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sneumann / mtblsHops

The ISAtab and supporting informtion for the data behind http://dx.doi.org/10.1007/s11306-011-0335-y
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Fails to load into BII #7

Closed sneumann closed 10 years ago

sneumann commented 10 years ago

Hi,

below are the errors when importing the study into a BII. [Hint: load the study from a directory, as currently creating ZIP files fails.]

warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'sample amount' not found in the protocol 'GC-MS extraction', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'extraction solvent' not found in the protocol 'GC-MS extraction', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'sample amount' not found in the protocol 'GC mass spectrometry', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'scanning' not found in the protocol 'GC mass spectrometry', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'ionization mode' not found in the protocol 'GC mass spectrometry', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'ionization voltage' not found in the protocol 'GC mass spectrometry', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'software' not found in the protocol 'data transformation', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'sample amount' not found in the protocol 'GC-MS extraction', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'extraction solvent' not found in the protocol 'GC-MS extraction', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'sample amount' not found in the protocol 'GC mass spectrometry', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'scanning' not found in the protocol 'GC mass spectrometry', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'ionization mode' not found in the protocol 'GC mass spectrometry', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'ionization voltage' not found in the protocol 'GC mass spectrometry', creating it automatically
warning - a_mtbls-hops-gcms.txt
Parameter referred in protocol application 'software' not found in the protocol 'data transformation', creating it automatically
warning - a_mtbls-hops-nmr.txt
WARNING: The field "NMR Assay Name" should be preceded by the field "Labeled Extract Name"
warning - a_mtbls-hops-nmr.txt
WARNING: The field "NMR Assay Name" should be preceded by the field "Labeled Extract Name"
warning - a_mtbls-hops-lcms.txt
WARNING: The field "MS Assay Name" should be preceded by the field "Labeled Extract Name"
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'sample amount' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'ionization mode' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'ionization voltage' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'internal standard amount' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'elution buffer' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
WARNING: The field "MS Assay Name" should be preceded by the field "Labeled Extract Name"
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'sample amount' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'ionization mode' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'ionization voltage' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'internal standard amount' not found in the protocol 'LC mass spectrometry', creating it automatically
warning - a_mtbls-hops-lcms.txt
Parameter referred in protocol application 'elution buffer' not found in the protocol 'LC mass spectrometry', creating it automatically
sneumann commented 10 years ago

Hi, I checked again, and get this error towards the end:

...
2014-02-18 14:40:37,319 []: Data file 'Derived Spectral Data File' / '/vol/bioinvindex/Submissions/mtblsHops/MTBLS-Hops/lcms/QHH033_TPE_3_pos.cdf' copied to '/vol/bioinvindex/data-1.6/meda_repo/ms/study_MTBLS-HOPS_zy62bCKPtj/processed_data'
2014-02-18 14:40:37,484 []: Some assays for the study #MTBLS-HOPS have both file link annotation comments and a data location defined. You should probably review the ISATAB or the configured data locations. Keeping the comments in the assay file and skipping the data location definition for this file
2014-02-18 14:40:38,183 []: not-null property references a null or transient value: uk.ac.ebi.bioinvindex.model.xref.ReferenceSource.acc
org.hibernate.PropertyValueException: not-null property references a null or transient value: uk.ac.ebi.bioinvindex.model.xref.ReferenceSource.acc
    at org.hibernate.engine.Nullability.checkNullability(Nullability.java:95)
    at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:313)
    at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:204)
    at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:144)
    at org.hibernate.ejb.event.EJB3SaveEventListener.saveWithGeneratedId(EJB3SaveEventListener.java:43)
    at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:210)
    at org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:56)
    at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:195)
    at org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:50)
    at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:93)
    at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:562)
    at org.hibernate.impl.SessionImpl.save(SessionImpl.java:550)
    at org.hibernate.impl.SessionImpl.save(SessionImpl.java:546)
    at uk.ac.ebi.bioinvindex.dao.ejb3.IdentifiableEJB3DAO.save(IdentifiableEJB3DAO.java:106)
    at uk.ac.ebi.bioinvindex.persistence.Persister.save(Persister.java:237)
    at uk.ac.ebi.bioinvindex.persistence.Persister.persist(Persister.java:202)
    at uk.ac.ebi.bioinvindex.persistence.OntologyEntryPersister.preProcess(OntologyEntryPersister.java:97)
    at uk.ac.ebi.bioinvindex.persistence.OntologyEntryPersister.preProcess(OntologyEntryPersister.java:70)
    at uk.ac.ebi.bioinvindex.persistence.Persister.persist(Persister.java:199)
    at uk.ac.ebi.bioinvindex.persistence.FreeTextTermPersister.preProcess(FreeTextTermPersister.java:92)
    at uk.ac.ebi.bioinvindex.persistence.FreeTextTermPersister.preProcess(FreeTextTermPersister.java:69)
    at uk.ac.ebi.bioinvindex.persistence.Persister.persist(Persister.java:199)
    at uk.ac.ebi.bioinvindex.persistence.AbstractPropertyValuePersister.preProcess(AbstractPropertyValuePersister.java:86)
    at uk.ac.ebi.bioinvindex.persistence.AbstractPropertyValuePersister.preProcess(AbstractPropertyValuePersister.java:63)
    at uk.ac.ebi.bioinvindex.persistence.Persister.persist(Persister.java:199)
    at uk.ac.ebi.bioinvindex.persistence.pipeline.MaterialPersister.preProcess(MaterialPersister.java:90)
    at uk.ac.ebi.bioinvindex.persistence.pipeline.MaterialPersister.preProcess(MaterialPersister.java:60)
    at uk.ac.ebi.bioinvindex.persistence.Persister.persist(Persister.java:199)
    at uk.ac.ebi.bioinvindex.persistence.pipeline.MaterialNodePersister.postProcess(MaterialNodePersister.java:75)
    at uk.ac.ebi.bioinvindex.persistence.pipeline.MaterialNodePersister.postProcess(MaterialNodePersister.java:52)
    at uk.ac.ebi.bioinvindex.persistence.Persister.persist(Persister.java:204)
    at uk.ac.ebi.bioinvindex.persistence.pipeline.GraphElementPersister.persist(GraphElementPersister.java:137)
    at uk.ac.ebi.bioinvindex.persistence.pipeline.GenericGraphElementPersister.persist(GenericGraphElementPersister.java:149)
    at uk.ac.ebi.bioinvindex.persistence.pipeline.GenericGraphElementPersister.persistCasted(GenericGraphElementPersister.java:162)
    at uk.ac.ebi.bioinvindex.persistence.pipeline.AssayMaterialPersister.persist(AssayMaterialPersister.java:123)
    at uk.ac.ebi.bioinvindex.persistence.AssayPersister.preProcess(AssayPersister.java:112)
    at uk.ac.ebi.bioinvindex.persistence.AssayPersister.preProcess(AssayPersister.java:64)
    at uk.ac.ebi.bioinvindex.persistence.Persister.persist(Persister.java:199)
    at uk.ac.ebi.bioinvindex.persistence.StudyPersister.postProcess(StudyPersister.java:156)
    at uk.ac.ebi.bioinvindex.persistence.StudyPersister.postProcess(StudyPersister.java:66)
    at uk.ac.ebi.bioinvindex.persistence.Persister.persist(Persister.java:204)
    at uk.ac.ebi.bioinvindex.persistence.StudyPersister.persist(StudyPersister.java:198)
    at org.isatools.isatab.ISATABPersister.persist(ISATABPersister.java:99)
    at org.isatools.isatab.gui_invokers.GUIISATABLoader.persist(GUIISATABLoader.java:119)
    at org.isatools.isatab.gui_invokers.GUIISATABLoader.persist(GUIISATABLoader.java:107)
    at org.isatools.isatab.gui_invokers.GUIISATABLoader.persist(GUIISATABLoader.java:89)
    at org.isatools.gui.datamanager.DBLoader.loadToDatabase(DBLoader.java:79)
    at org.isatools.gui.datamanager.DataManagerToolUI.loadToDatabase(DataManagerToolUI.java:280)
    at org.isatools.gui.CommonUI$3.run(CommonUI.java:215)
    at java.lang.Thread.run(Thread.java:679)
2014-02-18 14:40:38,187 []: Rolling back transaction.
2014-02-18 14:40:38,189 []: Closing entity manager.
proccaserra commented 10 years ago

file names are the name for both raw data file and derived data in a_mtbls-hops-lcms.txt this is the root cause (most likely)

sneumann commented 10 years ago

No, just pushed 01c91468cc117d30345ee0860ef57d8f826dc19a which adds *.raw files and corresponding file paths in the assay file.

proccaserra commented 10 years ago

This one loads when I used BIImanager-1.6.5 against an out of the box H2 database.

the problem was caused by the FactorValue[]

s/Factor Value[selectively maintained organism,http://purl.obolibrary.org/obo/OBI_0001185,OBI]/Factor Value[selectively maintained organism]

because the Study Factor in the investigation already sets the Ontology Entry value, there is no need to include it in the header.

We need to document this better in the spec and the documentation. Note that the syntax is however valid when dealing with Characteristics[] and Parameter Value[]

I have not pushed as I was wondering if you were still editing. let me know.

sneumann commented 10 years ago

Thanks for fixing this. I have pushed my changes, but due to some merge problems I am unsure whether I was able to keep all your changes from Fri Feb 28.