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google-code-export / nmrrestrntsgrid

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Review of new stable version #283

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Please note that as of today the API related code in branch stable/ (so the 
CCPN SF repository) has major updates. All new stuff in the current trunk/ 
version has been merged with existing stable/.

I have not found any problems so far using it, also not with backward 
compatibility, but be aware that if you do an update of the repository, a 
complete regeneration of the API machinery will be required for sure.

Original issue reported on code.google.com by wfvran...@gmail.com on 16 Feb 2012 at 12:42

GoogleCodeExporter commented 9 years ago 
Thanks for the heads up Wim!

Original comment by jurge...@gmail.com on 16 Feb 2012 at 3:22

GoogleCodeExporter commented 9 years ago 
No problem for now. We might reopen this issue if it does come up.

Original comment by jurge...@gmail.com on 16 Feb 2012 at 3:22

GoogleCodeExporter commented 9 years ago 
On my development setup (MBP) using the stable branch, I have done:
svn update $WS/ccpn
got:
...
Updated to revision 7048.

python -u $CCPNMR_TOP_DIR/python/memops/scripts_v2/makePython.py

Original comment by jurge...@gmail.com on 17 Feb 2012 at 5:14

GoogleCodeExporter commented 9 years ago 
Sorry, I wasn't done typing.

The above worked fine.

Then using the machinery in CING:
python $CINGROOT/python/cing/PluginCode/test/test_ccpn.py

Also worked fine. 

I'll need to run a NRG proccessing here before handing it over to production 
with Chris.

Original comment by jurge...@gmail.com on 17 Feb 2012 at 5:19

GoogleCodeExporter commented 9 years ago 
I've updated the NRG-CING production setup now. The API rebuild wasn't very 
clean:

iLnmr/ccpn/ python -u $CCPNMR_TOP_DIR/python/memops/scripts_v2/makePython.py
Model read finished. Duration 0.877506971359 
WARNING, <MetaOperation: ccp.nmr.Nmr.DataDimRef.pointToValue>: single input 
parameter is not named 'value' but point
WARNING, <MetaRole: ccp.general.Citation.Citation.nmrEntriesPrimary> baseName 
'nmrEntryPrimary' dissimilar to name 'nmrEntriesPrimary'
Model validity checked. Duration 10.3875980377

  Memops made ModelPortal, time 0.0999879837036

WARNING, <MetaOperation: ccp.nmr.Nmr.DataDimRef.pointToValue>: single input 
parameter is not named 'value' but point
WARNING, <MetaRole: ccp.general.Citation.Citation.nmrEntriesPrimary> baseName 
'nmrEntryPrimary' dissimilar to name 'nmrEntriesPrimary'
WARNING - <MetaParameter: 
memops.Implementation.ComplexDataType.__init__.result> valueType 
<MetaDataObjType: memops.Implementation.ComplexDataType> does not descend from 
<MetaDataObjType: memops.Implementation.MemopsDataTypeObject>
ModelAdapt - Model validity check took 30.0977208614

  Memops done FileAdapt, time 42.0445351601

  Memops done XML map generation, time 4.1644411087

WARNING1: File 
'/home/i/workspace/ccpn/model/doc/html/diagram/cambridge__Cambridge_Diag.gif' 
does not exist
WARNING1: File 
'/home/i/workspace/ccpn/model/doc/html/diagram/ccp_nmr__NmrCalc_Diag.gif' does 
not exist
WARNING, memops.Implementation.AbstractMatrix.data has no documentation
WARNING, memops.Implementation.BooleanMatrix.data has no documentation
WARNING, memops.Implementation.FloatMatrix.data has no documentation
WARNING, memops.Implementation.IntMatrix.data has no documentation
WARNING, memops.Implementation.StringMatrix.data has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/memops_Implementation__BasicDataT
ypes-details_Diag.gif" does not exist
WARNING, memops.AccessControl.AccessObject has no documentation
WARNING, memops.AccessControl.Permission has no documentation
WARNING, memops.AccessControl.User has no documentation
WARNING, memops.AccessControl.UserGroup has no documentation
WARNING, ccp.general.KeywordDefinition.KeywordDefinition has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_general_KeywordDefinition__Ke
ywordDefinition-details_Diag.gif" does not exist
WARNING, ccp.general.DbRef.Entry.targetGroups has no documentation
WARNING, ccp.general.DbRef.Entry.targets has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_general_Template__Template-de
tails_Diag.gif" does not exist
WARNING, ccp.lims.Classification.HolderCategory.abstractHolderTypes has no 
documentation
WARNING, ccp.lims.Classification.HolderCategory.holders has no documentation
WARNING, ccp.lims.Classification.TargetScoreboard.targetStatus has no 
documentation
WARNING, ccp.lims.Classification.TargetStatus.blueprintStatuss has no 
documentation
WARNING, ccp.lims.Classification.TargetStatus.targetScoreboards has no 
documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_lims_Classification__Classifi
cation-details_Diag.gif" does not exist
WARNING, ccp.general.Affiliation.Person.dropAnnotations has no documentation
WARNING, ccp.molecule.ChemComp.NonStdChemComp.stdChemCompCode has no 
documentation
WARNING, ccp.molecule.ChemComp.StdChemComp.stdChemCompCode has no documentation
WARNING, ccp.lims.Location.Location.location has no documentation
WARNING, ccp.general.Citation.Citation.targetGroups has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccpnmr_AnalysisProfile__AnalysisP
rofile-details_Diag.gif" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccpnmr_AnalysisProfile__AnalysisP
rofile_Diag.gif" does not exist
WARNING, ccp.lims.Holder.AbstractHolderType.holderCategories has no 
documentation
WARNING, ccp.lims.Holder.Holder.endDate has no documentation
WARNING, ccp.lims.Holder.Holder.holderCategories has no documentation
WARNING, ccp.lims.Holder.Holder.startDate has no documentation
WARNING, ccp.lims.Holder.RefSamplePosition has no documentation
WARNING, ccp.molecule.Molecule.Molecule.compounds has no documentation
WARNING, ccp.general.Method.Software.dropAnnotations has no documentation
WARNING, ccp.molecule.MolSystem.MolSystem.nmrScreens has no documentation
WARNING, ccp.lims.RefSampleComponent.MolCompFeature.refMolComponent has no 
documentation
WARNING, ccp.lims.RefSampleComponent.MolComponent.blueprintComponents has no 
documentation
WARNING, ccp.lims.RefSampleComponent.MolComponent.refMolCompFeatures has no 
documentation
WARNING, ccp.lims.RefSampleComponent.MolComponent.relatedExpBlueprints has no 
documentation
WARNING, ccp.lims.RefSampleComponent.MolComponent.seqDetails has no 
documentation
WARNING, ccp.lims.RefSampleComponent.MolComponent.seqString has no documentation
WARNING, ccp.molecule.Validation.PeakValidation has no documentation
WARNING, ccp.molecule.Validation.ValidationResult has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_molecule_Validation__Validati
on-details_Diag.gif" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_molecule_Validation__Validati
on_Diag.gif" does not exist
WARNING, molsim.Symmetry.Symmetry.symmetryCode has no documentation
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/molsim_Symmetry__Symmetry_Diag.gi
f" does not exist
WARNING, ccp.lims.Sample.RefSample.refInputSamples has no documentation
WARNING, ccp.lims.Sample.RefSample.refOutputSamples has no documentation
WARNING, ccp.lims.Sample.RefSample.refSamplePositions has no documentation
WARNING, ccp.lims.Sample.Sample.dropAnnotations has no documentation
WARNING, ccp.lims.Sample.Sample.mixtures has no documentation
WARNING, ccp.lims.Sample.SampleComponent.blueprintComponent has no documentation
WARNING, ccp.lims.Target.Target.dbRefs has no documentation
WARNING, ccp.lims.Target.TargetGroup.annotations has no documentation
WARNING, ccp.lims.Target.TargetGroup.citations has no documentation
WARNING, ccp.lims.Target.TargetGroup.completeName has no documentation
WARNING, ccp.lims.Target.TargetGroup.entrys has no documentation
WARNING, ccp.lims.Crystallization has no documentation
WARNING, ccp.lims.Crystallization.Parameter.parameterDefinition has no 
documentation
WARNING, ccp.lims.Crystallization.ParameterDefinition.parameters has no 
documentation
WARNING, ccp.lims.Protocol.ParameterDefinition.parameters has no documentation
WARNING, ccp.lims.Protocol.RefInputSample.inputSamples has no documentation
WARNING, ccp.lims.Protocol.RefInputSample.refSample has no documentation
WARNING, ccp.lims.Protocol.RefOutputSample.outputSamples has no documentation
WARNING, ccp.lims.Protocol.RefOutputSample.refSample has no documentation
WARNING, ccp.lims.ExpBlueprint.BlueprintComponent.molComponent has no 
documentation
WARNING, ccp.lims.ExpBlueprint.BlueprintComponent.sampleComponents has no 
documentation
WARNING, ccp.lims.ExpBlueprint.BlueprintComponent.trialMolComponents has no 
documentation
WARNING, ccp.lims.ExpBlueprint.BlueprintStatus has no documentation
WARNING, ccp.nmr.Nmr.DataSource.refSpectra has no documentation
WARNING, ccp.nmr.Nmr.DataSource.trialExperiments has no documentation
WARNING, ccp.lims.Experiment.Experiment.blueprintStatuss has no documentation
WARNING, ccp.lims.Experiment.InputSample.refInputSample has no documentation
WARNING, ccp.lims.Experiment.OutputSample.refOutputSample has no documentation
WARNING, ccp.lims.Experiment.Parameter.parameterDefinition has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_lims_Experiment__Lims-details
_Diag.gif" does not exist
WARNING, ccp.nmr.NmrConstraint.CsaConstraintList has no documentation
WARNING, ccp.nmr.NmrConstraint.FixedResonance.csaConstraints has no 
documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_nmr_NmrEntry__NmrData-details
_Diag.gif" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_nmr_NmrEntry__NmrData_Diag.gi
f" does not exist
WARNING, ccpnmr.Analysis.AnalysisPeakList has no documentation
WARNING, ccp.nmr.NmrScreen.Compound has no documentation
WARNING, ccp.nmr.NmrScreen.ExperimentHit has no documentation
WARNING, ccp.nmr.NmrScreen.Mixture has no documentation
WARNING, ccp.nmr.NmrScreen.MixtureComponent has no documentation
WARNING, ccp.nmr.NmrScreen.NmrScreen has no documentation
WARNING, ccp.nmr.NmrScreen.NmrScreenStore has no documentation
WARNING, ccp.nmr.NmrScreen.RefSpectrum has no documentation
WARNING, ccp.nmr.NmrScreen.Trial has no documentation
WARNING, ccp.nmr.NmrScreen.TrialExperiment has no documentation
WARNING, ccp.nmr.NmrScreen.TrialGroup has no documentation
WARNING, ccp.nmr.NmrScreen.TrialHit has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_nmr_NmrScreen__NmrScreen-deta
ils_Diag.gif" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_nmr_NmrScreen__NmrScreen_Diag
.gif" does not exist
WARNING, ccp.general.Annotation.Annotation.targetGroups has no documentation
WARNING, utrecht.Haddock.HaddockPartner.isDna has no documentation
WARNING, utrecht.Haddock.Run.analysisClustRmsd has no documentation
WARNING, utrecht.Haddock.Run.analysisClustSize has no documentation
WARNING, utrecht.Haddock.Run.analysisDistHBond has no documentation
WARNING, utrecht.Haddock.Run.analysisDistNonbond has no documentation
WARNING, utrecht.Haddock.Run.annealProtocol has no documentation
WARNING, utrecht.Haddock.Run.calcDesolvation has no documentation
WARNING, utrecht.Haddock.Run.centerOfMassConstant has no documentation
WARNING, utrecht.Haddock.Run.doRigidTranslations has no documentation
WARNING, utrecht.Haddock.Run.initialRigidBodyMinim has no documentation
WARNING, utrecht.Haddock.Run.nTrails has no documentation
WARNING, utrecht.Haddock.Run.radomizeStartOriention has no documentation
WARNING, utrecht.Haddock.Run.randomSeed has no documentation
WARNING, utrecht.Haddock.Run.rotate180It0 has no documentation
WARNING, utrecht.Haddock.Run.rotate180It1 has no documentation
WARNING, utrecht.Haddock.Run.skipStructures has no documentation
WARNING, utrecht.Haddock.Run.solvent has no documentation
WARNING, utrecht.Haddock.Run.surfaceContactRestraints has no documentation
WARNING, utrecht.Haddock.Run.useHBondRestraints has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/cambridge_Dangle__Dangle-details_
Diag.gif" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/cambridge_Dangle__Dangle_Diag.gif
" does not exist
WARNING, ccp.nmr.NmrCalc.ExternalData.dataLocationStoreName has no documentation
WARNING, ccp.nmr.NmrCalc.ViolationListData.setViolationList has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_nmr_NmrCalc__NmrCalc-details_
Diag.gif" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/ccp_nmr_NmrCalc__NmrCalc_Diag.gif
" does not exist
WARNING, cambridge.WmsProtocol.ProtocolParam.rowspan has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/cambridge_WmsProtocol__WmsProtoco
l-details_Diag.gif" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/cambridge_WmsProtocol__WmsProtoco
l_Diag.gif" does not exist
WARNING, cambridge.Wms.ProjectVersion.createdByTask has no documentation
WARNING, cambridge.Wms.ProjectVersion.outputTasks has no documentation
WARNING, cambridge.Wms.Task.dateCompleted has no documentation
WARNING, cambridge.Wms.Task.dateStarted has no documentation
WARNING, cambridge.Wms.Task.generatedVersion has no documentation
WARNING, cambridge.Wms.Task.inputVersion has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/cambridge_Wms__Wms-details_Diag.g
if" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/cambridge_Wms__Wms_Diag.gif" 
does not exist
WARNING, cambridge.WmsQuery.AbstractQuery.criteria has no documentation
WARNING2: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/cambridge_WmsQuery__WmsQuery-deta
ils_Diag.gif" does not exist
WARNING3: File 
"/home/i/workspace/ccpn/model/doc/html/diagram/cambridge_WmsQuery__WmsQuery_Diag
.gif" does not exist

  Memops done ApiDocGen, time 42.1289439201

  Memops done Api generation, time 73.7480881214

  Memops start test importing

Model read finished. Duration 0.864551067352 
Model validity check skipped
WARNING, Import failed for ccpnmr.format.webServer.Util
WARNING, Import failed for ccpnmr.format.webServer.webFc
WARNING, Import failed for ccpnmr.format.help.makeDoc
WARNING, Import failed for memops.qtapp.BaseApplication
WARNING, Import failed for memops.scripts.PyDocGen
WARNING, Import failed for memops.scripts.odModelTemplateCreator
WARNING, Import failed for memops.scripts.JavaModelGen
WARNING, Import failed for memops.scripts.XmlSchemaGen
WARNING, Import failed for memops.scripts.XMLcheck
WARNING, Import failed for memops.scripts.makeJavaXml
WARNING, Import failed for memops.scripts.extendOdModel
WARNING, Import failed for memops.scripts.DiagDocGen
WARNING, Import failed for memops.scripts.makeDiagDoc
WARNING, Import failed for memops.scripts.PyXmlGen
WARNING, Import failed for memops.scripts.makeSql
WARNING, Import failed for memops.scripts.makeModel
WARNING, Import failed for memops.scripts.makePython
WARNING, Import failed for memops.scripts.JavaImpl
WARNING, Import failed for memops.scripts.ModelGen
WARNING, Import failed for memops.scripts.JavaApiGen
WARNING, Import failed for memops.scripts.makeJava
WARNING, Import failed for memops.scripts.SqlSchemaGen
WARNING, Import failed for memops.scripts.JavaXmlApiGen
WARNING, Import failed for memops.scripts.makeJavaForEclipse
WARNING, Import failed for memops.scripts.JavaXmlGen
WARNING, Import failed for memops.scripts.makeJavaApi
WARNING, Import failed for molsim.xml.NmrSim
WARNING, Import failed for molsim.api.NmrSim
WARNING, Import failed for pdbe.software.vascoReferenceCheck
  Warning need to install sbb/ directory for NRG-CING downloads!
WARNING, Import failed for ccp.qtgui.Molecule.ChainFrame
WARNING, Import failed for ccp.qtgui.Molecule.MoleculeFrame
WARNING, Import failed for ccp.qtgui.Molecule.MolSystemFrame
WARNING, Import failed for ccp.qtgui.Molecule.ResidueFrame
WARNING, Import failed for ccp.qtgui.Molecule.MoleculeTabbedFrame
WARNING, Import failed for ccp.qtgui.Molecule.model.ResidueModel
WARNING, Import failed for ccp.qtgui.Molecule.model.MolSystemModel
WARNING, Import failed for ccp.qtgui.Molecule.model.ChainModel
WARNING, Import failed for ccp.qtgui.Spectrum.OpenSpectrum
Error, the ViewStructureFrame module will not work, something is wrong with the 
C code.
Exception: cannot import name StructAtom
Will continue without Analysis structure viewing functionality
Error, the ViewChemCompVar module will not work, something is wrong with the C 
code.
Exception: cannot import name StructAtom
Will continue without viewing functionality

  Memops done Test Importing, time 10.3647770882

Original comment by jurge...@gmail.com on 24 Feb 2012 at 9:05