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TranSyT
transyt-service
Commits
c82612ac
Commit
c82612ac
authored
Sep 21, 2018
by
Davide Lagoa
Browse files
ModelSEED relations using file created
parent
030482b8
Changes
43
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0 → 100644
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pom.xml
View file @
c82612ac
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
<modelVersion>
4.0.0
</modelVersion>
<groupId>
Biosynth
</groupId>
...
...
@@ -16,7 +17,7 @@
<url>
http://193.137.11.210/nexus/content/groups/public/
</url>
</repository>
</repositories>
<build>
<plugins>
<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-compiler-plugin</artifactId>
...
...
@@ -54,6 +55,10 @@
<groupId>
ch.qos.logback
</groupId>
<artifactId>
logback-core
</artifactId>
</exclusion>
<exclusion>
<groupId>
org.apache.logging.log4j
</groupId>
<artifactId>
log4j-slf4j-impl
</artifactId>
</exclusion>
</exclusions>
</dependency>
...
...
@@ -233,23 +238,20 @@
<artifactId>
json-simple
</artifactId>
<version>
1.1.1
</version>
</dependency>
<dependency>
<groupId>
org.apache.logging.log4j
</groupId>
<artifactId>
log4j-api
</artifactId>
<version>
2.7
</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
<dependency>
<groupId>
org.
apache.logging.log
4j
</groupId>
<artifactId>
log4j-core
</artifactId>
<version>
2
.7
</version>
<groupId>
org.
slf
4j
</groupId>
<artifactId>
slf4j-api
</artifactId>
<version>
1
.7
.25
</version>
</dependency>
<!-- https://mvnrepository.com/artifact/ch.qos.logback/logback-classic -->
<dependency>
<groupId>
ch.qos.logback
</groupId>
<artifactId>
logback-classic
</artifactId>
<version>
1.
1.7
</version>
<version>
1.
2.3
</version>
</dependency>
</dependencies>
</project>
src/main/java/biosynth/BuildDatabase.java
View file @
c82612ac
...
...
@@ -17,18 +17,6 @@ public class BuildDatabase {
GraphDatabaseService
graphDatabaseService
=
HelperNeo4jConfigInitializer
.
initializeNeo4jDataDatabaseConstraints
(
"C:\\Users\\Davide\\Documents\\BASE DE DADOS BIOSYNTH\\db3_0"
);
// System.out.println("opening ModelSEED...");
//
// EtlTransform<ModelSeedMetaboliteEntity, GraphMetaboliteEntity> t0 = ModelSEED.getMetaboliteTransform();
//
// MetaboliteDao<ModelSeedMetaboliteEntity> dao0 = ModelSEED.getMetaboliteDatabase();
//
// System.out.println("transforming...");
//
// ModelSEED.etl(dao0 , t0, graphDatabaseService);
//
// System.out.println("ModelSEED complete...");
//
// ///////////////////////////////////////////////////////////
// System.out.println();
// System.out.println("requesting kegg compounds...");
...
...
@@ -84,25 +72,34 @@ public class BuildDatabase {
// ///////////////////////////////////////////////////////////
// System.out.println();
System
.
out
.
println
(
"opening Metacyc ECOLI..."
);
EtlTransform
<
BioCycMetaboliteEntity
,
GraphMetaboliteEntity
>
t4
=
Metacyc
.
getMetacycMetaboliteTransform
();
// MetaboliteDao<BiggMetaboliteEntity> daoBigg = getBigg1MetaboliteDatabase();
MetaboliteDao
<
BioCycMetaboliteEntity
>
daoBiocyc4
=
Metacyc
.
getMetacycMetaboliteDao
(
"ECOLI"
);
System
.
out
.
println
(
"transforming..."
);
Metacyc
.
etl
(
daoBiocyc4
,
t4
,
graphDatabaseService
);
System
.
out
.
println
(
"Metacyc ECOLI complete..."
);
// System.out.println("opening Metacyc ECOLI...");
//
// EtlTransform<BioCycMetaboliteEntity, GraphMetaboliteEntity> t4 = Metacyc.getMetacycMetaboliteTransform();
// MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc4 = Metacyc.getMetacycMetaboliteDao("ECOLI");
//
// System.out.println("transforming...");
//
// Metacyc.etl(daoBiocyc4 , t4, graphDatabaseService);
//
// System.out.println("Metacyc ECOLI complete...");
//////////////////////////////////////////////
// System.out.println("
requesting kegg drugs
...");
// System.out.println("
opening ModelSEED
...");
//
// etl(getKeggDrugMetaboliteDao() , getKeggDrugTransform(), graphDatabaseService);
System
.
out
.
println
(
"database load complete..."
);
// EtlTransform<ModelSeedMetaboliteEntity, GraphMetaboliteEntity> t0 = ModelSEED.getMetaboliteTransform();
//
// MetaboliteDao<ModelSeedMetaboliteEntity> dao0 = ModelSEED.getMetaboliteDatabase();
//
// System.out.println("transforming...");
//
// ModelSEED.etl(dao0 , t0, graphDatabaseService);
//
// System.out.println("ModelSEED complete...");
//
ModelSEED
.
createModelSEEDRelationships
(
graphDatabaseService
);
// System.out.println("database load complete...");
//
graphDatabaseService
.
shutdown
();
System
.
out
.
println
(
"shutdown..."
);
...
...
src/main/java/biosynth/ModelSEED.java
View file @
c82612ac
package
biosynth
;
import
java.io.BufferedReader
;
import
java.io.File
;
import
java.io.FileNotFoundException
;
import
java.io.FileReader
;
import
java.io.IOException
;
import
java.util.HashMap
;
import
java.util.HashSet
;
import
java.util.Map
;
import
java.util.Set
;
import
org.neo4j.graphdb.GraphDatabaseService
;
import
org.neo4j.graphdb.Relationship
;
import
org.neo4j.graphdb.RelationshipType
;
import
org.neo4j.graphdb.Transaction
;
import
org.slf4j.Logger
;
import
org.slf4j.LoggerFactory
;
import
org.springframework.core.io.FileSystemResource
;
import
files.FilesUtils
;
import
internalDB.WriteByMetabolitesID
;
import
pt.uminho.sysbio.biosynth.integration.GraphMetaboliteEntity
;
import
pt.uminho.sysbio.biosynth.integration.etl.CentralMetaboliteEtlDataCleansing
;
import
pt.uminho.sysbio.biosynth.integration.etl.DefaultMetaboliteEtlExtract
;
...
...
@@ -12,36 +27,42 @@ import pt.uminho.sysbio.biosynth.integration.etl.EtlTransform;
import
pt.uminho.sysbio.biosynth.integration.etl.HbmNeo4jHybridMetaboliteEtlPipeline
;
import
pt.uminho.sysbio.biosynth.integration.etl.HeterogenousMetaboliteEtlLoad
;
import
pt.uminho.sysbio.biosynth.integration.etl.biodb.ModelSeedMetaboliteTransform
;
import
pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.MetaboliteMajorLabel
;
import
pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.Neo4jGraphMetaboliteDaoImpl
;
import
pt.uminho.sysbio.biosynth.integration.neo4j.BiodbMetaboliteNode
;
import
pt.uminho.sysbio.biosynthframework.BiodbGraphDatabaseService
;
import
pt.uminho.sysbio.biosynthframework.Metabolite
;
import
pt.uminho.sysbio.biosynthframework.chemanalysis.cdk.CdkWrapper
;
import
pt.uminho.sysbio.biosynthframework.io.MetaboliteDao
;
import
utilities.triage_utilities.Utilities
;
public
class
ModelSEED
{
// public static void main(String[] args) {
//
// System.out.println("opening...");
//
// EtlTransform<ModelSeedMetaboliteEntity, GraphMetaboliteEntity> t = getMetaboliteTransform();
//
// MetaboliteDao<ModelSeedMetaboliteEntity> dao = getMetaboliteDatabase();
//
// System.out.println("transforming...");
//
// etl(dao , t);
//
// System.out.println("finnish...");
//
// }
private
static
final
Logger
logger
=
LoggerFactory
.
getLogger
(
WriteByMetabolitesID
.
class
);
// public static void main(String[] args) {
//
// System.out.println("opening...");
//
// EtlTransform<ModelSeedMetaboliteEntity, GraphMetaboliteEntity> t = getMetaboliteTransform();
//
// MetaboliteDao<ModelSeedMetaboliteEntity> dao = getMetaboliteDatabase();
//
// System.out.println("transforming...");
//
// etl(dao , t);
//
// System.out.println("finnish...");
//
// }
public
static
Json2ModelSeedMetaboliteDaoImpl
getMetaboliteDatabase
()
{
Json2ModelSeedMetaboliteDaoImpl
dao
=
new
Json2ModelSeedMetaboliteDaoImpl
(
new
FileSystemResource
(
new
File
(
"C:\\
\\
Users\\
\\
Davide\\
\\
Desktop\\
\\
compounds.json"
)));
Json2ModelSeedMetaboliteDaoImpl
dao
=
new
Json2ModelSeedMetaboliteDaoImpl
(
new
FileSystemResource
(
new
File
(
"C:\\Users\\Davide\\Desktop\\compounds.json"
)));
return
dao
;
}
public
static
ModelSeedMetaboliteTransform
getMetaboliteTransform
()
{
...
...
@@ -68,7 +89,148 @@ public class ModelSEED {
etlPipeline
.
setLoadSubsystem
(
new
HeterogenousMetaboliteEtlLoad
<
GraphMetaboliteEntity
>(
dst
));
etlPipeline
.
setTransformSubsystem
(
t
);
etlPipeline
.
etl
();
}
public
static
void
createModelSEEDRelationships
(
GraphDatabaseService
graphDatabaseService
)
{
Map
<
MetaboliteMajorLabel
,
Map
<
String
,
Set
<
String
>>>
data
=
readSEEDRelationshipsFile
();
Transaction
dataTx
=
graphDatabaseService
.
beginTx
();
BiodbGraphDatabaseService
service
=
new
BiodbGraphDatabaseService
(
graphDatabaseService
);
for
(
MetaboliteMajorLabel
label
:
data
.
keySet
())
{
for
(
String
modelSEEDid
:
data
.
get
(
label
).
keySet
())
{
BiodbMetaboliteNode
node
=
service
.
getMetabolite
(
modelSEEDid
,
MetaboliteMajorLabel
.
ModelSeed
);
if
(
node
!=
null
)
{
for
(
String
externalID
:
data
.
get
(
label
).
get
(
modelSEEDid
))
{
if
(
node
!=
null
)
{
try
{
BiodbMetaboliteNode
node2
=
service
.
getMetabolite
(
externalID
,
label
);
node
.
createRelationshipTo
(
node2
,
RelationshipType
.
withName
(
"has_crossreference_to"
));
String
msg
=
"Relationship created between compound "
.
concat
(
externalID
).
concat
(
" with source "
).
concat
(
label
.
toString
())
.
concat
(
" and ModelSEED compound "
).
concat
(
modelSEEDid
);
logger
.
info
(
msg
);
}
catch
(
Exception
e
)
{
String
msg
=
"Compound "
.
concat
(
externalID
).
concat
(
" with source "
).
concat
(
label
.
toString
())
.
concat
(
" not found to create relationship with ModelSEED compound "
).
concat
(
modelSEEDid
);
logger
.
warn
(
msg
);
}
}
else
{
String
msg
=
"Compound "
.
concat
(
externalID
).
concat
(
" with source "
).
concat
(
label
.
toString
())
.
concat
(
" not found to create relationship with ModelSEED compound "
).
concat
(
modelSEEDid
);
logger
.
warn
(
msg
);
}
}
}
else
logger
.
warn
(
"Relationship NOT created for ModelSEED compound {}"
,
modelSEEDid
);
}
}
dataTx
.
success
();
logger
.
info
(
"All reationships created!"
);
dataTx
.
close
();
service
.
shutdown
();
}
public
static
Map
<
MetaboliteMajorLabel
,
Map
<
String
,
Set
<
String
>>>
readSEEDRelationshipsFile
()
{
Map
<
MetaboliteMajorLabel
,
Map
<
String
,
Set
<
String
>>>
data
=
new
HashMap
<>();
String
path
=
System
.
getProperty
(
"user.dir"
).
concat
(
"\\src\\main\\resources\\Compounds_Aliases.tsv"
);
logger
.
info
(
"Reading external references file at: {}"
,
path
);
try
{
BufferedReader
reader
=
new
BufferedReader
(
new
FileReader
(
path
));
String
line
;
while
((
line
=
reader
.
readLine
())
!=
null
)
{
if
(!
line
.
isEmpty
())
{
Map
<
String
,
Set
<
String
>>
submap
=
new
HashMap
<>();
String
[]
text
=
line
.
split
(
"\t"
);
String
id
=
text
[
0
].
trim
();
String
externalID
=
text
[
2
];
String
source
=
text
[
3
].
trim
();
if
(
text
.
length
==
3
)
{
externalID
=
text
[
1
].
trim
();
}
MetaboliteMajorLabel
label
=
null
;
if
(
source
.
equalsIgnoreCase
(
"BiGG1"
))
label
=
MetaboliteMajorLabel
.
BiGG2
;
else
if
(
source
.
equalsIgnoreCase
(
"KEGG"
))
{
label
=
MetaboliteMajorLabel
.
LigandCompound
;
if
(
externalID
.
startsWith
(
"G"
))
label
=
MetaboliteMajorLabel
.
LigandGlycan
;
}
else
if
(
source
.
equalsIgnoreCase
(
"MetaCyc"
))
{
label
=
MetaboliteMajorLabel
.
MetaCyc
;
externalID
=
"META:"
.
concat
(
externalID
);
}
if
(
source
.
equalsIgnoreCase
(
"BiGG"
))
label
=
MetaboliteMajorLabel
.
BiGG
;
if
(
label
!=
null
&&
!
id
.
isEmpty
()
&&
!
externalID
.
isEmpty
())
{
if
(!
data
.
containsKey
(
label
))
data
.
put
(
label
,
new
HashMap
<>());
submap
=
data
.
get
(
label
);
if
(
submap
.
containsKey
(
id
))
{
submap
.
get
(
id
).
add
(
externalID
);
}
else
{
Set
<
String
>
set
=
new
HashSet
<>();
set
.
add
(
externalID
);
submap
.
put
(
id
,
set
);
}
data
.
put
(
label
,
submap
);
}
}
}
reader
.
close
();
}
catch
(
FileNotFoundException
e
)
{
e
.
printStackTrace
();
}
catch
(
IOException
e
)
{
e
.
printStackTrace
();
}
return
data
;
}
}
src/main/java/internalDB/WriteByMetabolitesID.java
View file @
c82612ac
...
...
@@ -27,6 +27,7 @@ import reactions.IdentifyReactionsMetabolites;
import
reactions.TransportReactionsBuilder
;
import
relations.MetabolitesChilds
;
import
tcdb.capsules.BiosynthMetaboliteProperties
;
import
tcdb.capsules.ReactionContainer
;
import
tcdb.capsules.TcNumberContainer2
;
import
triageDatabase.PopulateTriageNeo4jDatabase
;
import
utilities.FileUtils
;
...
...
@@ -65,14 +66,16 @@ public class WriteByMetabolitesID {
BiosynthMetabolites
namesAndIDsContainer
=
getBiosynthDataByName
(
service
,
true
);
//154225 names
// BiosynthMetabolites namesAndIDsContainer = null;
//
// FileUtils.saveMapInFile2("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getMetabolitesIDs5.txt", namesAndIDsContainer.getMetabolitesIDs());
// FilesUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCase5.txt", namesAndIDsContainer.getNamesLowerCase());
// FilesUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCaseWithoutSigns5.txt", namesAndIDsContainer.getNamesLowerCaseWithoutSigns());
// FilesUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesWithoutSigns5.txt", namesAndIDsContainer.getNamesWithoutSigns());
// FileUtils.saveMapInFile2("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getMetabolitesIDs3.txt", namesAndIDsContainer.getMetabolitesIDs());
// FilesUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCase3.txt", namesAndIDsContainer.getNamesLowerCase());
// FilesUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCaseWithoutSigns3.txt", namesAndIDsContainer.getNamesLowerCaseWithoutSigns());
// FilesUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesWithoutSigns3.txt", namesAndIDsContainer.getNamesWithoutSigns());
Map
<
String
,
Set
<
TcNumberContainer2
>>
reactionsData
=
JSONFilesUtils
.
readJSONtcdbReactionsFile
();
Map
<
String
,
Set
<
TcNumberContainer2
>>
reactionsData
=
JSONFilesUtils
.
readJSONtcdbReactionsFile
();
//uncomment
// Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>();
//
// reactionsData2.put("O51235", reactionsData.get("O51235"));
...
...
@@ -86,8 +89,8 @@ public class WriteByMetabolitesID {
int
n
=
1
;
while
(
n
!=
99
)
{
test
(
namesAndIDsContainer
,
data
,
service
,
null
,
reactionsData
,
null
);
test
(
namesAndIDsContainer
,
data
,
service
,
null
,
reactionsData
,
null
);
//uncomment
System
.
out
.
println
(
"Enter a random number to repeat (100 to repeat data retrieval) or 99 to finish: "
);
...
...
@@ -110,34 +113,59 @@ public class WriteByMetabolitesID {
e
.
printStackTrace
();
}
}
public
static
void
test
(
BiosynthMetabolites
namesAndIDsContainer
,
Map
<
String
,
BiosynthMetaboliteProperties
>
data
,
BiodbGraphDatabaseService
service
,
Map
<
String
,
Map
<
String
,
MetaboliteMajorLabel
>>
tcdbMetabolitesIDs
,
Map
<
String
,
Set
<
TcNumberContainer2
>>
reactionsData
2
,
Map
<
String
,
String
[]>
forChildsSearch
)
{
Map
<
String
,
Set
<
TcNumberContainer2
>>
reactionsData
,
Map
<
String
,
String
[]>
forChildsSearch
)
{
try
{
// Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>();
//
// reactionsData2.put("Q1D027", reactionsData.get("Q1D027"));
IdentifyReactionsMetabolites
metabolitesIdentification
=
new
IdentifyReactionsMetabolites
(
reactionsData2
,
namesAndIDsContainer
,
service
);
// reactionsData2.put("P0AAG8", reactionsData.get("P0AAG8"));
IdentifyReactionsMetabolites
metabolitesIdentification
=
new
IdentifyReactionsMetabolites
(
reactionsData
,
namesAndIDsContainer
,
service
);
tcdbMetabolitesIDs
=
metabolitesIdentification
.
getTcdbMetabolitesIDs
();
forChildsSearch
=
metabolitesIdentification
.
getforChildsSearch
();
forChildsSearch
=
metabolitesIdentification
.
getforChildsSearch
();
//uncomment
// Map<String, Set<TcNumberContainer2>> reactionsData3 = new HashMap<>();
// reactionsData3.put("O51235", reactionsData.get("O51235"));
/////TRIAGE
Map
<
String
,
Set
<
TcNumberContainer2
>>
newData
=
new
TransportReactionsBuilder
(
tcdbMetabolitesIDs
,
reactionsData
2
,
forChildsSearch
,
service
,
data
).
getResults
();
Map
<
String
,
Set
<
TcNumberContainer2
>>
newData
=
new
TransportReactionsBuilder
(
tcdbMetabolitesIDs
,
reactionsData
,
forChildsSearch
,
service
,
data
,
namesAndIDsContainer
.
getMetabolitesIDs
()
).
getResults
();
//uncomment
// JSONFilesUtils.writeJSONTriageReactions(newData);
// Map<String, Set<TcNumberContainer2>> newData2 = new Has
new
PopulateTriageNeo4jDatabase
(
newData
);
///////////////////////////
Set
<
TcNumberContainer2
>
containers
=
newData
.
get
(
"P0AAG8"
);
for
(
TcNumberContainer2
container
:
containers
)
{
if
(
container
.
getTcNumber
().
equalsIgnoreCase
(
"3.A.1.2.3"
))
{
Set
<
Integer
>
ids
=
container
.
getAllReactionsIds
();
for
(
Integer
id
:
ids
)
{
ReactionContainer
rcont
=
container
.
getReactionContainer
(
id
);
System
.
out
.
println
(
rcont
.
getReaction
());
System
.
out
.
println
(
rcont
.
getReactionMetaCyc
());
System
.
out
.
println
(
rcont
.
getReactionModelSEED
());
System
.
out
.
println
(
rcont
.
getReactionKEGG
());
}
}
}
////////////////////////////
// new PopulateTriageNeo4jDatabase(newData); //uncomment
////COUNTS
...
...
@@ -592,11 +620,11 @@ public class WriteByMetabolitesID {
if
(
useCache
)
{
namesLowerCaseWithoutSigns
=
FilesUtils
.
readMapFromFile
(
"C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCaseWithoutSigns
3
.txt"
);
namesWithoutSigns
=
FilesUtils
.
readMapFromFile
(
"C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesWithoutSigns
3
.txt"
);
namesLowerCase
=
FilesUtils
.
readMapFromFile
(
"C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCase
3
.txt"
);
namesLowerCaseWithoutSigns
=
FilesUtils
.
readMapFromFile
(
"C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCaseWithoutSigns
5
.txt"
);
namesWithoutSigns
=
FilesUtils
.
readMapFromFile
(
"C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesWithoutSigns
5
.txt"
);
namesLowerCase
=
FilesUtils
.
readMapFromFile
(
"C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCase
5
.txt"
);
compounds
=
FileUtils
.
readMapFromFile2
(
"C:\\Users\\Davide\\Documents\\InternalDB\\info\\getMetabolitesIDs
3
.txt"
);
compounds
=
FileUtils
.
readMapFromFile2
(
"C:\\Users\\Davide\\Documents\\InternalDB\\info\\getMetabolitesIDs
5
.txt"
);
return
new
BiosynthMetabolites
(
compounds
,
namesLowerCaseWithoutSigns
,
namesWithoutSigns
,
namesLowerCase
);
}
...
...
@@ -608,11 +636,13 @@ public class WriteByMetabolitesID {
Set
<
BiodbMetaboliteNode
>
allMetabolites
=
service
.
listMetabolites
();
// Set<BiodbMetaboliteNode> allMetabolites = new HashSet<>();
// allMetabolites.add(service.getMetabolite("C05359", MetaboliteMajorLabel.LigandCompound));
// allMetabolites.add(service.getMetabolite("glu-L", MetaboliteMajorLabel.BiGG));
// allMetabolites.add(service.getMetabolite("META:CU+2", MetaboliteMajorLabel.MetaCyc));
// allMetabolites.add(service.getMetabolite("cpd12713", MetaboliteMajorLabel.ModelSeed));
// allMetabolites.add(service.getMetabolite("glu__L", MetaboliteMajorLabel.BiGGMetabolite));
// allMetabolites.add(service.getMetabolite("cpd00009", MetaboliteMajorLabel.ModelSeed));
// allMetabolites.add(service.getMetabolite("C00009", MetaboliteMajorLabel.LigandCompound));
// allMetabolites.add(service.getMetabolite("pi", MetaboliteMajorLabel.BiGG));
// allMetabolites.add(service.getMetabolite("ECOLI:Phosphates", MetaboliteMajorLabel.MetaCyc));
// allMetabolites.add(service.getMetabolite("META:CPD-20124", MetaboliteMajorLabel.MetaCyc));
// allMetabolites.add(service.getMetabolite("cpd11715", MetaboliteMajorLabel.ModelSeed));
// allMetabolites.add(service.getMetabolite("pi", MetaboliteMajorLabel.BiGGMetabolite));
// Set<String> allDatabases = new HashSet<>();
...
...
@@ -649,9 +679,21 @@ public class WriteByMetabolitesID {
// System.out.println(formula + "\t" + names);
names
.
remove
(
"co2"
);
// to avoid errors with cobalt ions
names
.
remove
(
"h"
);
names
.
remove
(
"H"
);
if
(
names
.
contains
(
"glucose"
)
||
names
.
contains
(
"Glucose"
)
||
names
.
contains
(
"d-glucose"
)
||
names
.
contains
(
"D-glucose"
))
{
names
.
remove
(
"sugar"
);
names
.
remove
(
"D-Glucopyranose"
);
names
.
remove
(
"d-glucopyranose"
);
}
for
(
String
name
:
names
)
{
// if(name.equals("glucose"))
// System.out.println("found");
// System.out.println();
//
// System.out.println(name + " >>>>> " + formula);
...
...
@@ -691,10 +733,6 @@ public class WriteByMetabolitesID {
for
(
String
name
:
names
)
{
// if(name.equals("Cu2+"))
// System.out.println("coiso");
// System.out.println("name>>" + name);
if
(!
found
)
{
...
...
@@ -712,6 +750,7 @@ public class WriteByMetabolitesID {
// System.out.println("alias>>> " + alias.get(name));
for
(
String
name2
:
alias
.
get
(
name
))
{
if
(
compounds
.
containsKey
(
name2
))
ids
.
putAll
(
compounds
.
get
(
name2
));
}
...
...
src/main/java/kbase/ModelSEEDCompoundsFileReader.java
0 → 100644
View file @
c82612ac
package
kbase
;
import
java.io.FileReader
;
import
java.util.HashMap
;
import
java.util.Map
;
import
java.util.Set
;
import
org.json.simple.JSONObject
;
import
org.json.simple.parser.JSONParser
;
import
enumerators.TypeOfTransporter
;
import
tcdb.capsules.ReactionContainer
;
import
tcdb.capsules.TcNumberContainer
;
public
class
ModelSEEDCompoundsFileReader
{
/**
* Method to read JSON exceptions file.
*
* @return
*/
public
static
Map
<
String
,
Map
<
String
,
String
>>
readFile
()
{
JSONParser
parser
=
new
JSONParser
();
Map
<
String
,
Map
<
String
,
String
>>
data
=
new
HashMap
<>();
try
{
Object
obj
=
parser
.
parse
(
new
FileReader
(
"C:\\Users\\Davide\\Desktop\\Compounds.json"
));
JSONObject
allObjects
=
(
JSONObject
)
obj
;
@SuppressWarnings
(
"unchecked"
)
Set
<
String
>
keys
=
allObjects
.
keySet
();
for
(
String
met
:
keys
)
{
Map
<
String
,
String
>
metProperties
=
new
HashMap
<>();
JSONObject
properties
=
(
JSONObject
)
allObjects
.
get
(
met
);
if
(
properties
.
get
(
"abbreviation"
)
!=
null
)
metProperties
.
put
(
"abbreviation"
,
properties
.
get
(
"abbreviation"
).
toString
());
if
(
properties
.
get
(
"abstract_compound"
)
!=
null
)
metProperties
.
put
(
"abstract_compound"
,
properties
.
get
(
"abstract_compound"
).
toString
());
if
(
properties
.
get
(
"aliases"
)
!=
null
)
metProperties
.
put
(
"aliases"
,
properties
.
get
(
"aliases"
).
toString
());
if
(
properties
.
get
(
"charge"
)
!=
null
)
metProperties
.
put
(
"charge"
,
properties
.
get
(
"charge"
).
toString
());
if
(
properties
.
get
(
"deltag"
)
!=
null
)
metProperties
.
put
(
"deltag"
,
properties
.
get
(
"deltag"
).
toString
());