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smarru pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git
commit b1320cef005d06cb8bd44a2892023dab8d86ec6b
Author: Bhavesh Asanabada <asanabhav...@gmail.com>
AuthorDate: Mon Jun 27 14:16:25 2022 +0530
Added CRUD methods to MolData
---
.../java/com/smiles/calcinfo/CalcInfoImpl.java | 2 -
.../java/com/smiles/calcinfo/CalcInfoRepo.java | 2 +-
.../java/com/smiles/calcprops/CalcPropsEntity.java | 2 +
.../java/com/smiles/calcprops/CalcPropsImpl.java | 15 ++--
.../java/com/smiles/calcprops/CalcPropsRepo.java | 4 +-
.../com/smiles/calctopology/CalcTopologyImpl.java | 4 +-
.../main/java/com/smiles/molData/MoleculeImpl.java | 82 +++++++++++++++++++++-
7 files changed, 98 insertions(+), 13 deletions(-)
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java
index 3798ca5e..221bf9cc 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java
@@ -77,7 +77,6 @@ public class CalcInfoImpl extends
CalcInfoServiceGrpc.CalcInfoServiceImplBase {
responseObserver.onCompleted();
}
-
@Override
public void deleteCalcInfo(com.smiles.CalcInfoRequest request,
io.grpc.stub.StreamObserver<com.smiles.CalcInfo> responseObserver) {
@@ -87,5 +86,4 @@ public class CalcInfoImpl extends
CalcInfoServiceGrpc.CalcInfoServiceImplBase {
responseObserver.onNext(calcInfo);
responseObserver.onCompleted();
}
-
}
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoRepo.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoRepo.java
index 37611c92..2abe1fb0 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoRepo.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoRepo.java
@@ -4,7 +4,7 @@ import
org.springframework.data.mongodb.repository.MongoRepository;
public interface CalcInfoRepo extends MongoRepository<CalcInfoEntity, String> {
- public CalcInfoEntity findByNalpha(long nalpha);
+// public CalcInfoEntity findByNalpha(long nalpha);
public CalcInfoEntity findBySMILES(String SMILES);
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsEntity.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsEntity.java
index e9b495c3..dbcbb1bd 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsEntity.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsEntity.java
@@ -1,11 +1,13 @@
package com.smiles.calcprops;
import org.springframework.data.annotation.Id;
+import org.springframework.data.mongodb.core.mapping.Document;
import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.List;
+@Document("calcProps")
public class CalcPropsEntity {
@Id
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsImpl.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsImpl.java
index 3aec2474..47ca39c7 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsImpl.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsImpl.java
@@ -15,8 +15,8 @@ public class CalcPropsImpl extends
CalcPropsServiceGrpc.CalcPropsServiceImplBase
public void getCalcProps(CalcPropsRequest request,
StreamObserver<CalcProps> responseObserver) {
// super.getCalcInfo(request, responseObserver);
- CalcPropsEntity calcProps =
repo1.findByPDB(request.getCalcPropsQuery());
- System.out.println(calcProps);
+ CalcPropsEntity calcProps =
repo1.findBySMILES(request.getCalcPropsQuery());
+ System.out.println(calcProps.toString());
CalcProps reply = CalcProps.newBuilder()
.setInChI(calcProps.getInChI())
@@ -69,7 +69,9 @@ public class CalcPropsImpl extends
CalcPropsServiceGrpc.CalcPropsServiceImplBase
calcProps.getOtherinfo(), calcProps.getComments(),
calcProps.getNAtom(),
calcProps.getHomosList(), calcProps.getScfEnergiesList(),
calcProps.getMoEnergiesList(),
calcProps.getAtomCoordsList(), calcProps.getNmo(),
calcProps.getNBasis());
-
+ repo1.save(c2001);
+ responseObserver.onNext(calcProps);
+ responseObserver.onCompleted();
}
@Override
@@ -77,7 +79,7 @@ public class CalcPropsImpl extends
CalcPropsServiceGrpc.CalcPropsServiceImplBase
// super.updateCalcProps(request, responseObserver);
CalcProps calcProps = request.getCalcProp();
System.out.println(request.getAllFields());
- CalcPropsEntity c2001 = (CalcPropsEntity)
repo1.findByPDB(calcProps.getPDB());
+ CalcPropsEntity c2001 = (CalcPropsEntity)
repo1.findBySMILES(calcProps.getSMILES());
System.out.println(c2001.getId());
c2001.setInChI(calcProps.getInChI());
c2001.setInChIKey(calcProps.getInChIKey());
@@ -134,13 +136,16 @@ public class CalcPropsImpl extends
CalcPropsServiceGrpc.CalcPropsServiceImplBase
c2001.setNAtom(calcProps.getNAtom());
c2001.setNmo(calcProps.getNmo());
c2001.setNBasis(calcProps.getNBasis());
+ repo1.save(c2001);
+ responseObserver.onNext(calcProps);
+ responseObserver.onCompleted();
}
@Override
public void deleteCalcProps(CalcPropsRequest request,
StreamObserver<CalcProps> responseObserver) {
// super.deleteCalcProps(request, responseObserver);
CalcProps calcProps = request.getCalcProp();
- CalcPropsEntity c2001 = (CalcPropsEntity)
repo1.findByPDB(calcProps.getSDF());
+ CalcPropsEntity c2001 = (CalcPropsEntity)
repo1.findBySMILES(calcProps.getSMILES());
repo1.delete(c2001);
responseObserver.onNext(calcProps);
responseObserver.onCompleted();
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsRepo.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsRepo.java
index aa084e0a..ef71a7e6 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsRepo.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsRepo.java
@@ -4,5 +4,7 @@ import
org.springframework.data.mongodb.repository.MongoRepository;
public interface CalcPropsRepo extends MongoRepository<CalcPropsEntity,
String> {
- public CalcPropsEntity findByPDB(String PDB);
+// public CalcPropsEntity findByPDB(String PDB);
+ public CalcPropsEntity findBySMILES(String SMILES);
+
}
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyImpl.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyImpl.java
index a12aa07d..2b143010 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyImpl.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyImpl.java
@@ -16,7 +16,7 @@ public class CalcTopologyImpl extends
CalcTopologyServiceGrpc.CalcTopologyServic
// super.getCalcTopology(request, responseObserver);
System.out.println(request.getAllFields());
- CalcTopologyEntity calcTopology =
repo.findBySymbols(request.getCalcTopologyQuery());
+ CalcTopologyEntity calcTopology =
repo.findBySymbols(request.getcalcTopologyQuery());
System.out.println(calcTopology.toString());
CalcTopology reply = CalcTopology.newBuilder()
@@ -37,7 +37,7 @@ public class CalcTopologyImpl extends
CalcTopologyServiceGrpc.CalcTopologyServic
// super.createCalcTopology(request, responseObserver);
CalcTopology calcTopology = request.getCalcTopology();
System.out.println(request.getAllFields());
-
+
}
@Override
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/molData/MoleculeImpl.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/molData/MoleculeImpl.java
index 782ed68c..6cf4a7b5 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/molData/MoleculeImpl.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/molData/MoleculeImpl.java
@@ -87,11 +87,89 @@ public class MoleculeImpl extends
MoleculeServiceGrpc.MoleculeServiceImplBase {
@Override
public void updateMolecule(MoleculeRequest request,
StreamObserver<Molecule> responseObserver) {
- super.updateMolecule(request, responseObserver);
+// super.updateMolecule(request, responseObserver);
+ Molecule molecule = request.getMolecule();
+ System.out.println(request.getAllFields());
+ MoleculeEntity c4001 = (MoleculeEntity)
repo.findBySmiles(molecule.getSmiles());
+ System.out.println(c4001.getId());
+ c4001.setCas_nr(molecule.getCasNr());
+ c4001.setSmiles(molecule.getSmiles());
+ c4001.setSmiles_stereo(molecule.getSmilesStereo());
+ c4001.setInchi(molecule.getInchi());
+ c4001.setMolfile_blob_source(molecule.getMolfileBlobSource());
+ c4001.setEmp_formula(molecule.getEmpFormula());
+ c4001.setEmp_formula_sort(molecule.getEmpFormulaSort());
+ c4001.setEmp_formula_source(molecule.getEmpFormulaSource());
+ c4001.setMw(molecule.getMw());
+ c4001.setMw_monoiso(molecule.getMwMonoiso());
+ c4001.setRdb(molecule.getRdb());
+ c4001.setMw_source(molecule.getMwSource());
+ c4001.setValidated_by(molecule.getValidatedBy());
+ c4001.setJournal(molecule.getJournal());
+ c4001.setAuth_of_intr(molecule.getAuthOfIntr());
+ c4001.setJour_cit(molecule.getJourCit());
+ c4001.setYear_publ(molecule.getYearPubl());
+ c4001.setDoi_link(molecule.getDoiLink());
+ c4001.setComp_class(molecule.getCompClass());
+ c4001.setCuniq(molecule.getCuniq());
+ c4001.setCalc_perf(molecule.getCalcPerf());
+ c4001.setOrg_met(molecule.getOrgMet());
+ c4001.setMol_chrg(molecule.getMolChrg());
+ c4001.setState_ofmat(molecule.getStateOfmat());
+ c4001.setColor_white(molecule.getColorWhite());
+ c4001.setColor_uv(molecule.getColorUv());
+ c4001.setAbsorb_max(molecule.getAbsorbMax());
+ c4001.setSolvent_ae(molecule.getSolventAe());
+ c4001.setAbsorb(molecule.getAbsorb());
+ c4001.setConc(molecule.getConc());
+ c4001.setExtinc(molecule.getExtinc());
+ c4001.setEmis_max(molecule.getEmisMax());
+ c4001.setTemp_abs(molecule.getTempAbs());
+ c4001.setEmis_qy(molecule.getEmisQy());
+ c4001.setTemp_ems(molecule.getTempEms());
+ c4001.setLifetime(molecule.getLifetime());
+ c4001.setTemp_cv(molecule.getTempCv());
+ c4001.setReduc_pot(molecule.getReducPot());
+ c4001.setHw_or_pk_rp(molecule.getHwOrPkRp());
+ c4001.setOxid_pot(molecule.getOxidPot());
+ c4001.setHw_or_pk_op(molecule.getHwOrPkOp());
+ c4001.setSolvent_cv(molecule.getSolventCv());
+ c4001.setElectrolyte(molecule.getElectrolyte());
+ c4001.setRef_electrd(molecule.getRefElectrd());
+ c4001.setInter_thngs(molecule.getInterThngs());
+ c4001.setDensity_20(molecule.getDensity20());
+ c4001.setDensity_20_source(molecule.getDensity20Source());
+ c4001.setDefault_warn_level(molecule.getDefaultWarnLevel());
+ c4001.setN_20(molecule.getN20());
+ c4001.setN_20_source(molecule.getN20Source());
+ c4001.setMp_low(molecule.getMpLow());
+ c4001.setMp_high(molecule.getMpHigh());
+ c4001.setMp_source(molecule.getMpSource());
+ c4001.setBp_low(molecule.getBpLow());
+ c4001.setBp_high(molecule.getBpHigh());
+ c4001.setBp_press(molecule.getBpPress());
+ c4001.setPress_unit(molecule.getPressUnit());
+ c4001.setBp_source(molecule.getBpSource());
+ c4001.setSafety_r(molecule.getSafetyR());
+ c4001.setSafety_h(molecule.getSafetyH());
+ c4001.setSafety_s(molecule.getSafetyS());
+ c4001.setSafety_p(molecule.getSafetyP());
+ c4001.setSafety_text(molecule.getSafetyText());
+ c4001.setSafety_sym(molecule.getSafetySym());
+ c4001.setSafety_sym_ghs(molecule.getSafetySymGhs());
+ c4001.setComment_mol(molecule.getCommentMol());
+ repo.save(c4001);
+ responseObserver.onNext(molecule);
+ responseObserver.onCompleted();
}
@Override
public void deleteMolecule(MoleculeRequest request,
StreamObserver<Molecule> responseObserver) {
- super.deleteMolecule(request, responseObserver);
+// super.deleteMolecule(request, responseObserver);
+ Molecule molecule = request.getMolecule();
+ MoleculeEntity c4001 = (MoleculeEntity)
repo.findBySmiles(molecule.getSmiles());
+ repo.delete(c4001);
+ responseObserver.onNext(molecule);
+ responseObserver.onCompleted();
}
}
