 |
Page History
| Scrollbar | ||
|---|---|---|
|
...
| Page info | ||||
|---|---|---|---|---|
|
| Panel | ||||
|---|---|---|---|---|
| ||||
|
This page is intended to provide a ready-reference for LexBIG system administrators and candidate material for inclusion in the next release of the LexBIG Administration Guide.
As primary reference, see the Installation and Administration Guide in the GForge archive.
Building the LexBIG Installer from CVS
LexBIG CVS
LexBIG source folders have been distributed to the NCI CVS repository:
| Code Block |
|---|
:title} {panel:title=Contents} {toc:minLevel=2} {panel} This page is intended to provide a ready-reference for LexBIG system administrators and candidate material for inclusion in the next release of the LexBIG Administration Guide. As primary reference, see the Installation and Administration Guide: {code}Link provided for historical purposes; contact the page author for access: https://gforge.nci.nih.gov/frs/?group_id=14{code} h2. Building the LexBIG Installer from CVS h3. LexBIG CVS LexBIG source folders have been distributed to the NCI CVS repository: {code}Link provided for historical purposes: cbiocvs2.nci.nih.gov:/share/content/gforge/lexbig{code} |
This
...
location
...
is
...
maintained
...
as
...
a
...
mirror
...
for
...
all
...
source
...
and
...
packaging
...
materials
...
required
...
to
...
build
...
LexBIG
...
product
...
installers.
...
Files
...
are
...
refreshed
...
from
...
the
...
primary
...
development
...
repository
...
(maintained
...
internally
...
by
...
Mayo
...
Clinic)
...
for
...
each
...
milestone
...
release.
...
Development
...
and
...
build
...
processes
...
are
...
not
...
dependent
...
on
...
a
...
particular
...
CVS
...
client
...
or
...
programming
...
environment.
...
However,
...
files
...
with
...
the
...
extension
...
'.classpath'
...
and
...
'.project'
...
have
...
been
...
inserted
...
into
...
each
...
project
...
folder
...
to
...
help
...
facilitate
...
compilation
...
and
...
use
...
within
...
the
...
...
| Multiexcerpt include | ||||||
|---|---|---|---|---|---|---|
|
Folder content and purpose
- lbCVSDeploy: Contains build and packaging resources. This includes third party jar files, sample vocabularies, and scripts used to build the LexBIG installer.
- lbAdminDist: Contains source for command-line driven programs related to LexBIG administrative functions.
- lbExamplesDist: Contains source for command-line driven programs used to provide interactive examples of basic operations running against the LexBIG API.
- lbGUIDist: Contains source for the LexBIG graphical user interface.
- lbInterfacesDist: Contains source for the LexBIG API definition.
- lbImplDist: Contains source for the LexBIG API implementation.
- lgModelDist: Contains source for the LexGrid vocabulary data model.
- lbModelDist: Contains source for LexBIG extensions to the LexGrid data model.
- lbTestDist: Contains source for programs used to perform automated validation of the LexBIG runtime environment.
- lgUtilityDist: Contains source for various utility classes (e.g. persistence functions) required by the LexBIG API.
How to produce the installer
- Command line: Download and unzip the latest stable version of Ant from the Apache site
. Check out all project folders from CVS, and then run the Ant command against the build.xml file provided in lbCVSDeploy. If successful, files will be created in /lbCVSDeploy/dist/.Multiexcerpt include nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include - Eclipse: Open the build.xml file in the Eclipse Ant view and run the default task. If successful, refresh the /lbCVSDeploy folder; files will be created in /lbCVSDeploy/dist.
How to enable ydoc
- yDoc
offers the capability to add UML diagrams to the generated LexBIG JavaDoc.Multiexcerpt include nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include
If the yDoc directory is present and a valid license is located in the /yDoc/resources directory, the enhanced yDoc support is automatically enabled and used. If not, standard JavaDoc is produced.
Other notes
- Some classpath and jar dependencies have been documented for reference in file /lbCVSDeploy/ClasspathConfig.txt.
- Notes on the origin of the files are noted in /lbCVSDeploy/FILESOURCEs.txt.
JBoss Memory Settings
JBoss tends to run out of memory while running with the default settings of JBoss. To fix the problem, modify the run.conf file under JBOSS_home/bin to change the memory setting and how frequently the rmi garbage collector runs, by editing the JAVA_OPTS line as follows:
| Code Block | ||||
|---|---|---|---|---|
| ||||
environment|http://www.eclipse.org/]. h3. Folder content and purpose * lbCVSDeploy: Contains build and packaging resources. This includes third party jar files, sample vocabularies, and scripts used to build the LexBIG installer. * lbAdminDist: Contains source for command-line driven programs related to LexBIG administrative functions. * lbExamplesDist: Contains source for command-line driven programs used to provide interactive examples of basic operations running against the LexBIG API. * lbGUIDist: Contains source for the LexBIG graphical user interface. * lbInterfacesDist: Contains source for the LexBIG API definition. * lbImplDist: Contains source for the LexBIG API implementation. * lgModelDist: Contains source for the LexGrid vocabulary data model. * lbModelDist: Contains source for LexBIG extensions to the LexGrid data model. * lbTestDist: Contains source for programs used to perform automated validation of the LexBIG runtime environment. * lgUtilityDist: Contains source for various utility classes (e.g. persistence functions) required by the LexBIG API. h3. How to produce the installer * Command line: Download and unzip the latest stable version of Ant from the [Apache site|[http://ant.apache.org/bindownload.cgi]. Check out all project folders from CVS, and then run the Ant command against the build.xml file provided in lbCVSDeploy. If successful, files will be created in /lbCVSDeploy/dist/. * Eclipse: Open the build.xml file in the Eclipse Ant view and run the default task. If successful, refresh the /lbCVSDeploy folder; files will be created in /lbCVSDeploy/dist. h3. How to enable ydoc * [yDoc|http://www.yworks.com/en/products_ydoc.htm] offers the capability to add UML diagrams to the generated LexBIG JavaDoc. If the yDoc directory is present and a valid license is located in the /yDoc/resources directory, the enhanced yDoc support is automatically enabled and used. If not, standard JavaDoc is produced. h3. Other notes * Some classpath and jar dependencies have been documented for reference in file /lbCVSDeploy/ClasspathConfig.txt. * Notes on the origin of the files are noted in /lbCVSDeploy/FILESOURCEs.txt. h2. JBoss Memory Settings JBoss tends to run out of memory while running with the default settings of JBoss. To fix the problem, modify the run.conf file under JBOSS_home/bin to change the memory setting and how frequently the rmi garbage collector runs, by editing the JAVA_OPTS line as follows: {code:none} if [[ "x$JAVA_OPTS" = "x" ]; then JAVA_OPTS="-server -XX:!MaxPermSize=128m -Xms256m -Xmx2000m -Dsun.rmi.dgc.client.gcInterval=120000 -Dsun.rmi.dgc.server.gcInterval=120000" fi {code} h2. Improving Performance on |
Improving Performance on MySQL/Windows
...
MySQL
...
can
...
be
...
passed
...
a
...
jdbc
...
option
...
for
...
the
...
Windows
...
local
...
environment
...
that
...
may
...
improve
...
perfomance
...
30
...
to
...
50%.
...
Try
...
the
...
following
...
values
...
in
...
the
...
config.props
...
file
...
for
...
the
...
DB_URL:
| Code Block | ||||
|---|---|---|---|---|
| ||||
{code:none} SINGLE_DB_MODE=true DB_URL=jdbc:mysql:///<dbname>?socketFactory=com.mysql.jdbc.NamedPipeSocketFactory DB_DRIVER=org.gjt.mm.mysql.Driver DB_USER=root DB_PASSWORD= DB_PREFIX=lb DB_PARAM= {code} |
This
...
uses
...
Windows
...
Named
...
Pipe
...
function
...
and
...
avoids
...
use
...
of
...
the
...
TCP/IP
...
protocol.
...
It
...
only
...
works
...
when
...
connecting
...
with
...
a
...
local
...
iteration
...
of
...
the
...
MySQL
...
database
...
on
...
Windows.
...
Error
...
Connecting
...
to
...
MySQL
...
LexBIG
...
is
...
distributed
...
with
...
an
...
older
...
version
...
of
...
the
...
Java
...
MySQL
...
driver
...
due
...
to
...
licensing
...
concerns.
...
If
...
LexBIG
...
reports
...
an
...
error
...
concerning
...
establishing
...
a
...
connection
...
to
...
the
...
MySQL
...
server
...
yet
...
the
...
MySQL
...
CLI
...
is
...
able
...
to
...
connect,
...
a
...
new
...
version
...
of
...
Connector/J
...
may
...
be
...
required.
...
The
...
latest
...
version
...
of
...
Connector/J
...
is
...
available
...
from
...
MySQL.org.
...
The
...
new
...
jar
...
should
...
be
...
placed
...
in
...
the
...
LexGrid/LexBIG/2.0.0/runtime/sqlDrivers/
...
directory.
...
Remove
...
the
...
existing
...
mm.mysql-2.0.6.jar
...
to
...
ensure
...
that
...
the
...
class
...
loader
...
does
...
not
...
incorrectly
...
load
...
the
...
older
...
driver
...
file
...
.
...
Configuring
...
Manifest
...
Files
...
Using
...
Coding
...
Scheme
...
Manifest
...
Entries
...
LexBIG
...
Release
...
July/Aug
...
2007
...
What
...
is
...
"Coding
...
Scheme
...
Manifest"?
...
A
...
"Coding
...
Scheme
...
Manifest"
...
(or
...
simply
...
"manifest"
...
as
...
used
...
interchangeably
...
in
...
this
...
document)
...
encapsulates
...
the
...
user
...
supplied
...
values
...
to
...
set
...
for
...
a
...
coding
...
scheme
...
while
...
loading
...
or
...
converting
...
an
...
OWL
...
(currently
...
it
...
is
...
supported
...
only
...
for
...
OWL
...
type
...
of
...
files)
...
source
...
to
...
LexGrid
...
format
...
.
...
What
...
is
...
"Coding
...
Scheme"?
...
Coding
...
Scheme
...
is
...
the
...
term
...
that
...
is
...
used
...
to
...
represent
...
an
...
ontology/terminology
...
being
...
loaded
...
or
...
converted.
...
In
...
the
...
LexGrid
...
data
...
model
...
a
...
terminology
...
is
...
represented
...
as
...
a
...
coding
...
scheme
...
and
...
it
...
can
...
reference
...
other
...
coding
...
schemes.
...
An
...
example
...
of
...
coding
...
scheme
...
is
...
"Amino
...
Acid"
...
which
...
is
...
described
...
in
...
the
...
"amino-acid.owl"
...
file.
...
A
...
Coding
...
Scheme
...
has
...
some
...
meta
...
information
...
about
...
it;
...
values
...
like
...
'formal
...
name',
...
'local
...
names',
...
'default
...
language',
...
'version',
...
'copyright',
...
'sources'
...
to
...
name
...
some.
...
Why
...
do
...
we
...
need
...
a
...
"Coding
...
Scheme
...
Manifest"?
...
When
...
a
...
terminology
...
is
...
being
...
converted
...
to
...
the
...
LexGrid
...
data
...
model
...
from
...
its
...
native
...
format
...
(in
...
this
...
case
...
OWL),
...
Coding
...
Scheme
...
information
...
is
...
read
...
from
...
the
...
source
...
file.
...
Sometimes
...
values
...
may
...
be
...
missing
...
(not
...
provided
...
or
...
invalid)
...
or
...
the
...
author/user
...
of
...
the
...
terminology
...
wants
...
to
...
override
...
or
...
set
...
default
...
values
...
despite
...
(or
...
in
...
addition
...
to)
...
what
...
is
...
provided
...
in
...
the
...
source
...
file.
...
This
...
can
...
be
...
accomplished
...
using
...
"manifest"
...
files
...
along
...
with
...
the
...
source
...
file.
...
How
...
do
...
we
...
create
...
a
...
"Coding
...
Scheme
...
Manifest"
...
file?
...
A
...
coding
...
scheme
...
manifest
...
file
...
is
...
a
...
valid
...
XML
...
file,
...
conforming
...
to
...
the
...
schema
...
defined
...
by
...
http://LexGrid.org/schema/LexBIG/
...
2007/01/CodingSchemeManifestList.xsd
| Multiexcerpt include | ||||||
|---|---|---|---|---|---|---|
|
This XML file can define values for one or more coding schemes you are dealing with. Some coding scheme meta-information may not easily map to information in the source file. In this case a manifest file is of great help to bridge the gap and control the information flow while mapping to the LexGrid model. A detailed model of the LexGrid Coding Scheme and its fields can be found online. Structure of the schema for the manifest file is explained in the following table (manifest components refer to the original LexGrid model schema namespaces and types):
- Coding Scheme Manifest entry field: '''id'''
...
- Type:
...
- lgCommon:registeredName
...
- Required:
...
- Yes
...
- Override
...
- flag
...
- set:
...
- Not
...
- applicable
...
Description:
...
The
...
registered
...
name
...
is
...
the
...
key
...
used
...
to
...
find
...
a
...
coding
...
scheme
...
(for
...
example
...
a
...
unique
...
URL
...
or
...
namespace
...
by
...
which
...
other
...
people
...
access
...
same
...
coding
...
scheme).
...
This
...
String
...
value
...
will
...
be
...
used
...
to
...
identify
...
the
...
manifest
...
entry
...
in
...
the
...
manifest
...
file
...
for
...
the
...
coding
...
scheme
...
too.
...
For
...
example
...
the
...
registered
...
name
...
for
...
coding
...
scheme
...
"Amino-acid"
...
isÂ
Code Block Historical link http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#
...
This
...
string
...
is
...
also
...
set
...
as
...
the
...
coding
...
scheme's
...
registered
...
name
...
field
...
in
...
the
...
LexGrid
...
model.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''codingScheme'''
...
- Type:
...
- lgBuiltin:localId
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''entityDescription'''
...
- Type:
...
- lgCommon:entityDescription
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- description'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''formalName'''
...
- Type:
...
- lgBuiltin:tsCaseIgnoreIA5String
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- formal
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''registeredName'''
...
- Type:
...
- lgCommon:registeredName
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- registered
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''defaultLanguage'''
...
- Type:
...
- lgCommon:defaultLanguage
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- default
...
- language'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''representsVersion'''
...
- Type:
...
- lgCommon:version
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- version'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''localName'''
...
- Type:
...
- lgBuiltin:tsCaseIgnoreIA5String
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- local
...
- names'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- local
...
- names
...
- (if
...
- not
...
- there
...
- already).
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''source'''
...
- Type:
...
- lgCommon:source
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- sources'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- sources
...
- (if
...
- not
...
- there
...
- already).
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''copyright'''
...
- Type:
...
- lgCommon:text
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- copyright'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''mappings'''
...
- Type:
...
- lgCS:mappings
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- mappings'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- mappings
...
- (if
...
- not
...
- there
...
- already).
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''associationDefinitions'''
...
- Type:
...
- lgRel:association
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- associations'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- associations
...
- (if
...
- not
...
- there
...
- already).
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
(Note:
...
- This
...
- option
...
- is
...
- used
...
- internally
...
- by
...
- the
...
- system
...
- to
...
- provide
...
- default
...
- recognition
...
- of
...
- some
...
- common
...
- associations.
...
It
...
- is
...
- typically
...
- not
...
- necessary
...
- to
...
- provide
...
- this
...
- value,
...
- however,
...
- since
...
- association
...
- definitions
...
- are
...
- automatically
...
- derived
...
- from
...
- the
...
- source.)
Could you please provide some example entries in a manifest file?
Here are some example coding scheme manifest entries:
| Code Block | ||||
|---|---|---|---|---|
| ||||
_ h3. Could you please provide some example entries in a manifest file? Here are some example coding scheme manifest entries: {code:none} <CodingSchemeManifestList xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList http://LexGrid.org/schema/LexBIG/2007/01/CodingSchemeManifestList.xsd" xmlns:owldef="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList" xmlns="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList"> <entry id="http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#"> <codingScheme>amino</codingScheme> <entityDescription>This is AminoAcide Description from Manifest.</entityDescription> <formalName>Amino Acid Ontology</formalName> <defaultLanguage>en</defaultLanguage> <representsVersion>2005/10/11</representsVersion> <localName>myLocalName</localName> <source subRef="ontologies">COODE</source> <copyright>This is copyright</copyright> <owldef:mappings dc="mappings" xmlns="http://LexGrid.org/schema/2006/01/LexGrid/codingSchemes"> <supportedLanguage localId="en" urn="urn:oid:2.16.840.1.113883.6.84:en"/> <supportedFormat localId="text_plain" urn="urn:oid:2.16.840.1.113883.6.10:text_plain"/> <supportedSource localId="COODE" urn="http://www.co-ode.org/"/> </owldef:mappings> <associationDefinitions> <assoc association="testRelation" forwardName="testRelation" reverseName="testRelationInverse" isTransitive="true" isReflexive="true" targetCodingScheme= "http://www.co-ode.org/ontologies/amino-acid/2006/05/18/outside#"/> </associationDefinitions> </entry> <entry id="urn:oid:2.16.840.1.113883.3.26.1.1"> <codingScheme>NCI Thesaurus CS Manifest</codingScheme> <entityDescription>This is NCI Thesaurus Description from Manifest.</entityDescription> <formalName>NCI Thesaurus Formal From Manifest</formalName> <defaultLanguage>en</defaultLanguage> <representsVersion>manifestVersion</representsVersion> <localName>NCILocalName</localName> <source subRef="ontologies" >NCIManifestSource</source> <copyright>This is copyright for NCI Thesaurus</copyright> %%% <owldef:mappings dc="mappings" xmlns="http://LexGrid.org/schema/2006/01/LexGrid/codingSchemes"> <supportedSource localId="COODE" urn="http://www.co-ode.org/"/> </owldef:mappings> <associationDefinitions> <assoc association="testRelation" forwardName="testRelation" reverseName="testRelationInverse" isTransitive="true" isReflexive="true" targetCodingScheme= "urn:oid:2.16.840.1.113883.3.26.1.1"/> </associationDefinitions> </entry> </CodingSchemeManifestList> {code} h3. What code changes may be required to use a manifest file? Currently a coding scheme manifest file is only supported when loading OWL sources. Support for other formats is in-works. If you want to use the manifest file, you can supply the manifest file URI to the following methods: {code:none} |
What code changes may be required to use a manifest file?
Currently a coding scheme manifest file is only supported when loading OWL sources. Support for other formats is in-works. If you want to use the manifest file, you can supply the manifest file URI to the following methods:
| Code Block | ||||
|---|---|---|---|---|
| ||||
"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.load()"
"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.validate()"
{code}
|
An
...
example
...
code
...
snippet:
| Code Block | ||||
|---|---|---|---|---|
| ||||
{code:none} LexBIGService lbs = new LexBIGServiceImpl(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); OWL_Loader loader = (OWL_Loader) lbsm.getLoader("OWLLoader"); if (toValidateOnly) { loader.'''validate'''(source, manifest, vl); System.out.println("VALIDATION SUCCESSFUL"); } else { loader.'''load'''(new File("resources/testData/amino-cid.owl").toURI(),%%%new File ("resources/testData/aa-manifest.xml").toURI(), true, true); } {code} h2. Generating RRF Files from UMLS When generating source RRF files from the Metathesaurus, the UMLS Metamorphosys tool should be set to output versionless source abbreviations rather than versioned source abbreviations in any RRF subset to be loaded to LexGrid. Failing to do so will create an incomplete database leaving the association and concept tables empty. {scrollbar:icons=false} |
Generating RRF Files from UMLS
When generating source RRF files from the Metathesaurus, the UMLS Metamorphosys tool should be set to output versionless source abbreviations rather than versioned source abbreviations in any RRF subset to be loaded to LexGrid. Failing to do so will create an incomplete database leaving the association and concept tables empty.
| Scrollbar | ||
|---|---|---|
|
