OMERO search

Beginning with 3.0-Beta3, the OMERO server will use  Lucene to index all string and timestamp information in the database, as well as all OriginalFiles which can be parsed to simple text (see File parsers for more information). The index is stored under /OMERO/FullText (or the FullText subdirectory of your ${omero.data.dir}, and can be searched with Google-like queries.

Field names

Each row in the database becomes a single Lucene Document parsed into the several Fields. A field is referenced by prefixing a search term with the field name followed by a colon. For example, name:myImage searches for myImage anywhere in the name field.

Field	Comments
	Any unprefixed field searches the combination of all fields together i.e. a search for cell AND name:myImage gets translated to combined_fields:cell AND name:myImage.
<field name>	Each string, timestamp, or Details field of the entity also gets its own Field entry, like the name field above
details.owner.omeName	Login name of the owner of the object
details.owner.firstName	First name of the owner of the object
details.owner.lastName	Last name of the owner of the object
details.group.name	Group name of the owning group of the object
details.creationEvent.id	Id of the Event of this objects creation
details.creationEvent.time	When that Event took place
details.updateEvent.id	Id of the Event of this objects last modification
details.updateEvent.time	When that Event took place
details.permissions	Permissions in the form rwrwrw or rw-
tag	Contents from a TagAnnotation.
annotation	Contents from any annotations, including TagAnnotation and any TextAnnotation on another TextAnnotation (a.k.a. a description)
annotation.ns	Namespace (if present) for any annotations on an object
annotation.type	Short type name, e.g. TextAnnotation or FileAnnotation for any annotations on an object
file.name	For FileAnnotations and objects they are attached to, the name of the OriginalFile
file.format	For FileAnnotations and objects they are attached to, the format of the OriginalFile
file.path	For FileAnnotations and objects they are attached to, the path of the OriginalFile
file.sha1	For FileAnnotations and objects they are attached to, the sha1 of the OriginalFile
file.contents	For FileAnnotations and objects they are attached to as well as the OriginalFile itself, the file contents themselves if their Format is configured with the File parsers.
Internal,
combined_fields	The default field prefix.
_hibernate_class	Used by Hibernate Search to record the entity type. The class value, e.g. ome.model.core.Image is also entered in combined_fields. Unimportant for the casual users.
id	The primary key of the entity. Unimportant for the casual user

Queries

Search queries are very similar to Google searches. When search terms are entered without a prefix (“name:”), then the default field will be used which combines all available fields. Otherwise, a prefix can be added to restrict the search.

Indexing

Successful searching depends on understanding how the text is indexed. The default analyzer used is the FullTextAnalyzer.

1. Desktop/image_GFP-H2B_1.dv  --->  "desktop", "image", "gfp", "h2b", "1", "dv"
2. Desktop/image_GFP-H2B_2.dv  --->  "desktop", "image", "gfp", "h2b", "2", "dv
3. Desktop/image_GFP_01-H2B.dv --->  "desktop", "image", "gfp", "01", "h2b", "dv"
4. Desktop/image_GFP-CSFV_a.dv --->  "desktop", "image", "gfp", "csfv", "a", "dv"

Assuming these entries above for Image.name:

• searching for GFP-H2B returns 1 and 2.
• searching for “GFP H2B” also returns 1 and 2.
• searching for GFP H2B returns 1, 2, and 3, since the two terms are joined by an OR.

Information for developers and system administrators

Scheduling indexing

Indexing is not driven by the user, but happens automatically in the background. Automatic indexing occurs at the frequency defined in etc/omero.properties:

omero.search.cron=0,30 * * * * ?
omero.search.batch=100

which implies every thirty seconds of every hour, day, month, year, etc. During each iteration, 100 EventLogs will be loaded from the database and processed. Upon successful completion, the persistent count in the configuration table, will be incremented.

omero3=# select value from configuration where name = 'PersistentEventLogLoader.current_id';
 value
-------
 30983
(1 row)

If you have more than one PersistentEventLogLoader.* value in your database, then you have run indexing with multiple versions of the server. This is fine. To allow a new server version to force an update, the configuration key may be changed. For example,

PersistentEventLogLoader.currend_id

became

PersistentEventLogLoader.v2.current_id

in r2460.

Once an entity is indexed, it is possible to start writing querying against the server via IQuery.findAllByFullText(). Use new Parameters(new Filter().owner()) and .group() to restrict your search. Or alternatively use the oma.api.Search interface (below).

Re-indexing

If you need to re-index your database, stop your server, and:

• (Optionally) Delete the /OMERO/FullText directory

• Delete or set to 0 the entry from the configuration table: update configuration set value = 0 where name like 'PersistentEventLogLoader%';

• If it is necessary to force re-indexing, use:

  cd $OMERO_PREFIX
  CLASSPATH=etc:`find lib/server | xargs | sed 's/ /:/g'`
  java -Dlog4j.configuration=log4j-cli.properties -Xmx512M ome.services.fulltext.Main full
  

or alternatively for particular types, ...

java -Dlog4j.configuration=log4j-cli.properties -Xmx512M ome.services.fulltext.Main reindex ome.model.core.Image

This functionality is still being tested, but will be made more available in future versions.

ome.api.IQuery

The current IQuery implementation restricts searches to a single class at a time.

• findAllByFullText(Image.class, "metaphase") – Images which contain or are annotated with “metaphase”
• findAllByFullText(Image.class, "annotation:metaphase") – Images which are annotated with “metaphase”
• findAllByFullText(Image.class, "tag:metaphase") – Images which are tagged with “metaphase” (specialization of the previous)
• findAllByFullText(Image.class, "file.contents:metaphase") – Images which have files attached containing “metaphase”
• findAllByFullText(OriginalFile.class, "file.contents:metaphase") – File containing “metaphase”

ome.api.Search

The Search API offers a number of different queries along with various filters and settings which are all maintained on the server.

The matrix below show which combinations of parameters and queries are supported (S), will throw an exception (X), and which will simply silently be ignored (I).

Query Method –>	byFullText/SomeMustNone	byGroupForTags/byTagsForGroup	byAnnotatedWith
Parameters
annotated between	S	S	S
annotated by	S	S	S
annotated with	S	I	I
created between	S	S	S
modified between	S	I (Immutable)	S
owned by	S	S	S
all types	X	I	X
1 type	S	I	S
N types	X	I	X
only ids	S	I	S
Ordering / Fetches
orderBy	S	I	S
fetchAnnotations	[1]	I	[2]
Other
setProjections [3]	X	X	X
current*Metdata [4]	X	X	X
setProjections [3]	X	X	X

Footnotes

[1]	Any fetchAnnotation() argument to byFullText() or related queries, returns all annotations.

[2]	byAnnotatedWith() does not accept a fetchAnnotation() argument of Annotation.class.

[3]	(1, 2) setProjects may need to be removed if Lucene cannot handle OMERO’s security requirements.

[4]	Not yet implemented.

Leading wildcard searches

Leading wildcard searches are disallowed by default. ”?omething” or “*hatever”, for example, would both throw exceptions. They can be run by using:

Search search = serviceFactory.createSearchService();
search.setAllowLeadingWildcards(true);

There is a performance penalty, however. In addition, wildcard searches get expanded on the server to boolean queries. For example, assuming “ACELL”, “BCELL”, and “CCELL” are all terms in your index, then the query:

*CELL

gets expanded to:

ACELL OR BCELL OR CCELL

If there are more than “omero.search.maxclause” terms in the expansion (default is 4096), then an exception will be thrown. This requires the user to enter a more refined search, but not because there are too many results, only because there is not enough room in memory to search on all terms at once.

Extension points

Two extension points are currently available for searching. The first are the File parsers mentioned above. By configuring the map of Formats (roughly mime-types) of files to parser instances, extracting information from attached binary files can be made quick and straightforward.

Similarly, Search bridges provide a mechanism for parsing all metadata entering the system. One built in bridge (the FullTextBridge) parses out the fields mentioned above, but by creating your own bridge it is possible to extract more information specific to your site.

See also

Structured annotations, Search bridges, File parsers, Query Parser Syntax,

 Luke

a Java application which you can download and point at your /OMERO/FullText directory to get a better feeling for Lucene queries.