com.eldrix.hermes.impl.store — com.eldrix/hermes 0.9.362

Store provides access to a key value store.

all-transitive-synonyms clj

(all-transitive-synonyms store concept-id)

(all-transitive-synonyms store concept-id {:keys [include-inactive?]})

Returns all of the synonyms of the specified concept, including those of its descendants.

close clj

(close store)

compact clj

(compact store)

ConceptSerializer clj

default-opts clj

DescriptionSerializer clj

get-all-children clj

(get-all-children store concept-id)

(get-all-children store concept-id type-id)

Returns all child concepts for the concept. It takes 3500 milliseconds on my 2013 laptop to return all child concepts of the root SNOMED CT concept, so this should only be used for more granular concepts generally, or used asynchronously / via streaming. Parameters:

• store
• concept-id
• type-id, defaults to 'IS-A' (116680003).

get-all-parents clj

(get-all-parents store concept-id)

(get-all-parents store concept-id type-id)

Returns all parent concepts for the concept, including self. Parameters:

• store the MapDBStore
• concept-id
• type-id, defaults to 'IS-A' (116680003).

get-child-relationships-of-type clj

(get-child-relationships-of-type store concept-id type-concept-id)

Returns a collection of identifiers representing the parent relationships of the specified type of the specified concept.

get-component-refset-items clj

(get-component-refset-items store component-id)

(get-component-refset-items store component-id refset-id)

Get the refset items for the given component, optionally limited to the refset specified.

• store : MapDBStore
• component-id : id of the component (e.g concept-id or description-id)
• refset-id : (optional) - limit to this refset.

get-component-refsets clj

(get-component-refsets store component-id)

Return the refset-id's to which this component belongs.

get-concept clj

(get-concept store concept-id)

Returns the concept specified.

get-concept-descriptions clj

(get-concept-descriptions store concept-id)

Return the descriptions for the concept specified.

get-description clj

(get-description store description-id)

Return the description with the given description-id. This uses the descriptionId-conceptId index to determine the concept-id, as all descriptions are actually stored by conceptId-descriptionId-concept because that's a more common operation that finding a description by identifier alone.

get-description-refsets clj

(get-description-refsets store description-id)

Get the refsets and language applicability for a description. Returns a map containing:

• refsets : a set of refsets to which this description is a member
• preferredIn : refsets for which this description is preferred
• acceptableIn : refsets for which this description is acceptable.

Example: (map #(merge % (get-description-refsets store (:id %))) (get-concept-descriptions store 24700007))

get-extended-concept clj

(get-extended-concept store concept-id)

get-fully-specified-name clj

(get-fully-specified-name store concept-id)

(get-fully-specified-name store concept-id language-refset-ids fallback?)

Return the fully specified name for the concept specified. If no language preferences are provided the first description of type FSN will be returned. If language preferences are provided, but there is no match and fallback? is true, then the first description of type FSN will be returned.

get-grouped-properties clj

(get-grouped-properties store concept-id)

(get-grouped-properties store concept-id type-id)

Return a concept's properties as a collection of maps, each map representing related properties in a 'relationshipGroup'. By default, all groups are returned, but this can optionally be limited to those containing a specific relationship type.

get-installed-reference-sets clj

(get-installed-reference-sets store)

Returns the installed reference sets. While it is possible to use the SNOMED ontology to find all reference sets:

(get-leaves store (get-all-children store 900000000000455006))

This will return reference sets with no actual members in the installed edition. Instead, we keep track of installed reference sets as we import reference set items, thus ensuring we have a list that contains only reference sets with members.

get-leaves clj

(get-leaves store concept-ids)

Returns the subset of the specified concept-ids such that no member of the subset is subsumed by another member. Parameters:

• concept-ids : a collection of concept identifiers

get-parent-relationships clj

(get-parent-relationships store concept-id)

Returns the parent relationships of the specified concept. Returns a map key: concept-id of the relationship type (e.g. identifier representing finding site) value: a set of concept identifiers for that property.

See get-parent-relationships-expanded to get each target expanded via transitive closure tables.

get-parent-relationships-expanded clj

(get-parent-relationships-expanded store concept-id)

Returns all of the parent relationships, expanded to include each target's transitive closure table. This makes it trivial to build queries that find all concepts with, for example, a common finding site at any level of granularity.

get-parent-relationships-of-type clj

(get-parent-relationships-of-type store concept-id type-concept-id)

Returns a collection of identifiers representing the parent relationships of the specified type of the specified concept.

get-parent-relationships-of-types clj

(get-parent-relationships-of-types store concept-id type-concept-ids)

get-preferred-description clj

(get-preferred-description store
                           concept-id
                           description-type-id
                           language-refset-id)

Return the preferred description for the concept specified as defined by the language reference set specified for the description type.

• store :
• concept-id :
• description-type-id : type of description (e.g. synonym or FSN)
• language-refset-id : language reference set

Possible description-type-ids: 900000000000013009: synonym (core metadata concept) 900000000000003001: fully specified name

Example language-refset-ids: 900000000000509007: US English language reference set 999001261000000100: UK English (clinical) language reference set.

get-preferred-fully-specified-name clj

(get-preferred-fully-specified-name store concept-id language-refset-ids)

get-preferred-synonym clj

(get-preferred-synonym store concept-id language-refset-ids)

Returns the preferred synonym for the concept specified, looking in the language reference sets specified in order, returning the first 'preferred' value. The ordering of the reference set identifiers is therefore significant.

• store : store
• concept-id : concept-id
• language-refset-ids : an ordered list of language reference set identifiers

Notes: We have a frustrating situation in that there are three language reference sets in the UK that might give a 'good' answer to the 'preferred' description for any given concept. 900000000000508004 : Great Britain English language reference set 999001261000000100 : NHS realm language (clinical part) 999000691000001104 : NHS Realm language (pharmacy part) (supercedes the old dm+d realm subset 30001000001134). This means that we need to be able to submit multiple language reference set identifiers.

get-refset-item clj

(get-refset-item store uuid)

(get-refset-item store msb lsb)

Get the specified refset item. Parameters:

• store : MapDBStore
• UUID : the UUID of the refset item to fetch
• msb/lsb : the most and least significant 64-bit longs representing the UUID.

get-relationship clj

(get-relationship store relationship-id)

get-release-information clj

(get-release-information st)

Returns descriptions representing the installed distributions. Ordering will be by date except that the description for the 'core' module will always be first. See https://confluence.ihtsdotools.org/display/DOCTIG/4.1.+Root+and+top-level+Concepts

get-reverse-map clj

(get-reverse-map store refset-id s)

Returns the reverse mapping from the reference set and mapTarget specified.

get-reverse-map-range clj

(get-reverse-map-range store refset-id prefix)

(get-reverse-map-range store refset-id lower-bound upper-bound)

Returns the reverse mapping from the reference set specified, performing what is essentially a prefix search using the parameters. For example (get-reverse-map-range store "D86.") will return all items with a map target with prefix 'D86.'

Parameters:

• store : a MapDBStore
• refset-id : the reference set in which to search
• lower-bound : lower bound prefix, inclusive
• upper-bound : upper bound prefix, exclusive
• prefix : prefix; lower and upper bounds derived automatically

Prefixes are case sensitive, with natural string sorting used.

get-source-association-referenced-components clj

(get-source-association-referenced-components store component-id refset-id)

Returns a sequence of component identifiers that reference the specified component in the specified association reference set.

get-source-associations clj

(get-source-associations store component-id)

(get-source-associations store component-id refset-id)

Returns the associations in which this component is the target. targetComponentId - refsetId - itemId1 -itemId2.

has-property? clj multimethod

is-a? clj multimethod

make-extended-concept clj

(make-extended-concept store concept)

open-store clj

(open-store)

(open-store filename)

(open-store filename opts)

paths-to-root clj

(paths-to-root store concept-id)

Return a sequence of paths from the concept to root node. Each path is a sequence of identifiers, starting with the concept itself and ending with the root node. e.g. (sort-by count (paths-to-root store 24700007)) result (truncated): ((24700007 414029004 64572001 404684003 138875005) (24700007 6118003 80690008 362975008 64572001 404684003 138875005) (24700007 39367000 23853001 246556002 118234003 404684003 138875005) (24700007 6118003 80690008 23853001 246556002 118234003 404684003 138875005))

prefix-upper-bound clj

(prefix-upper-bound s)

Given a string, generate an upper bound suitable for a prefix search. For example, 123 should give 124.

RefsetItemSerializer clj

RelationshipSerializer clj

status clj

(status store)

stream-all-concepts clj

(stream-all-concepts store ch)

(stream-all-concepts store ch close?)

Asynchronously stream all concepts to the channel specified, and, by default, closing the channel when done unless specified. Returns a channel which, by default, will be closed when done.

write-batch clj multimethod

write-batch-one-by-one clj

(write-batch-one-by-one batch store)

Write out a batch one item at a time.

write-batch-with-fallback clj

(write-batch-with-fallback batch store)