hupo-psi / mzidentml-validator Goto Github PK

Failed to execute goal on project mzIdentMLValidator: 
Could not resolve dependencies for project psidev.psi.pi:mzIdentMLValidator:jar:1.4.35-SNAPSHOT: 
Failed to collect dependencies at psidev.psi.tools:validator:jar:2.0.10 
-> psidev.psi.tools:ontology-manager:jar:2.0.10 
-> uk.ac.ebi.ols:ols-core:jar:1.19 
-> proteomics:proteomics-common:jar:1.5: 
Failed to read artifact descriptor for proteomics:proteomics-common:jar:1.5: 
Could not transfer artifact proteomics:proteomics-common:pom:1.5 from/to maven-default-http-blocker (http://0.0.0.0/): 

Blocked mirror for repositories: 
[
nexus-ebi-repo-old (http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/, default, releases+snapshots), 
nexus-ebi-release-repo (http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/, default, releases+snapshots), 
nexus-ebi-snapshot-repo (http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/, default, releases+snapshots), 
ebi-repo (http://www.ebi.ac.uk/~maven/m2repo, default, releases+snapshots), 
ibiblio-repo (http://mirrors.ibiblio.org/pub/mirrors/maven2/, default, releases+snapshots), 
java-repo (http://download.java.net/maven/2/, default, releases+snapshots)
] 
-> [Help 1]

  <ProteinAmbiguityGroup id="PAG_13">
    <ProteinDetectionHypothesis dBSequence_ref="dbseq_XXXXX_target" passThreshold="false" id="PAG_13_PDH_0">
      ...
      <cvParam cvRef="PSI-MS" accession="MS:1002677" name="residue-pair-level global FDR" value="151808167.a:214:0.0:true"></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002677" name="residue-pair-level global FDR" value="151808167.b:141:0.0:true"></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002677" name="residue-pair-level global FDR" value="151808167.b:149:0.0:true"></cvParam>

Message 14497:
    Level: ERROR
    --> Interaction score is not paired for XL interaction ID 151810610 and score 0.0 (has only 1 entries for : PAG: PAG_13 and PDH: PAG_13_PDH_0

    <SpectrumIdentificationProtocol id="SIP" analysisSoftware_ref="AS_mascot_server">
      <SearchType>
        <cvParam accession="MS:1002755" name="combined ms-ms + spectral library search" cvRef="PSI-MS" value="" />
      </SearchType>

id: MS:1002755
name: combined ms-ms + spectral library search
def: "A combined MS2 (with fragment ions) and spectral library search." [PSI:PI]
is_a: MS:1001080 ! search type

Message 2:
    Rule ID: SearchTypeObjectRule
    Level: ERROR
    Context(/MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol )
    --> At least one child term of 'search type' must occur in SearchType of the SpectrumIdentificationProtocol (id='SIP') element at /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol
    Tip: The SearchType element of SpectrumIdentificationProtocol must contain a CV term.

Message 3:
    Rule ID: SearchType_must_rule
    Level: ERROR
    Context(/searchType/cvParam/@accession ) in 2 locations
    --> The result found at: /searchType/cvParam/@accession for which the values is  ''MS:1002755'' didn't match any of the 6 specified CV terms:
  - The sole term MS:1001010 (de novo search) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
  - The sole term MS:1001031 (spectral library search) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
  - The sole term MS:1001081 (pmf search) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
  - The sole term MS:1001082 (tag search) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
  - The sole term MS:1001083 (ms-ms search) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
  - The sole term MS:1001584 (combined pmf + ms-ms search) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name

      <Threshold>
        <cvParam accession="MS:1001214" name="protein-level global FDR" cvRef="PSI-MS" value="0.0562" />
      </Threshold>
    </ProteinDetectionProtocol>

id: MS:1001214
name: protein-level global FDR
def: "Estimation of the global false discovery rate of proteins." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002705 ! protein-level result list statistic

Message 1:
    Rule ID: ProteinDetectionProtocolThreshold_must_rule
    Level: ERROR
    Context(/threshold/cvParam/@accession ) in 2 locations
    --> The result found at: /threshold/cvParam/@accession for which the values is  ''MS:1001214'' didn't match any of the 5 specified CV terms:
  - Any children term of MS:1001153 (search engine specific score). The term can be repeated. The matching value has to be the identifier of the term, not its name.
  - Any children term of MS:1001302 (search engine specific input parameter). The term can be repeated. The matching value has to be the identifier of the term, not its name.
  - The sole term MS:1001494 (no threshold) or any of its children. The term can be repeated. The matching value has to be the identifier of the term, not its name.
  - Any children term of MS:1002572 (protein detection statistical threshold). The term can be repeated. The matching value has to be the identifier of the term, not its name.
  - Any children term of MS:1002706 (protein group-level result list statistic). The term can be repeated. The matching value has to be the identifier of the term, not its name.

Message 5:
    Rule ID: CrosslinkingPeptideModification_may_rule
    Level: ERROR
    Context(Flaw in the rule definition: CrosslinkingPeptideModification_may_rule )
    --> Could not find property 'Peptide' of the xpath expression '/Peptide/modification/cvParam/@accession' (element position: 1) in the given object of: uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection - Did you mean 'peptide' ?