com.eldrix.hermes.impl.store — com.eldrix/hermes 1.0.822

Store provides access to a key value store.

close clj

compact clj

extended-refset-item clj

(extended-refset-item store
                      {:keys [refsetId] :as item}
                      &
                      {:keys [attr-ids?] :or {attr-ids? true}})

Merges a map of extended attributes to the specified reference set item. The attributes will be keyed based on information from the reference set descriptor information and known field names.

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
• 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 set of identifiers representing the parent relationships of the specified type of the specified concept.

get-component-refset-ids clj

get-component-refset-items clj

get-concept clj

get-concept-descriptions clj

get-description clj

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 an extended concept for the concept specified.

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-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 a map of the parent relationships, with each value a set of identifiers representing the targets of each relationship. 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)

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

Returns a map of the parent relationships, with each value a set of identifiers representing the targets and their transitive closure tables. 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 set 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-raw-child-relationships clj

get-raw-parent-relationships clj

get-refset-descriptor-attribute-ids clj

(get-refset-descriptor-attribute-ids store refset-id)

Return a vector of attribute description concept ids for the given reference set.

get-refset-descriptors clj

(get-refset-descriptors store refset-id)

get-refset-field-names clj

get-refset-item clj

get-relationship clj

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-source-association-referenced-components clj

has-property? clj multimethod

history-profile clj

(history-profile st)

(history-profile st profile)

Return a sequence of reference set identifiers representing the history profile requested, or HISTORY-MAX, if not specified. See https://confluence.ihtsdotools.org/display/DOCECL/6.11+History+Supplements

index clj

(index store)

is-a? clj multimethod

make-extended-concept clj

(make-extended-concept store concept)

open-store clj

(open-store)

(open-store f)

(open-store f 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))

refset-counts clj

(refset-counts store)

Returns a map of reference set counts keyed by type. This simply iterates over all stored items Example results from the UK distribution:

{com.eldrix.hermes.snomed.SimpleMapRefsetItem        508618,      ;; ~4 %
 com.eldrix.hermes.snomed.LanguageRefsetItem         5829820,     ;; ~45 %
 com.eldrix.hermes.snomed.ExtendedMapRefsetItem      1858024,     ;; ~14 %
 com.eldrix.hermes.snomed.SimpleRefsetItem           1972073,     ;; ~15 %
 com.eldrix.hermes.snomed.AttributeValueRefsetItem   1261587,     ;; ~10 %
 com.eldrix.hermes.snomed.AssociationRefsetItem      1263064,     ;; ~10 %
 com.eldrix.hermes.snomed.RefsetDescriptorRefsetItem 1131}        ;; 0.01 %
 ```.

reify-refset-item clj

(reify-refset-item store item)

Reifies a refset item when possible, turning it into a concrete class. Suitable for use at import as long as refset descriptor refsets have already been imported.

source-associations clj

source-historical clj

(source-historical st component-id)

(source-historical st component-id refset-ids)

Return the requested historical associations for the component of types as defined by refset-ids, or all association refsets if omitted.

status clj

stream-all-concepts clj

stream-all-refset-items clj

transitive-synonyms clj

(transitive-synonyms store concept-id)

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

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

with-historical clj

(with-historical st concept-ids)

(with-historical st concept-ids historical-refset-ids)

For a given sequence of concept identifiers, expand to include historical associations both backwards and forwards in time.

For a currently active concept, this will return historic inactivated concepts in which it is the target. For a now inactive concept, this will return the active associations and their historic associations.

By default, all types of historical associations except MoveTo and MovedFrom are included, but this is configurable.

write-batch clj multimethod

Write a batch of SNOMED components to the store. Returns nil. Parameters:

• batch - a map containing :type and :data keys
• store - SNOMED CT store implementation

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)