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commit 451792418d020430d32d735a55d04e40c14d2401 Author: Bhavesh Asanabada <asanabhav...@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