OMERO search

OMERO.server uses Lucene to index all string and timestamp information in the database, as well as all OriginalFile 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.

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 ome.api.Search interface (below).

See also

Search and indexing configuration

Section of the sysadmin documentation describing the configuration of the search and indexing for the server.

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 annotations, including TagAnnotation and any TextAnnotation on another TextAnnotation (a.k.a. a description). Non-string annotations like FileAnnotation are not covered by this definition and are handled separately. See below.
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
channel.name	Name of the Channel object
channel.fluor	Fluor value of the Channel object (e.g. “Alex Fluor 488” or “DAPI”)
channel.mode	Mode of the Channel object (e.g. “BrightField” or “SPIM”)
channel.photometricInterpretation	Name of the Channel object (e.g. “RGB” or “Monochrome”)
file.name	For FileAnnotation and objects they are attached to, the name of the OriginalFile
file.format	For FileAnnotation and objects they are attached to, the format of the OriginalFile
file.path	For FileAnnotation and objects they are attached to, the path of the OriginalFile
file.sha1	For FileAnnotation and objects they are attached to, the sha1 of the OriginalFile
file.contents	For FileAnnotation 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.
fileset.entry.name	Name of an imported file.
fileset.entry.clientPath	Original, client-side path of an imported file.
fileset.templatePrefix	Location of the import in the managed repository.
${NAME}	For MapAnnotation and objects they are attached to, dynamic fields are generated for each of the NamedValue entries in the annotation. For example, if NamedValue('temperature', '37') is one such value, a field named temperature will exist.
has_key	As ${NAME}, but a single field of name has_key is generated for each NamedValue entry with a value of the key such that a search for has_key:temperature in the example above is possible.
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. The search term is first split into “tokens” and these are combined into a search query. The tokenizing happens on all non-alpha-numerical characters, such as space, underscore, hyphen etc. The query is built by combining the tokens with an “OR” operator (see examples in the “Indexing” paragraph). The search terms or the tokens created from them as above must precisely match the indexed entries. This means for example that a search term tes will not match the indexed entry test and the search will accordingly give no result.

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, 2, 3 and 4, because of the tokenizing on the hyphen and joining of the tokens by an OR.

• searching for “GFP H2B” or “GFP-H2B” only returns 1 and 2, since the quotes enforce the exact sequence of the tokens and the query is built with an AND.

• searching for GFP H2B returns 1, 2, 3 and 4, since the two tokens are joined by an OR.

With the same entries as above and adding a wildcard:

• searching for *FP returns 1, 2, 3 and 4. As this example shows, leading wildcards in the Graphical User Interface are allowed, but must be explicitly enabled when using the API directly, see below in the developers section.

• searching for GF* returns 1, 2, 3 and 4.

• searching for GFP-* returns no results, but GFP.* returns 1, 2, 3 and 4. Only hyphen and underscore do not return results in this situation, the other non-alpha-numerical characters do.

Wildcards and quotations:

Wildcard inside quotations is not parsed as a wilcard, but as a non-alpha-numerical character on which the tokenizing happens.

• searching for “*FP-H2B” returns no results, since it is the same as searching for “FP-H2B”.

• searching for “GF*” returns no results, since it is the same as searching for “GF”.

• searching for “GFP-*” returns 1, 2, 3 and 4, since it is the same as searching for “GFP-”.

• searching for “GFP*H2B” returns 1 and 2, since it is the same as searching for “GFP H2B”.

Information for developers

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 –>	byGroupForTags/byTagsForGroup	byFullText/SomeMustNone	byAnnotatedWith
Parameters
annotated between	S	S	S
annotated by	S	S	S
annotated by	S	I	I
created between	S	I	I
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

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

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 too many terms in the expansion 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

Working with 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.