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Posted to commits@airavata.apache.org by sm...@apache.org on 2022/09/12 17:16:29 UTC
[airavata-sandbox] 04/26: Resolved issues in calc_topology builder
This is an automated email from the ASF dual-hosted git repository.
smarru pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git
commit 451792418d020430d32d735a55d04e40c14d2401
Author: Bhavesh Asanabada <as...@gmail.com>
AuthorDate: Tue Jun 28 12:03:12 2022 +0530
Resolved issues in calc_topology builder
---
.../com/smiles/calctopology/CalcTopologyImpl.java | 18 ++-
.../com/smiles/calctopology/CalcTopologyRepo.java | 1 +
.../main/java/com/smiles/molData/MoleculeImpl.java | 146 ++++++++++-----------
.../Server/src/main/proto/calc_topology.proto | 6 +-
4 files changed, 88 insertions(+), 83 deletions(-)
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 2b143010..22fa6ec2 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
@@ -7,6 +7,7 @@ import com.smiles.SpringContext;
import io.grpc.stub.StreamObserver;
import javax.swing.*;
+import java.util.ArrayList;
public class CalcTopologyImpl extends CalcTopologyServiceGrpc.CalcTopologyServiceImplBase {
@@ -16,20 +17,23 @@ public class CalcTopologyImpl extends CalcTopologyServiceGrpc.CalcTopologyServic
// super.getCalcTopology(request, responseObserver);
System.out.println(request.getAllFields());
- CalcTopologyEntity calcTopology = repo.findBySymbols(request.getcalcTopologyQuery());
+ ArrayList<String> input = new ArrayList<String>();
+ input.add(request.getCalcTopologyQuery());
+ CalcTopologyEntity calcTopology = repo.findBySymbols(input);
System.out.println(calcTopology.toString());
CalcTopology reply = CalcTopology.newBuilder()
- .setSymbols(calcTopology.getSymbols())
- .setGeometry(calcTopology.getGeometry())
+ .addAllSymbols(calcTopology.getSymbols())
+ .addAllGeometry(calcTopology.getGeometry())
.setMolCharge(calcTopology.getMol_charge())
.setMolMultiplicity(calcTopology.getMol_multiplicity())
.setName(calcTopology.getName())
.setComment(calcTopology.getComment())
- .setMassNumbers(calcTopology.getMass_numbers())
- .setMasses(calcTopology.getMasses())
- .setAtomicNumber(calcTopology.getAtomic_number())
- .setAtomLabels(calcTopology.getAtomic_labels()).build();
+ .addAllMassNumbers(calcTopology.getMass_numbers())
+ .addAllMasses(calcTopology.getMasses())
+ .addAllAtomicNumber(calcTopology.getAtomic_number())
+ .addAllAtomLabels(calcTopology.getAtomic_labels()).build();
+
}
@Override
diff --git a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyRepo.java b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyRepo.java
index a4fd1b98..2efbebea 100644
--- a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyRepo.java
+++ b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyRepo.java
@@ -7,4 +7,5 @@ import java.util.List;
public interface CalcTopologyRepo extends MongoRepository<CalcTopologyEntity, String> {
public CalcTopologyEntity findBySymbols(List<String> symbols);
+
}
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 6cf4a7b5..1b961a1a 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
@@ -55,7 +55,7 @@ public class MoleculeImpl extends MoleculeServiceGrpc.MoleculeServiceImplBase {
// super.createMolecule(request, responseObserver);
Molecule molecule = request.getMolecule();
System.out.println(request.getAllFields());
- MoleculeEntity c4001 = new MoleculeEntity(molecule.getCasNr(),
+ MoleculeEntity moleculeEntity = new MoleculeEntity(molecule.getCasNr(),
molecule.getSmiles(), molecule.getSmilesStereo(),
molecule.getInchi(), molecule.getMolfileBlobSource(),
molecule.getEmpFormula(), molecule.getEmpFormulaSort(),
@@ -78,7 +78,7 @@ public class MoleculeImpl extends MoleculeServiceGrpc.MoleculeServiceImplBase {
molecule.getBpSource(), molecule.getSafetyR(), molecule.getSafetyH(), molecule.getSafetyS(),
molecule.getSafetyP(), molecule.getSafetyText(), molecule.getSafetySym(),
molecule.getSafetySymGhs(), molecule.getSafetySource(), molecule.getCommentMol());
- repo.save(c4001);
+ repo.save(moleculeEntity);
responseObserver.onNext(molecule);
responseObserver.onCompleted();
@@ -90,75 +90,75 @@ public class MoleculeImpl extends MoleculeServiceGrpc.MoleculeServiceImplBase {
// 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);
+ MoleculeEntity moleculeEntity = (MoleculeEntity) repo.findBySmiles(molecule.getSmiles());
+ System.out.println(moleculeEntity.getId());
+ moleculeEntity.setCas_nr(molecule.getCasNr());
+ moleculeEntity.setSmiles(molecule.getSmiles());
+ moleculeEntity.setSmiles_stereo(molecule.getSmilesStereo());
+ moleculeEntity.setInchi(molecule.getInchi());
+ moleculeEntity.setMolfile_blob_source(molecule.getMolfileBlobSource());
+ moleculeEntity.setEmp_formula(molecule.getEmpFormula());
+ moleculeEntity.setEmp_formula_sort(molecule.getEmpFormulaSort());
+ moleculeEntity.setEmp_formula_source(molecule.getEmpFormulaSource());
+ moleculeEntity.setMw(molecule.getMw());
+ moleculeEntity.setMw_monoiso(molecule.getMwMonoiso());
+ moleculeEntity.setRdb(molecule.getRdb());
+ moleculeEntity.setMw_source(molecule.getMwSource());
+ moleculeEntity.setValidated_by(molecule.getValidatedBy());
+ moleculeEntity.setJournal(molecule.getJournal());
+ moleculeEntity.setAuth_of_intr(molecule.getAuthOfIntr());
+ moleculeEntity.setJour_cit(molecule.getJourCit());
+ moleculeEntity.setYear_publ(molecule.getYearPubl());
+ moleculeEntity.setDoi_link(molecule.getDoiLink());
+ moleculeEntity.setComp_class(molecule.getCompClass());
+ moleculeEntity.setCuniq(molecule.getCuniq());
+ moleculeEntity.setCalc_perf(molecule.getCalcPerf());
+ moleculeEntity.setOrg_met(molecule.getOrgMet());
+ moleculeEntity.setMol_chrg(molecule.getMolChrg());
+ moleculeEntity.setState_ofmat(molecule.getStateOfmat());
+ moleculeEntity.setColor_white(molecule.getColorWhite());
+ moleculeEntity.setColor_uv(molecule.getColorUv());
+ moleculeEntity.setAbsorb_max(molecule.getAbsorbMax());
+ moleculeEntity.setSolvent_ae(molecule.getSolventAe());
+ moleculeEntity.setAbsorb(molecule.getAbsorb());
+ moleculeEntity.setConc(molecule.getConc());
+ moleculeEntity.setExtinc(molecule.getExtinc());
+ moleculeEntity.setEmis_max(molecule.getEmisMax());
+ moleculeEntity.setTemp_abs(molecule.getTempAbs());
+ moleculeEntity.setEmis_qy(molecule.getEmisQy());
+ moleculeEntity.setTemp_ems(molecule.getTempEms());
+ moleculeEntity.setLifetime(molecule.getLifetime());
+ moleculeEntity.setTemp_cv(molecule.getTempCv());
+ moleculeEntity.setReduc_pot(molecule.getReducPot());
+ moleculeEntity.setHw_or_pk_rp(molecule.getHwOrPkRp());
+ moleculeEntity.setOxid_pot(molecule.getOxidPot());
+ moleculeEntity.setHw_or_pk_op(molecule.getHwOrPkOp());
+ moleculeEntity.setSolvent_cv(molecule.getSolventCv());
+ moleculeEntity.setElectrolyte(molecule.getElectrolyte());
+ moleculeEntity.setRef_electrd(molecule.getRefElectrd());
+ moleculeEntity.setInter_thngs(molecule.getInterThngs());
+ moleculeEntity.setDensity_20(molecule.getDensity20());
+ moleculeEntity.setDensity_20_source(molecule.getDensity20Source());
+ moleculeEntity.setDefault_warn_level(molecule.getDefaultWarnLevel());
+ moleculeEntity.setN_20(molecule.getN20());
+ moleculeEntity.setN_20_source(molecule.getN20Source());
+ moleculeEntity.setMp_low(molecule.getMpLow());
+ moleculeEntity.setMp_high(molecule.getMpHigh());
+ moleculeEntity.setMp_source(molecule.getMpSource());
+ moleculeEntity.setBp_low(molecule.getBpLow());
+ moleculeEntity.setBp_high(molecule.getBpHigh());
+ moleculeEntity.setBp_press(molecule.getBpPress());
+ moleculeEntity.setPress_unit(molecule.getPressUnit());
+ moleculeEntity.setBp_source(molecule.getBpSource());
+ moleculeEntity.setSafety_r(molecule.getSafetyR());
+ moleculeEntity.setSafety_h(molecule.getSafetyH());
+ moleculeEntity.setSafety_s(molecule.getSafetyS());
+ moleculeEntity.setSafety_p(molecule.getSafetyP());
+ moleculeEntity.setSafety_text(molecule.getSafetyText());
+ moleculeEntity.setSafety_sym(molecule.getSafetySym());
+ moleculeEntity.setSafety_sym_ghs(molecule.getSafetySymGhs());
+ moleculeEntity.setComment_mol(molecule.getCommentMol());
+ repo.save(moleculeEntity);
responseObserver.onNext(molecule);
responseObserver.onCompleted();
}
@@ -167,8 +167,8 @@ public class MoleculeImpl extends MoleculeServiceGrpc.MoleculeServiceImplBase {
public void deleteMolecule(MoleculeRequest request, StreamObserver<Molecule> responseObserver) {
// super.deleteMolecule(request, responseObserver);
Molecule molecule = request.getMolecule();
- MoleculeEntity c4001 = (MoleculeEntity) repo.findBySmiles(molecule.getSmiles());
- repo.delete(c4001);
+ MoleculeEntity moleculeEntity = (MoleculeEntity) repo.findBySmiles(molecule.getSmiles());
+ repo.delete(moleculeEntity);
responseObserver.onNext(molecule);
responseObserver.onCompleted();
}
diff --git a/gsoc2022/smilesdb/Server/src/main/proto/calc_topology.proto b/gsoc2022/smilesdb/Server/src/main/proto/calc_topology.proto
index 3f55f6b9..c09f04b8 100644
--- a/gsoc2022/smilesdb/Server/src/main/proto/calc_topology.proto
+++ b/gsoc2022/smilesdb/Server/src/main/proto/calc_topology.proto
@@ -14,11 +14,11 @@ message CalcTopology{
string name = 5; //The name of the molecule.
string comment = 6; //Any additional comment one would attach to the molecule.
// int[] mass_numbers; //(nat, ) mass numbers for atoms, if known isotope, else -1.
- repeated int64 mass_numbers = 7;
+ repeated int64 mass_numbers = 7 [packed = true];
// double[] masses; //(nat, ) atom masses [u]; canonical weights assumed if not given.
- repeated double masses = 8;
+ repeated double masses = 8 [packed = true];
// double[] atomic_numbers; //(nat, ) atomic numbers, nuclear charge for atoms. Ghostedness should be indicated through ‘real’ field, not zeros here.
- repeated double atomic_number = 9;
+ repeated double atomic_number = 9 [packed = true];
// string[] atom_labels; //(nat, ) atom labels with any user tagging information.
repeated string atom_labels = 10;
// atomic_numbers