inst/unitTests/test_main.R
In girke-lab/eiR-release: Accelerated similarity searching of small molecules
library(eiR)
library(snow)
library(DBI)
options(warn=2)
#options(error=dump.frames)
options(warnPartialMatchDollar=TRUE)
test_dir="test_workspace"
r<- 50
d<- 40
N<- 100
numUniqueDescriptors=96
j=1 #can only use 1 when using sqlite
runDir<-file.path(test_dir,paste("run",r,d,sep="-"))
fpDir=file.path(test_dir,"fp_test")
descType="ap"
sqliteSource=function(reset=FALSE){
require(eiR)
require(RSQLite)
path = file.path(test_dir,"data")
if(!file.exists(path))
dir.create(path,recursive=TRUE)
conn=initDb(file.path(path,"chem.db"))
#checkTrue(file.exists(file.path(test_dir,"data","chem.db")))
conn
}
resetDb <- function(conn){
tables = dbListTables(conn)
print(tables)
for(table in tables)
dbGetQuery(conn, paste("DROP TABLE ",table," CASCADE"))
initDb(conn)
}
pgSource=function(reset=FALSE){
require(eiR)
require(RPostgreSQL)
conn=dbConnect(dbDriver("PostgreSQL"),user="chemminer_tests",password="40ersfdv90erijgfk",
dbname="chemminer_tests",host="girke-db-1.bioinfo.ucr.edu")
if(reset)
resetDb(conn)
initDb(conn)
eiR:::setDefaultConn(conn)
conn
}
connSource = sqliteSource
#connSource = pgSource
connSource(TRUE) # reset postgres
lastRunId=0
#debug=TRUE
debug=FALSE
test_aa.eiInit <- function() {
#DEACTIVATED("slow")
cleanup()
connSource() #sets default connection
checkData <- function(cids,dir=test_dir){
checkTrue(file.exists(file.path(dir,"data","main.iddb")))
i <- readLines(file.path(dir,"data","main.iddb"))
checkEquals(length(i),N)
checkEquals(length(cids),N)
sdfFromDb = getCompounds(connSource(),cids)
checkEquals(length(sdfFromDb),N)
}
message("eiInit tests")
setDefaultDistance("dummy",function(x,y) x-y)
checkTrue(!is.null(eiR:::getDefaultDist("dummy")))
addTransform("dummy","d2",toObject=function(x,conn=NA,dir=".")x)
checkTrue(!is.null(eiR:::getTransform("dummy","d2")))
message("default descriptor")
data(sdfsample)
compoundIds = eiInit(sdfsample[1:N],descriptorType=descType,dir=test_dir)
#checkData(compoundIds)
message("fp descriptor")
dir.create(fpDir)
write.SDF(sdfsample[1:30],file.path(fpDir,"f1"))
write.SDF(sdfsample[31:60],file.path(fpDir,"f2"))
write.SDF(sdfsample[61:100],file.path(fpDir,"f3"))
# we just test with one node as SQLite does not support parallel writes
cl=makeCluster(1,type="SOCK",outfile=file.path(test_dir,"eiInit.snow"))
fpCids = eiInit(file.path(fpDir,c("f1","f2","f3")),dir=fpDir,descriptorType="fp",cl=cl,
connSource=connSource )
stopCluster(cl)
#checkData(fpCids)
}
testRefs <- function(){
200+c(1,2,5,8,9,10,11,17,18,19,20,23,24,25,26,29,31,33,34,36,38,43,45,46,47,48,49,51,53,66,67,70,71,72,73,74,75,77,78,79,80,81,82,83,87,88,89,91,99,100)
}
test_ba.parDist <- function(){
#DEACTIVATED("slow")
conn = connSource()
distance = eiR:::getDefaultDist("ap")
require(snow)
cl = makeSOCKcluster(3,outfile="")
set1=eiR:::readIddb(conn,file.path(test_dir,"data","main.iddb"))
set2 = testRefs()
if(debug){
print("set1")
print(set1)
print("set2")
print(set2)
}
eiR:::IddbVsIddbDist(conn,set1,set2, distance,"ap",file=file.path(test_dir,"parDist.final"),
cl=cl, connSource= connSource )
stopCluster(cl)
#
# checkTrue(file.exists(file.path(test_dir,"parDist.final")))
}
test_bb.eiMakeDb <- function() {
#DEACTIVATED("slow")
message(" eiMakeDb ")
conn = connSource()
runDbChecks = function(rid,targetSampleNum=20){
parameters = eiR:::runQuery(conn,paste("SELECT e.name,e.embedding_id,dimension,num_references FROM runs as r JOIN embeddings as e USING(embedding_id)
WHERE r.run_id = ",rid))
#print(parameters)
checkEquals(d,parameters$dimension)
checkEquals(r,parameters$num_references)
numRefs = eiR:::runQuery(conn,paste("SELECT count(*) FROM runs as r JOIN embeddings as e USING(embedding_id)
JOIN compound_group_members as refs ON(e.references_group_id=refs.compound_group_id)
WHERE r.run_id = ",rid))[[1]]
message("found ",numRefs," refs")
checkEquals(r,numRefs)
numCompounds = eiR:::runQuery(conn,paste("SELECT count(*) FROM runs as r
JOIN compound_group_members as cgm ON(r.compound_group_id=cgm.compound_group_id)
WHERE r.run_id = ",rid))[[1]]
checkEquals(N,numCompounds)
numSamples = eiR:::runQuery(conn,paste("SELECT count(*) FROM runs as r
JOIN compound_group_members as cgm ON(r.sample_group_id=cgm.compound_group_id)
WHERE r.run_id = ",rid))[[1]]
message("found ",numSamples," samples")
checkEquals(targetSampleNum,numSamples)
numDescriptors = eiR:::runQuery(conn,paste("SELECT count(distinct descriptor_id) FROM runs as r JOIN embedded_descriptors as ed USING(embedding_id)
WHERE r.run_id = ",rid))[[1]]
#checkEquals(N,numDescriptors)
#this should be 96 now because some descriptors are identical
# and we now only store a unique set
checkEquals(96,numDescriptors)
message("checking descriptors")
for(i in 1:numDescriptors)
checkDescriptor(conn,rid,descriptorIndex=i)
checkTrue(file.info(file.path(runDir,sprintf("matrix.%d-%d",r,d)))$size>0)
checkTrue(file.info(file.path(runDir,sprintf("matrix.query.%d-%d",r,d)))$size>0)
}
cl=makeCluster(j,type="SOCK",outfile="")
print("by file name")
refFile = file.path(test_dir,"reference_file.cdb")
eiR:::writeIddbFile((1:r)+200,refFile)
rid=eiMakeDb(refFile,d,cl=cl,descriptorType=descType,dir=test_dir,
connSource=connSource )
runDbChecks(rid,targetSampleNum = N*0.1)
unlink(runDir,recursive=TRUE)
print("by number")
rid=eiMakeDb(r,d,numSamples=20,cl=cl,descriptorType=descType,dir=test_dir,
connSource=connSource )
runDbChecks(rid)
unlink(runDir,recursive=TRUE)
print("by vector")
rid=eiMakeDb(testRefs(),d,numSamples=20,cl=cl,descriptorType=descType, dir=test_dir,
connSource=connSource )
stopCluster(cl)
runDbChecks(rid)
lastRunId<<-rid
}
test_ca.eiQuery <- function(){
#DEACTIVATED("slow")
message("eiQuery")
conn=connSource()
data(sdfsample)
runId = lastRunId
message("using runId ",runId)
message("eiQuery test 1")
results = eiQuery(runId,sdfsample[1:2],K=15,asSimilarity=TRUE,dir=test_dir)
checkTrue(length(results$similarity) != 0)
checkTrue(all(results$similarity>= 0))
checkEquals(results$similarity[16],1)
message("eiQuery test 2")
results=eiQuery(runId,203:204,format="compound_id",K=15,asSimilarity=TRUE,dir=test_dir)
checkEquals(results$similarity[1],1)
message("eiQuery test 3")
results=eiQuery(runId,c("650002","650003"), format="name",K=15,dir=test_dir)
checkEquals(results$distance[1],0)
#checkEquals(results$distance[9],0) # not reliable
message("eiQuery test 4")
lshData = loadLSHData(r,d,dir=test_dir)
results=eiQuery(runId,c("650002","650003"), format="name",K=15,lshData=lshData,dir=test_dir)
freeLSHData(lshData)
}
test_da.eiPerformanceTest <- function() {
#DEACTIVATED("slow")
runId = lastRunId
eiPerformanceTest(runId,K=22,dir=test_dir)
checkMatrix("chemical-search.results$",20, N,file.path(test_dir,"data"))
#only 19 queries where since some have dup descriptors
checkMatrix(sprintf("eucsearch.%d-%d",r,d),15:20,numUniqueDescriptors)
checkMatrix("indexed.performance",20,1)
}
test_ea.eiAdd<- function(){
#DEACTIVATED("slow")
conn = connSource()
data(example_compounds)
cat(paste(paste(example_compounds,collapse="\n"),"\n",sep=""),
file=file.path(test_dir,"example_compounds.sdf"))
options(warn=-1)
examples=read.SDFset(file.path(test_dir,"example_compounds.sdf"))
options(warn=2)
runId = lastRunId
message("using runId ",runId)
message("eiAdd test1")
newCompoundIds = eiAdd(runId,examples[1:2],dir=test_dir)
results = eiQuery(runId,examples[1:2],dir=test_dir)
print(results)
checkEquals(results$distance[1],0)
message("checking descriptors")
for(i in newCompoundIds)
checkDescriptor(conn,runId,compoundId=i,printAll=F)
message("eiAdd test2")
newCompoundIds2 = eiAdd(runId,examples[4:8],dir=test_dir)
results = eiQuery(runId,examples[4],dir=test_dir)
checkEquals(results$distance[1],0)
print(results)
message("checking descriptors")
for(i in newCompoundIds2)
checkDescriptor(conn,runId,compoundId=i,printAll=F)
}
test_fa.eiCluster <- function(){
#DEACTIVATED("off")
numNbrs=5
minNbrs=2
cutoff=0.5
runId = lastRunId
#normal clustering
clustering=eiCluster(runId,K=numNbrs,minNbrs=minNbrs,cutoff=1-cutoff,dir=test_dir)
print(byCluster(clustering))
checkTrue(length(clustering) >= numUniqueDescriptors) #eiAdd will add some stuff
conn=connSource()
compoundIds=names(clustering)
compoundNames=getCompoundNames(conn,compoundIds)
names(clustering)=compoundNames
sizes= clusterSizes(clustering)
print(sizes)
# checkTrue(nrow(sizes) %in% c(6))
checkTrue(nrow(sizes) %in% c(5))
checkTrue(all(sizes[,2]==2))
#returning just the matrix file and then clustering manually
nnm=eiCluster(runId,K=numNbrs,minNbrs=minNbrs,type="matrix",cutoff=1-cutoff,dir=test_dir)
clustering = jarvisPatrick(nnm,k=minNbrs,mode="a1b")
sizes= clusterSizes(clustering)
print(clusterSizes(clustering))
checkTrue(length(clustering) >= N) #eiAdd will add some stuff
# checkTrue(nrow(sizes) %in% c(6))
checkTrue(nrow(sizes) %in% c(5))
checkTrue(all(sizes[,2]==2))
#clustering a subset
message("subset clustering")
compoundIds= eiR:::readIddb(conn, file.path(test_dir,eiR:::Main))
clustering=eiCluster(runId,compoundIds=compoundIds[1:70],K=numNbrs,minNbrs=minNbrs,cutoff=1-cutoff,dir=test_dir)
print(byCluster(clustering))
checkTrue(length(clustering) >= 66)
compoundIds=names(clustering)
compoundNames=getCompoundNames(conn,compoundIds)
names(clustering)=compoundNames
sizes= clusterSizes(clustering)
print(sizes)
# checkTrue(nrow(sizes) %in% c(3))
checkTrue(nrow(sizes) %in% c(2))
checkTrue(all(sizes[,2]==2))
}
clusterSizes <- function(clustering) {
sizes=Reduce(rbind,lapply(unique(clustering),function(cid)
cbind(cid=cid,size=sum(clustering==cid))))
sizes[sizes[,2]>1,]
}
cleanup<- function(){
conn=connSource()
# if(inherits(conn,"PostgreSQLConnection"))
# {
# message("resetting postgres")
# resetDb(conn)
# }else
# message("not resetting postgres")
#unlink(test_dir,recursive=T) #doesn't work
system(paste("rm -rf ",test_dir))
dir.create(test_dir)
# setwd(test_dir) # this breaks check
#junk <- c("data","example_compounds.sdf","example_queries.sdf",paste("run",r,d,sep="-"),fpDir)
#junk <- c("example_compounds.sdf","example_queries.sdf",paste("run",r,d,sep="-"))
#unlink(junk,recursive=T)
}
findRefIddb <- function(runDir){
matches<-dir(runDir,pattern=".cdb$",full.names=T)
checkEquals(length(matches),1)
matches[1]
}
checkMatrix <- function(pattern,x,y,dir=runDir){
if(debug) print(paste("searching for ",pattern," expected dims: ",x,y))
matches<-dir(dir,pattern=pattern,full.names=T)
if(debug) print(matches)
checkEquals(length(matches),1)
file <- matches[1]
checkTrue(file.info(file)$size>0)
d = dim(read.table(file))
if(debug) print(paste("found dims: ",d))
#checkEquals(d,c(x,y))
checkTrue(d[1] %in% x)
checkTrue(d[2] %in% y)
}
checkDescriptor = function(conn,rid,descriptorIndex=NULL,
compoundId = eiR:::readIddb(conn,
file.path(test_dir,eiR:::Main))[descriptorIndex],
printAll=FALSE) {
parameters = eiR:::runQuery(conn,paste("SELECT e.name,e.embedding_id,dimension,num_references FROM runs as r JOIN embeddings as e USING(embedding_id)
WHERE r.run_id = ",rid))
#check that embedded descriptor values are stored in correct order
#message("checking descriptor of compound id ",compoundId)
descId = eiR:::runQuery(conn,paste("SELECT descriptor_id FROM compound_descriptors where
compound_id=",compoundId))[[1]]
desc = eiR:::getDescriptors(conn,descType,compoundId)[[1]]
embeddedDesc = eiR:::embedDescriptor(conn,r,d,parameters$name,desc,
descriptorType=descType,dir=test_dir)
dbEmbeddedDesc = eiR:::runQuery(conn,paste("SELECT value FROM embedded_descriptors WHERE
embedding_id=",parameters$embedding_id," and descriptor_id=",descId ,
" ORDER BY ordering"))[[1]]
#if(!all(as.vector(embeddedDesc) == dbEmbeddedDesc)){
if(printAll){
print(desc)
print(as.vector(embeddedDesc))
print(dbEmbeddedDesc)
}
checkEquals(as.vector(embeddedDesc),dbEmbeddedDesc)
}
girke-lab/eiR-release documentation built on May 17, 2019, 5:27 a.m.
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library(eiR)
library(snow)
library(DBI)
options(warn=2)
#options(error=dump.frames)
options(warnPartialMatchDollar=TRUE)
test_dir="test_workspace"
r<- 50
d<- 40
N<- 100
numUniqueDescriptors=96
j=1 #can only use 1 when using sqlite
runDir<-file.path(test_dir,paste("run",r,d,sep="-"))
fpDir=file.path(test_dir,"fp_test")
descType="ap"
sqliteSource=function(reset=FALSE){
require(eiR)
require(RSQLite)
path = file.path(test_dir,"data")
if(!file.exists(path))
dir.create(path,recursive=TRUE)
conn=initDb(file.path(path,"chem.db"))
#checkTrue(file.exists(file.path(test_dir,"data","chem.db")))
conn
}
resetDb <- function(conn){
tables = dbListTables(conn)
print(tables)
for(table in tables)
dbGetQuery(conn, paste("DROP TABLE ",table," CASCADE"))
initDb(conn)
}
pgSource=function(reset=FALSE){
require(eiR)
require(RPostgreSQL)
conn=dbConnect(dbDriver("PostgreSQL"),user="chemminer_tests",password="40ersfdv90erijgfk",
dbname="chemminer_tests",host="girke-db-1.bioinfo.ucr.edu")
if(reset)
resetDb(conn)
initDb(conn)
eiR:::setDefaultConn(conn)
conn
}
connSource = sqliteSource
#connSource = pgSource
connSource(TRUE) # reset postgres
lastRunId=0
#debug=TRUE
debug=FALSE
test_aa.eiInit <- function() {
#DEACTIVATED("slow")
cleanup()
connSource() #sets default connection
checkData <- function(cids,dir=test_dir){
checkTrue(file.exists(file.path(dir,"data","main.iddb")))
i <- readLines(file.path(dir,"data","main.iddb"))
checkEquals(length(i),N)
checkEquals(length(cids),N)
sdfFromDb = getCompounds(connSource(),cids)
checkEquals(length(sdfFromDb),N)
}
message("eiInit tests")
setDefaultDistance("dummy",function(x,y) x-y)
checkTrue(!is.null(eiR:::getDefaultDist("dummy")))
addTransform("dummy","d2",toObject=function(x,conn=NA,dir=".")x)
checkTrue(!is.null(eiR:::getTransform("dummy","d2")))
message("default descriptor")
data(sdfsample)
compoundIds = eiInit(sdfsample[1:N],descriptorType=descType,dir=test_dir)
#checkData(compoundIds)
message("fp descriptor")
dir.create(fpDir)
write.SDF(sdfsample[1:30],file.path(fpDir,"f1"))
write.SDF(sdfsample[31:60],file.path(fpDir,"f2"))
write.SDF(sdfsample[61:100],file.path(fpDir,"f3"))
# we just test with one node as SQLite does not support parallel writes
cl=makeCluster(1,type="SOCK",outfile=file.path(test_dir,"eiInit.snow"))
fpCids = eiInit(file.path(fpDir,c("f1","f2","f3")),dir=fpDir,descriptorType="fp",cl=cl,
connSource=connSource )
stopCluster(cl)
#checkData(fpCids)
}
testRefs <- function(){
200+c(1,2,5,8,9,10,11,17,18,19,20,23,24,25,26,29,31,33,34,36,38,43,45,46,47,48,49,51,53,66,67,70,71,72,73,74,75,77,78,79,80,81,82,83,87,88,89,91,99,100)
}
test_ba.parDist <- function(){
#DEACTIVATED("slow")
conn = connSource()
distance = eiR:::getDefaultDist("ap")
require(snow)
cl = makeSOCKcluster(3,outfile="")
set1=eiR:::readIddb(conn,file.path(test_dir,"data","main.iddb"))
set2 = testRefs()
if(debug){
print("set1")
print(set1)
print("set2")
print(set2)
}
eiR:::IddbVsIddbDist(conn,set1,set2, distance,"ap",file=file.path(test_dir,"parDist.final"),
cl=cl, connSource= connSource )
stopCluster(cl)
#
# checkTrue(file.exists(file.path(test_dir,"parDist.final")))
}
test_bb.eiMakeDb <- function() {
#DEACTIVATED("slow")
message(" eiMakeDb ")
conn = connSource()
runDbChecks = function(rid,targetSampleNum=20){
parameters = eiR:::runQuery(conn,paste("SELECT e.name,e.embedding_id,dimension,num_references FROM runs as r JOIN embeddings as e USING(embedding_id)
WHERE r.run_id = ",rid))
#print(parameters)
checkEquals(d,parameters$dimension)
checkEquals(r,parameters$num_references)
numRefs = eiR:::runQuery(conn,paste("SELECT count(*) FROM runs as r JOIN embeddings as e USING(embedding_id)
JOIN compound_group_members as refs ON(e.references_group_id=refs.compound_group_id)
WHERE r.run_id = ",rid))[[1]]
message("found ",numRefs," refs")
checkEquals(r,numRefs)
numCompounds = eiR:::runQuery(conn,paste("SELECT count(*) FROM runs as r
JOIN compound_group_members as cgm ON(r.compound_group_id=cgm.compound_group_id)
WHERE r.run_id = ",rid))[[1]]
checkEquals(N,numCompounds)
numSamples = eiR:::runQuery(conn,paste("SELECT count(*) FROM runs as r
JOIN compound_group_members as cgm ON(r.sample_group_id=cgm.compound_group_id)
WHERE r.run_id = ",rid))[[1]]
message("found ",numSamples," samples")
checkEquals(targetSampleNum,numSamples)
numDescriptors = eiR:::runQuery(conn,paste("SELECT count(distinct descriptor_id) FROM runs as r JOIN embedded_descriptors as ed USING(embedding_id)
WHERE r.run_id = ",rid))[[1]]
#checkEquals(N,numDescriptors)
#this should be 96 now because some descriptors are identical
# and we now only store a unique set
checkEquals(96,numDescriptors)
message("checking descriptors")
for(i in 1:numDescriptors)
checkDescriptor(conn,rid,descriptorIndex=i)
checkTrue(file.info(file.path(runDir,sprintf("matrix.%d-%d",r,d)))$size>0)
checkTrue(file.info(file.path(runDir,sprintf("matrix.query.%d-%d",r,d)))$size>0)
}
cl=makeCluster(j,type="SOCK",outfile="")
print("by file name")
refFile = file.path(test_dir,"reference_file.cdb")
eiR:::writeIddbFile((1:r)+200,refFile)
rid=eiMakeDb(refFile,d,cl=cl,descriptorType=descType,dir=test_dir,
connSource=connSource )
runDbChecks(rid,targetSampleNum = N*0.1)
unlink(runDir,recursive=TRUE)
print("by number")
rid=eiMakeDb(r,d,numSamples=20,cl=cl,descriptorType=descType,dir=test_dir,
connSource=connSource )
runDbChecks(rid)
unlink(runDir,recursive=TRUE)
print("by vector")
rid=eiMakeDb(testRefs(),d,numSamples=20,cl=cl,descriptorType=descType, dir=test_dir,
connSource=connSource )
stopCluster(cl)
runDbChecks(rid)
lastRunId<<-rid
}
test_ca.eiQuery <- function(){
#DEACTIVATED("slow")
message("eiQuery")
conn=connSource()
data(sdfsample)
runId = lastRunId
message("using runId ",runId)
message("eiQuery test 1")
results = eiQuery(runId,sdfsample[1:2],K=15,asSimilarity=TRUE,dir=test_dir)
checkTrue(length(results$similarity) != 0)
checkTrue(all(results$similarity>= 0))
checkEquals(results$similarity[16],1)
message("eiQuery test 2")
results=eiQuery(runId,203:204,format="compound_id",K=15,asSimilarity=TRUE,dir=test_dir)
checkEquals(results$similarity[1],1)
message("eiQuery test 3")
results=eiQuery(runId,c("650002","650003"), format="name",K=15,dir=test_dir)
checkEquals(results$distance[1],0)
#checkEquals(results$distance[9],0) # not reliable
message("eiQuery test 4")
lshData = loadLSHData(r,d,dir=test_dir)
results=eiQuery(runId,c("650002","650003"), format="name",K=15,lshData=lshData,dir=test_dir)
freeLSHData(lshData)
}
test_da.eiPerformanceTest <- function() {
#DEACTIVATED("slow")
runId = lastRunId
eiPerformanceTest(runId,K=22,dir=test_dir)
checkMatrix("chemical-search.results$",20, N,file.path(test_dir,"data"))
#only 19 queries where since some have dup descriptors
checkMatrix(sprintf("eucsearch.%d-%d",r,d),15:20,numUniqueDescriptors)
checkMatrix("indexed.performance",20,1)
}
test_ea.eiAdd<- function(){
#DEACTIVATED("slow")
conn = connSource()
data(example_compounds)
cat(paste(paste(example_compounds,collapse="\n"),"\n",sep=""),
file=file.path(test_dir,"example_compounds.sdf"))
options(warn=-1)
examples=read.SDFset(file.path(test_dir,"example_compounds.sdf"))
options(warn=2)
runId = lastRunId
message("using runId ",runId)
message("eiAdd test1")
newCompoundIds = eiAdd(runId,examples[1:2],dir=test_dir)
results = eiQuery(runId,examples[1:2],dir=test_dir)
print(results)
checkEquals(results$distance[1],0)
message("checking descriptors")
for(i in newCompoundIds)
checkDescriptor(conn,runId,compoundId=i,printAll=F)
message("eiAdd test2")
newCompoundIds2 = eiAdd(runId,examples[4:8],dir=test_dir)
results = eiQuery(runId,examples[4],dir=test_dir)
checkEquals(results$distance[1],0)
print(results)
message("checking descriptors")
for(i in newCompoundIds2)
checkDescriptor(conn,runId,compoundId=i,printAll=F)
}
test_fa.eiCluster <- function(){
#DEACTIVATED("off")
numNbrs=5
minNbrs=2
cutoff=0.5
runId = lastRunId
#normal clustering
clustering=eiCluster(runId,K=numNbrs,minNbrs=minNbrs,cutoff=1-cutoff,dir=test_dir)
print(byCluster(clustering))
checkTrue(length(clustering) >= numUniqueDescriptors) #eiAdd will add some stuff
conn=connSource()
compoundIds=names(clustering)
compoundNames=getCompoundNames(conn,compoundIds)
names(clustering)=compoundNames
sizes= clusterSizes(clustering)
print(sizes)
# checkTrue(nrow(sizes) %in% c(6))
checkTrue(nrow(sizes) %in% c(5))
checkTrue(all(sizes[,2]==2))
#returning just the matrix file and then clustering manually
nnm=eiCluster(runId,K=numNbrs,minNbrs=minNbrs,type="matrix",cutoff=1-cutoff,dir=test_dir)
clustering = jarvisPatrick(nnm,k=minNbrs,mode="a1b")
sizes= clusterSizes(clustering)
print(clusterSizes(clustering))
checkTrue(length(clustering) >= N) #eiAdd will add some stuff
# checkTrue(nrow(sizes) %in% c(6))
checkTrue(nrow(sizes) %in% c(5))
checkTrue(all(sizes[,2]==2))
#clustering a subset
message("subset clustering")
compoundIds= eiR:::readIddb(conn, file.path(test_dir,eiR:::Main))
clustering=eiCluster(runId,compoundIds=compoundIds[1:70],K=numNbrs,minNbrs=minNbrs,cutoff=1-cutoff,dir=test_dir)
print(byCluster(clustering))
checkTrue(length(clustering) >= 66)
compoundIds=names(clustering)
compoundNames=getCompoundNames(conn,compoundIds)
names(clustering)=compoundNames
sizes= clusterSizes(clustering)
print(sizes)
# checkTrue(nrow(sizes) %in% c(3))
checkTrue(nrow(sizes) %in% c(2))
checkTrue(all(sizes[,2]==2))
}
clusterSizes <- function(clustering) {
sizes=Reduce(rbind,lapply(unique(clustering),function(cid)
cbind(cid=cid,size=sum(clustering==cid))))
sizes[sizes[,2]>1,]
}
cleanup<- function(){
conn=connSource()
# if(inherits(conn,"PostgreSQLConnection"))
# {
# message("resetting postgres")
# resetDb(conn)
# }else
# message("not resetting postgres")
#unlink(test_dir,recursive=T) #doesn't work
system(paste("rm -rf ",test_dir))
dir.create(test_dir)
# setwd(test_dir) # this breaks check
#junk <- c("data","example_compounds.sdf","example_queries.sdf",paste("run",r,d,sep="-"),fpDir)
#junk <- c("example_compounds.sdf","example_queries.sdf",paste("run",r,d,sep="-"))
#unlink(junk,recursive=T)
}
findRefIddb <- function(runDir){
matches<-dir(runDir,pattern=".cdb$",full.names=T)
checkEquals(length(matches),1)
matches[1]
}
checkMatrix <- function(pattern,x,y,dir=runDir){
if(debug) print(paste("searching for ",pattern," expected dims: ",x,y))
matches<-dir(dir,pattern=pattern,full.names=T)
if(debug) print(matches)
checkEquals(length(matches),1)
file <- matches[1]
checkTrue(file.info(file)$size>0)
d = dim(read.table(file))
if(debug) print(paste("found dims: ",d))
#checkEquals(d,c(x,y))
checkTrue(d[1] %in% x)
checkTrue(d[2] %in% y)
}
checkDescriptor = function(conn,rid,descriptorIndex=NULL,
compoundId = eiR:::readIddb(conn,
file.path(test_dir,eiR:::Main))[descriptorIndex],
printAll=FALSE) {
parameters = eiR:::runQuery(conn,paste("SELECT e.name,e.embedding_id,dimension,num_references FROM runs as r JOIN embeddings as e USING(embedding_id)
WHERE r.run_id = ",rid))
#check that embedded descriptor values are stored in correct order
#message("checking descriptor of compound id ",compoundId)
descId = eiR:::runQuery(conn,paste("SELECT descriptor_id FROM compound_descriptors where
compound_id=",compoundId))[[1]]
desc = eiR:::getDescriptors(conn,descType,compoundId)[[1]]
embeddedDesc = eiR:::embedDescriptor(conn,r,d,parameters$name,desc,
descriptorType=descType,dir=test_dir)
dbEmbeddedDesc = eiR:::runQuery(conn,paste("SELECT value FROM embedded_descriptors WHERE
embedding_id=",parameters$embedding_id," and descriptor_id=",descId ,
" ORDER BY ordering"))[[1]]
#if(!all(as.vector(embeddedDesc) == dbEmbeddedDesc)){
if(printAll){
print(desc)
print(as.vector(embeddedDesc))
print(dbEmbeddedDesc)
}
checkEquals(as.vector(embeddedDesc),dbEmbeddedDesc)
}
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