""" CCP4DbMackup.py: CCP4 GUI Project Copyright (C) 2012 STFC This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. """ """ Liz Potterton June 2012 - create and benchmark mock database """ from dbapi import CCP4DbApi,CCP4ModelData,CCP4XtalData class BuildDb: TASKS = { 'SCA' : { 'in' : ['UNM'], 'out' : ['OBS'] }, 'MR_1' : { 'in' : ['OBS', 'PDB', 'SEQ'], 'out' : ['PDB','PHZ'] }, 'MR_2' : { 'in' : ['OBS', 'PHZ', 'SEQ'], 'out' : ['PDB_6','PDB_7','PDB_8','PDB_9','PDB_10'], 'sub' : [ 'MR_2_A' , 'MR_2_B','MR_2_C', 'MR_2_D', 'MR_2_E','MR_2_F' ] }, 'BUCREF' : { 'in' : ['OBS', 'PHZ', 'PDB'], 'out' : ['PDB'], 'sub' : [ 'BUC','REF','BUC','REF','BUC','REF',] }, 'REF_1' : { 'in' : ['OBS', 'PHZ', 'PDB'], 'out' : ['PHZ','MAP','PDB' ] }, 'BLD_1' : { 'in' : ['OBS', 'PHZ', 'PDB'], 'out' : ['PDB'] }, 'MR_2_A' : { 'in' : ['OBS', 'PHZ', 'SEQ'], 'out' : ['PDB_1','PDB_2','PDB_3','PDB_4','PDB_5'] }, 'MR_2_B' : { 'in' : ['OBS', 'PHZ', 'PDB_1'], 'out' : ['PDB_6'] }, 'MR_2_C' : { 'in' : ['OBS', 'PHZ', 'PDB_2'], 'out' : ['PDB_7'] }, 'MR_2_D' : { 'in' : ['OBS', 'PHZ', 'PDB_3'], 'out' : ['PDB_8'] }, 'MR_2_E' : { 'in' : ['OBS', 'PHZ', 'PDB_4'], 'out' : ['PDB_9'] }, 'MR_2_F' : { 'in' : ['OBS', 'PHZ', 'PDB_5'], 'out' : ['PDB_10'] }, 'BUC' : { 'in' : ['OBS', 'PHZ', 'PDB'], 'out' : ['PDB'] }, 'REF' : { 'in' : ['OBS', 'PHZ', 'PDB'], 'out' : ['PDB','MAP'] } } PATTERNS = { 1 : [ 'SCA','SCA','MR_1','MR_2','BUCREF','REF_1','BLD_1','REF_1','BLD_1','REF_1','REF_1','BLD_1','REF_1' ] } FILECLASS = { 'PDB' : CCP4ModelData.CPdbDataFile, 'SEQ' : CCP4ModelData.CSeqDataFile, 'UNM' : CCP4XtalData.CUnmergedMtzDataFile, 'OBS' : CCP4XtalData.CObsDataFile, 'PHZ' : CCP4XtalData.CPhsDataFile, 'MAP' : CCP4XtalData.CMapCoeffsDataFile } FILETYPE = { 'PDB' : 2, 'SEQ' : 1, 'UNM' : 5, 'OBS' : 11, 'PHZ' : 12, 'MAP' : 13 } def __init__(self,fileName=None,mode='sqlite'): self.mode=mode self.db = CCP4DbApi.CDbApi(mode=mode,fileName=fileName,userName='me') self.db.setPreference('testFileExists',False) self.projectNumber = 0 def makeProject(self,pattern=1): self.projectNumber = self.projectNumber + 1 topJobList = [] projectId = self.db.createProject(projectName='test_project_'+str(self.projectNumber),projectDirectory='/Users/lizp/Desktop/test_projects') for taskName in self.PATTERNS.get(pattern): if len(taskName)>0: if len(topJobList)>0: previousJobId = topJobList[-1] else: previousJobId = None jobId = self.makeJob(projectId=projectId,taskName=taskName,previousJobId=previousJobId) topJobList.append(jobId) else: topJobList = [] return projectId def makeJob(self,projectId,taskName=None,parentJobId=None,previousJobId=None,details=None): if details is None: details = self.TASKS.get(taskName) jobId = self.db.createJob(projectId,taskName,jobTitle='whatever',status=CCP4DbApi.JOB_STATUS_FINISHED,parentJobId=parentJobId) self.makeFilesIn(projectId,jobId,details.get('in',[]),previousJobId=previousJobId) self.makeFilesOut(projectId,jobId,details.get('out',[])) if details.get('sub',None) is not None: subJobId = None for subName in details['sub']: subJobId = self.makeJob(projectId,taskName=subName,parentJobId=jobId,previousJobId=subJobId) return jobId def makeFilesIn(self,projectId,jobId,fileInList,previousJobId=None): for fileIn in fileInList: if fileIn.count('_'): ftype,num = fileIn.split('_') else: ftype = fileIn num = 0 if previousJobId is not None: fileIdList = self.db.getFileByJobContext(contextJobId=previousJobId,fileType=self.FILETYPE[ftype],projectId=projectId) else: fileIdList = [] if len(fileIdList)>0: self.db.createFileUse(jobId=jobId,fileId=fileIdList[0],role=CCP4DbApi.FILE_ROLE_IN) else: fileObject = self.FILECLASS[ftype]() fileObject.baseName=fileIn+'.'+fileObject.qualifiers('fileExtensions')[0] self.db.createFile(jobId=jobId,projectId=projectId,fileObject=fileObject,sourceFileName='/foo/bar/'+fileIn) def makeFilesOut(self,projectId,jobId,fileOutList): for fileOut in fileOutList: if fileOut.count('_'): ftype,num = fileOut.split('_') else: ftype = fileOut num = 0 fileObject = self.FILECLASS[ftype]() fileObject.baseName=fileOut+'.'+fileObject.qualifiers('fileExtensions')[0] self.db.createFile(jobId=jobId,projectId=projectId,fileObject=fileObject) def makeDb(): import os try: os.remove('/Users/lizp/Desktop/mockDb.sqlite') os.remove('/Users/lizp/Desktop/mockDb.xml') except: pass mDb = BuildDb('/Users/lizp/Desktop/mockDb.sqlite') projectId = mDb.makeProject() err = mDb.db.exportProjectXml(projectId=projectId,fileName='/Users/lizp/Desktop/mockDb.xml') print err.report()