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A
AbstractSolrLoader
- Class in
owltools.solrj
Root class for loading ontologies or ontology-related data into a Solr instance using web services and the solrj library
AbstractSolrLoader(SolrServer)
- Constructor for class owltools.solrj.
AbstractSolrLoader
AbstractSolrLoader(String)
- Constructor for class owltools.solrj.
AbstractSolrLoader
add(FlexLine)
- Method in class owltools.flex.
FlexDocument
Add a line to the document.
add(SolrInputDocument)
- Method in class owltools.solrj.
AbstractSolrLoader
add(String)
- Method in class owltools.yaml.golrconfig.
ConfigManager
Work with a flexible document definition from a configuration file.
addAll(Collection<SolrInputDocument>)
- Method in class owltools.solrj.
AbstractSolrLoader
addAllAndCommit()
- Method in class owltools.solrj.
AbstractSolrLoader
addAssociatedGeneProduct(String, String)
- Method in class owltools.panther.
PANTHERTree
Add an associated id/label for a term in this tree.
associatedIdentifierSet()
- Method in class owltools.panther.
PANTHERTree
Return a set of all identifiers associated with this family.
B
boost_weights
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
boost_weights
- Variable in class owltools.yaml.golrconfig.
GOlrField
C
cardinality
- Variable in class owltools.yaml.golrconfig.
GOlrField
collect(FlexDocument)
- Method in class owltools.solrj.
FlexSolrDocumentLoader
Take args and add it index (no commits) Main wrapping for adding ontology documents to GOlr.
collect(OWLObject, OWLGraphWrapper)
- Method in class owltools.solrj.
OntologyGeneralSolrDocumentLoader
collect(OWLObject, OWLGraphWrapper)
- Method in class owltools.solrj.
OntologySolrLoader
Deprecated.
config
- Variable in class owltools.flex.
FlexCollection
ConfigManager
- Class in
owltools.yaml.golrconfig
ConfigManager()
- Constructor for class owltools.yaml.golrconfig.
ConfigManager
Constructor.
D
description
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
description
- Variable in class owltools.yaml.golrconfig.
GOlrField
display_name
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
display_name
- Variable in class owltools.yaml.golrconfig.
GOlrField
docs
- Variable in class owltools.flex.
FlexCollection
document_category
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
F
field
- Variable in class owltools.flex.
FlexLine
field()
- Method in class owltools.flex.
FlexLine
Return the field name.
fields
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
fileCount
- Variable in class owltools.panther.
PANTHERForest
filter_weights
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
filter_weights
- Variable in class owltools.yaml.golrconfig.
GOlrField
FlexCollection
- Class in
owltools.flex
Pull defined sources into a middle state for output, loading into Solr, etc.
FlexCollection(OWLGraphWrapper)
- Constructor for class owltools.flex.
FlexCollection
More fun init.
FlexCollection(ConfigManager, OWLGraphWrapper)
- Constructor for class owltools.flex.
FlexCollection
More fun init.
FlexDocument
- Class in
owltools.flex
Pull defined sources into a middle state for output, loading into Solr, etc.
FlexDocument()
- Constructor for class owltools.flex.
FlexDocument
Init.
FlexLine
- Class in
owltools.flex
Workalike for a singleton line in a Solr document.
FlexLine(String, String)
- Constructor for class owltools.flex.
FlexLine
Singleton init.
FlexLine(String, ArrayList<String>)
- Constructor for class owltools.flex.
FlexLine
List init.
FlexSolrDocumentLoader
- Class in
owltools.solrj
A slightly generic class for loading a Solr index compatible with the constraints defined by a BBOP-JS Solr index.
FlexSolrDocumentLoader(String, FlexCollection)
- Constructor for class owltools.solrj.
FlexSolrDocumentLoader
G
GafSolrDocumentLoader
- Class in
owltools.solrj
A very specific class for the specific use case of loading in a GAF-like document into a Solr index.
GafSolrDocumentLoader(String)
- Constructor for class owltools.solrj.
GafSolrDocumentLoader
getAncestorAnnotations(String)
- Method in class owltools.panther.
PANTHERTree
Return all annotations to ancestor nodes.
getAncestors(String)
- Method in class owltools.panther.
PANTHERTree
Return the ancestors of this node as an ID set.
getAssociatedGeneProductIDs()
- Method in class owltools.panther.
PANTHERTree
Return the associated gene/product ids for this tree.
getAssociatedGeneProductJSONMap()
- Method in class owltools.panther.
PANTHERTree
Return the mapping of associated gene/product ids to labels for this tree.
getAssociatedGeneProductLabels()
- Method in class owltools.panther.
PANTHERTree
Return the associated gene/product labels for this tree.
getAssociatedTrees(String)
- Method in class owltools.panther.
PANTHERForest
Return the number of unique bioentity identifiers found in the set.
getDescendantAnnotations(String)
- Method in class owltools.panther.
PANTHERTree
Return all annotations to descendant nodes.
getDescendants(String)
- Method in class owltools.panther.
PANTHERTree
Return the descendants of this node as an ID set.
getExtString(OWLObject, ArrayList<String>)
- Method in class owltools.flex.
FlexCollection
Get properly formatted output from the OWLGraphWrapper.
getExtStringList(OWLObject, ArrayList<String>)
- Method in class owltools.flex.
FlexCollection
Get properly formatted output from the OWLGraphWrapper.
getFieldComments(String)
- Method in class owltools.yaml.golrconfig.
ConfigManager
Return the comments associated with the GOlrCoreField id; empty list if there weren't any.
getFields()
- Method in class owltools.yaml.golrconfig.
ConfigManager
Get all the fields.
getGafDocument()
- Method in class owltools.solrj.
GafSolrDocumentLoader
getGraph()
- Method in class owltools.solrj.
AbstractSolrLoader
getNHXString()
- Method in class owltools.panther.
PANTHERTree
Return the raw Newick-type input string.
getNumberOfFilesInSet()
- Method in class owltools.panther.
PANTHERForest
Return the number of files read into the set.
getNumberOfIdentifiersInSet()
- Method in class owltools.panther.
PANTHERForest
Return the number of unique identifiers found in the set.
getOWLShuntGraph()
- Method in class owltools.panther.
PANTHERTree
Return the complete OWL shunt graph representation of the phylogenic tree.
getPANTHERID()
- Method in class owltools.panther.
PANTHERTree
Return the tree public (PANTHER) identifier.
getTreeByID(String)
- Method in class owltools.panther.
PANTHERForest
Return the tree for the tree unique identifier, If nothing was found, return null.
getTreeID()
- Method in class owltools.panther.
PANTHERTree
Return the tree internal identifier.
getTreeIDSet()
- Method in class owltools.panther.
PANTHERForest
Return the unique tree identifiers found in the forest.
getTreeLabel()
- Method in class owltools.panther.
PANTHERTree
Return the tree label.
GOlrConfig
- Class in
owltools.yaml.golrconfig
GOlrConfig()
- Constructor for class owltools.yaml.golrconfig.
GOlrConfig
GOlrDynamicField
- Class in
owltools.yaml.golrconfig
Deprecated.
GOlrDynamicField()
- Constructor for class owltools.yaml.golrconfig.
GOlrDynamicField
Deprecated.
GOlrField
- Class in
owltools.yaml.golrconfig
GOlrField()
- Constructor for class owltools.yaml.golrconfig.
GOlrField
GOlrFixedField
- Class in
owltools.yaml.golrconfig
Deprecated.
GOlrFixedField()
- Constructor for class owltools.yaml.golrconfig.
GOlrFixedField
Deprecated.
graph
- Variable in class owltools.flex.
FlexCollection
graph
- Variable in class owltools.solrj.
AbstractSolrLoader
I
id
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
id
- Variable in class owltools.yaml.golrconfig.
GOlrField
incrementalAddAndCommit()
- Method in class owltools.solrj.
AbstractSolrLoader
indexed
- Variable in class owltools.yaml.golrconfig.
GOlrField
isMulti()
- Method in class owltools.flex.
FlexLine
Return whether or not the line has a single value or multiple values.
isSingle()
- Method in class owltools.flex.
FlexLine
Return whether or not the line has a single value or multiple values.
iterator()
- Method in class owltools.flex.
FlexCollection
iterator()
- Method in class owltools.flex.
FlexDocument
iterator()
- Method in class owltools.flex.
FlexLine
L
lines
- Variable in class owltools.flex.
FlexDocument
load()
- Method in class owltools.solrj.
AbstractSolrLoader
load()
- Method in class owltools.solrj.
FlexSolrDocumentLoader
load()
- Method in class owltools.solrj.
GafSolrDocumentLoader
load()
- Method in class owltools.solrj.
OntologyGeneralSolrDocumentLoader
load()
- Method in class owltools.solrj.
OntologySolrLoader
Deprecated.
load()
- Method in class owltools.solrj.
OptimizeSolrDocumentLoader
load()
- Method in class owltools.solrj.
PANTHERGeneralSolrDocumentLoader
load()
- Method in class owltools.solrj.
PANTHERSolrDocumentLoader
O
OntologyGeneralSolrDocumentLoader
- Class in
owltools.solrj
A highly hard-wired class to specifically load the ontology graph into a set of hard-wired fields for the AmiGO 2/GOlr general-config.yaml schema.
OntologyGeneralSolrDocumentLoader(String, OWLGraphWrapper)
- Constructor for class owltools.solrj.
OntologyGeneralSolrDocumentLoader
OntologySolrLoader
- Class in
owltools.solrj
Deprecated.
OntologySolrLoader(String, OWLGraphWrapper)
- Constructor for class owltools.solrj.
OntologySolrLoader
Deprecated.
OptimizeSolrDocumentLoader
- Class in
owltools.solrj
A hard-wired optimize command for after we've done everything that we wanted to load.
OptimizeSolrDocumentLoader(String)
- Constructor for class owltools.solrj.
OptimizeSolrDocumentLoader
owltools.flex
- package owltools.flex
Flex Document
owltools.panther
- package owltools.panther
PANTHER Tree Tools
owltools.solrj
- package owltools.solrj
OWLTools and Solr
owltools.yaml.golrconfig
- package owltools.yaml.golrconfig
YAML GOlr Configuration
P
PANTHERForest
- Class in
owltools.panther
Methods to simplify the work with sets of PANTHER trees.
PANTHERForest(File)
- Constructor for class owltools.panther.
PANTHERForest
Create an instance for the given privitve array of files.
PANTHERGeneralSolrDocumentLoader
- Class in
owltools.solrj
A hard-wired loader for the general-config.yaml profile.
PANTHERGeneralSolrDocumentLoader(String)
- Constructor for class owltools.solrj.
PANTHERGeneralSolrDocumentLoader
PANTHERSolrDocumentLoader
- Class in
owltools.solrj
A hard-wired loader for the family-config.yaml profile.
PANTHERSolrDocumentLoader(String)
- Constructor for class owltools.solrj.
PANTHERSolrDocumentLoader
PANTHERTree
- Class in
owltools.panther
Methods to simplify the work with the Newick-ish output we get from PANTHER.
PANTHERTree(File)
- Constructor for class owltools.panther.
PANTHERTree
Create an instance for the given path
property
- Variable in class owltools.yaml.golrconfig.
GOlrField
R
required
- Variable in class owltools.yaml.golrconfig.
GOlrField
result_weights
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
result_weights
- Variable in class owltools.yaml.golrconfig.
GOlrField
S
schema()
- Method in class owltools.yaml.golrconfig.
SolrSchemaXMLWriter
Dump the necessary Solr schema as a String.
schema_generating
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
searchable
- Variable in class owltools.yaml.golrconfig.
GOlrField
server
- Variable in class owltools.solrj.
AbstractSolrLoader
setEcoTools(EcoTools)
- Method in class owltools.solrj.
GafSolrDocumentLoader
setGafDocument(GafDocument)
- Method in class owltools.solrj.
GafSolrDocumentLoader
setGraph(OWLGraphWrapper)
- Method in class owltools.solrj.
AbstractSolrLoader
setPANTHERSet(PANTHERForest)
- Method in class owltools.solrj.
GafSolrDocumentLoader
setPANTHERSet(PANTHERForest)
- Method in class owltools.solrj.
PANTHERGeneralSolrDocumentLoader
setPANTHERSet(PANTHERForest)
- Method in class owltools.solrj.
PANTHERSolrDocumentLoader
setTaxonTools(TaxonTools)
- Method in class owltools.solrj.
GafSolrDocumentLoader
SolrSchemaXMLWriter
- Class in
owltools.yaml.golrconfig
SolrSchemaXMLWriter(ConfigManager)
- Constructor for class owltools.yaml.golrconfig.
SolrSchemaXMLWriter
T
transform
- Variable in class owltools.yaml.golrconfig.
GOlrDynamicField
Deprecated.
transform
- Variable in class owltools.yaml.golrconfig.
GOlrField
type
- Variable in class owltools.yaml.golrconfig.
GOlrField
V
value
- Variable in class owltools.flex.
FlexLine
value()
- Method in class owltools.flex.
FlexLine
Return the first/only value.
values()
- Method in class owltools.flex.
FlexLine
Return all the values.
W
weight
- Variable in class owltools.yaml.golrconfig.
GOlrConfig
wring(OWLObject, ConfigManager)
- Method in class owltools.flex.
FlexCollection
Main wrapping for adding ontology documents to GOlr.
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