ch.epfl.bbp.uima

Class BlueUima

java.lang.Object

ch.epfl.bbp.uima.BlueUima

public final class BlueUima
extends Object

A place for constants. DO NOT CHANGE THEM BLINDLY, as they are hardcoded (text) in pipeline scripts

Author:

renaud.richardet@epfl.ch

Field Summary

Fields

Modifier and Type	Field and Description
static String	BLUE_UIMA_ROOT This is a central property, as many modules rely on it to find their resources (config files, models, etc).
static String	BLUE_UTILS_ROOT
static String	BLUE_UTILS_TEST_BASE
static String	PARAM_AND_QUERY
static String	PARAM_ANNOTATION_CLASS
static String	PARAM_ANNOTATION_CLASSES
static String	PARAM_ANNOTATION_FIELD
static String	PARAM_ANNOTATION_FIELDS
static String	PARAM_BETWEEN
static String	PARAM_CASE_SENSITIVE
static String	PARAM_COOCCURRENCE_TYPE
static String	PARAM_CORPUS_ANNOTATIONS_PATH
static String	PARAM_CORPUS_NAME
static String	PARAM_CORPUS_PATH
static String	PARAM_CORPUS_ROOT Root path of the corpus
static String	PARAM_DB_CONNECTION
static String	PARAM_DIRECTORY_ITERATOR
static String	PARAM_ENCLOSING_SCOPE
static String	PARAM_FEATURE_NAME
static String	PARAM_FIELD_NAME
static String	PARAM_FILE_EXTENSION_FILTER
static String	PARAM_FIRST_ANNOT
static String	PARAM_FIRST_ANNOT_ID_FIELD
static String	PARAM_FIRST_ANNOT_TYPE
static String	PARAM_FORMAT
static String	PARAM_INDEX_NAME
static String	PARAM_INPUT
static String	PARAM_INPUT_DIRECTORY
static String	PARAM_INPUT_FILE
static String	PARAM_IS_RECURSIVE
static String	PARAM_MAX_NR_RESULTS
static String	PARAM_MODE Corpus mode, either test or train or eval
static String	PARAM_MODEL
static String	PARAM_MODEL_FILE
static String	PARAM_OUTPUT_DIR
static String	PARAM_OUTPUT_FILE
static String	PARAM_PATH_PREFIX
static String	PARAM_QUERY
static String	PARAM_SECOND_ANNOT
static String	PARAM_SECOND_ANNOT_ID_FIELD
static String	PARAM_SECOND_ANNOT_TYPE
static String	PARAM_SKIP_EMPTY_DOCS Skip (PubMed) docs that have no (abstract)/text
static String	PARAM_VERBOSE
static String	PARAM_VIEW
static String	PATH_NFS4_EXTRACTED_PDFS
static String	PATH_NFS4_NLP Path to NLP root folder on storage array
static String	RESOURCES_PATH Path to main resources
static String	SECTION_TYPE_ABSTRACT
static String	SECTION_TYPE_COPYRIGHT
static String	SECTION_TYPE_REFERENCES
static String	SECTION_TYPE_TITLE
static String	TEST_RESOURCES_PATH Path to test resources
static String	VIEW_GOLD
static String	VIEW_SYSTEM

Constructor Summary

Constructors

Constructor and Description
BlueUima()

Method Summary

Methods

Modifier and Type	Method and Description
static String	getGitCommitId()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PARAM_QUERY

public static final String PARAM_QUERY

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Constant Field Values

PARAM_AND_QUERY

public static final String PARAM_AND_QUERY

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Constant Field Values

PARAM_MAX_NR_RESULTS

public static final String PARAM_MAX_NR_RESULTS

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Constant Field Values

PARAM_BETWEEN

public static final String PARAM_BETWEEN

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Constant Field Values

PARAM_FEATURE_NAME

public static final String PARAM_FEATURE_NAME

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Constant Field Values

PARAM_ANNOTATION_CLASS

public static final String PARAM_ANNOTATION_CLASS

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Constant Field Values

PARAM_ANNOTATION_CLASSES

public static final String PARAM_ANNOTATION_CLASSES

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Constant Field Values

PARAM_ANNOTATION_FIELD

public static final String PARAM_ANNOTATION_FIELD

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Constant Field Values

PARAM_ANNOTATION_FIELDS

public static final String PARAM_ANNOTATION_FIELDS

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Constant Field Values

PARAM_FIRST_ANNOT

public static final String PARAM_FIRST_ANNOT

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Constant Field Values

PARAM_SECOND_ANNOT

public static final String PARAM_SECOND_ANNOT

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Constant Field Values

PARAM_FIRST_ANNOT_ID_FIELD

public static final String PARAM_FIRST_ANNOT_ID_FIELD

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Constant Field Values

PARAM_SECOND_ANNOT_ID_FIELD

public static final String PARAM_SECOND_ANNOT_ID_FIELD

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Constant Field Values

PARAM_FIRST_ANNOT_TYPE

public static final String PARAM_FIRST_ANNOT_TYPE

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Constant Field Values

PARAM_SECOND_ANNOT_TYPE

public static final String PARAM_SECOND_ANNOT_TYPE

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Constant Field Values

PARAM_ENCLOSING_SCOPE

public static final String PARAM_ENCLOSING_SCOPE

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Constant Field Values

PARAM_COOCCURRENCE_TYPE

public static final String PARAM_COOCCURRENCE_TYPE

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Constant Field Values

PARAM_MODEL_FILE

public static final String PARAM_MODEL_FILE

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Constant Field Values

PARAM_MODEL

public static final String PARAM_MODEL

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Constant Field Values

PARAM_INPUT

public static final String PARAM_INPUT

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Constant Field Values

PARAM_INPUT_DIRECTORY

public static final String PARAM_INPUT_DIRECTORY

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Constant Field Values

PARAM_INPUT_FILE

public static final String PARAM_INPUT_FILE

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Constant Field Values

PARAM_OUTPUT_FILE

public static final String PARAM_OUTPUT_FILE

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Constant Field Values

PARAM_OUTPUT_DIR

public static final String PARAM_OUTPUT_DIR

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Constant Field Values

PARAM_PATH_PREFIX

public static final String PARAM_PATH_PREFIX

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Constant Field Values

PARAM_VERBOSE

public static final String PARAM_VERBOSE

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Constant Field Values

PARAM_CORPUS_PATH

public static final String PARAM_CORPUS_PATH

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Constant Field Values

PARAM_CORPUS_NAME

public static final String PARAM_CORPUS_NAME

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Constant Field Values

PARAM_CORPUS_ANNOTATIONS_PATH

public static final String PARAM_CORPUS_ANNOTATIONS_PATH

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Constant Field Values

PARAM_MODE

public static final String PARAM_MODE

Corpus mode, either test or train or eval

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Constant Field Values

PARAM_CORPUS_ROOT

public static final String PARAM_CORPUS_ROOT

Root path of the corpus

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Constant Field Values

PARAM_DIRECTORY_ITERATOR

public static final String PARAM_DIRECTORY_ITERATOR

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Constant Field Values

PARAM_IS_RECURSIVE

public static final String PARAM_IS_RECURSIVE

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Constant Field Values

PARAM_FILE_EXTENSION_FILTER

public static final String PARAM_FILE_EXTENSION_FILTER

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PARAM_FORMAT

public static final String PARAM_FORMAT

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Constant Field Values

PARAM_DB_CONNECTION

public static final String PARAM_DB_CONNECTION

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Constant Field Values

PARAM_INDEX_NAME

public static final String PARAM_INDEX_NAME

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Constant Field Values

PARAM_FIELD_NAME

public static final String PARAM_FIELD_NAME

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Constant Field Values

PARAM_SKIP_EMPTY_DOCS

public static final String PARAM_SKIP_EMPTY_DOCS

Skip (PubMed) docs that have no (abstract)/text

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Constant Field Values

PARAM_CASE_SENSITIVE

public static final String PARAM_CASE_SENSITIVE

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Constant Field Values

PARAM_VIEW

public static final String PARAM_VIEW

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Constant Field Values

VIEW_SYSTEM

public static final String VIEW_SYSTEM

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Constant Field Values

VIEW_GOLD

public static final String VIEW_GOLD

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Constant Field Values

PATH_NFS4_NLP

public static final String PATH_NFS4_NLP

Path to NLP root folder on storage array

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Constant Field Values

PATH_NFS4_EXTRACTED_PDFS

public static final String PATH_NFS4_EXTRACTED_PDFS

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Constant Field Values

SECTION_TYPE_REFERENCES

public static final String SECTION_TYPE_REFERENCES

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Constant Field Values

SECTION_TYPE_ABSTRACT

public static final String SECTION_TYPE_ABSTRACT

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Constant Field Values

SECTION_TYPE_TITLE

public static final String SECTION_TYPE_TITLE

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Constant Field Values

SECTION_TYPE_COPYRIGHT

public static final String SECTION_TYPE_COPYRIGHT

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Constant Field Values

BLUE_UIMA_ROOT

public static final String BLUE_UIMA_ROOT

This is a central property, as many modules rely on it to find their resources (config files, models, etc). It can be set on the command line, e.g.:
mvn exec:java \
-Dexec.mainClass="ch.epfl.bbp.uima.MyClass" \
-Dexec.classpathScope=runtime \
-Dbluima_home=/path/to/bluima
or as a system variable, e.g.:

• OS X / Linux: add export BLUIMA_HOME=/path/to/bluima to your .bashrc
• Win7: Control Panel > System & Security > System > Environment Variables

RESOURCES_PATH

public static final String RESOURCES_PATH

Path to main resources

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Constant Field Values

TEST_RESOURCES_PATH

public static final String TEST_RESOURCES_PATH

Path to test resources

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Constant Field Values

BLUE_UTILS_ROOT

public static final String BLUE_UTILS_ROOT

BLUE_UTILS_TEST_BASE

public static final String BLUE_UTILS_TEST_BASE

Constructor Detail

BlueUima

public BlueUima()

Method Detail

getGitCommitId

public static String getGitCommitId()