Note
This documentation is for the new OMERO 5.3 version. See the latest OMERO 5.2.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.
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 oma.api.Search interface (below).
See also
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 |
| 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. |
| ${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 |
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.
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:
The current IQuery implementation restricts searches to a single class at a time.
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 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.
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,