rmi.RemoteException

generate soybean network from arabidopsis network

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

moreSoybeanAnnotation

void moreSoybeanAnnotation()
                           throws java.rmi.RemoteException

create more soybean annotation

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

moreSoybeanPathwayCategory

void moreSoybeanPathwayCategory()
                                throws java.rmi.RemoteException

fill the category for soybean pathway

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

createBasicPathway

java.lang.Integer createBasicPathway(Blockunit blockunit,
                                     java.lang.String username)
                                     throws java.rmi.RemoteException

create pathway without the structure

Parameters:

blockunit - the blockunit information

username - user name

Returns:

the blockid of the pathway

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

changeSoybeanOR

java.util.Collection changeSoybeanOR()
                                     throws java.rmi.RemoteException

change the duplicate soybean probes in the network to the OR relation except for those exising OR relation, use flattern OR relation.

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

saveGraph

void saveGraph(java.lang.Integer pbid,
               MetnetPathway metnetPathway,
               org._3pq.jgrapht.DirectedGraph network,
               java.util.Map dataMap,
               org.apache.commons.collections.map.MultiKeyMap coeffMap,
               java.lang.String sessionUsername,
               java.lang.String sessionOrganism,
               boolean isAracycUpdate)
               throws java.rmi.RemoteException

save graph to the database. The pathway must have already been in te database. Otherwise, manually create the basic information of the pathway without structure information.

Parameters:

pbid - blockid of the pathway to be saved

metnetPathway - pathway information

network - the network

dataMap - the data map

coeffMap - the coefficient map

sessionUsername - session username

sessionOrganism - session organism

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findUser

java.util.Vector findUser(User userObject)
                          throws java.rmi.RemoteException

search by example

Parameters:

userObject -

Returns:

the list similar to the example case

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

permitOrganismList

java.util.Collection permitOrganismList(java.lang.String username)
                                        throws java.rmi.RemoteException

get all organism that the user allowed to edit

Parameters:

username -

Returns:

the organism list that the user can edit

Throws:

EJBException - any remote call exception

java.rmi.RemoteException