com.eldrix.hermes.impl.store — com.eldrix/hermes 1.2.1164

Store provides a store of SNOMED CT data with appropriate indices to permit fast lookup. It is currently implemented using two LMDB key value stores on the local filesystem.

all-children clj

(all-children store concept-id)

(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).

all-parents clj

(all-parents store concept-id-or-ids)

(all-parents store concept-id-or-ids type-id)

Returns all parent concepts for the concept(s), including that concept or those concepts, by design. Parameters:

• store
• concept-id-or-ids a concept identifier, or collection of identifiers
• type-id, defaults to 'IS-A' (116680003).

child-relationships-of-type clj

(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.

close clj

compact clj

component-refset-ids clj

component-refset-items clj

concept clj

concept-descriptions clj

concrete-values clj

description clj

description-refsets clj

(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 % (description-refsets store (:id %)))
     (concept-descriptions store 24700007))

extended-concept clj

(extended-concept store concept-id)

Get an extended concept for the concept specified.

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.

fully-specified-name clj

(fully-specified-name store concept-id)

(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.

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)

installed-reference-sets clj

is-a? clj multimethod

leaves clj

(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

make-extended-concept clj

(make-extended-concept store {concept-id :id :as c})

open-store clj

(open-store)

(open-store f)

(open-store f opts)

parent-relationships clj

(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.

parent-relationships-expanded clj

(parent-relationships-expanded store concept-id)

(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.

parent-relationships-of-type clj

(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.

parent-relationships-of-types clj

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

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))

preferred-description clj

(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

preferred-fully-specified-name clj

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

preferred-synonym clj

(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.

properties clj

(properties store concept-id)

Returns a concept's properties, including concrete values. Ungrouped properties are returned under key '0', with other groups returned with non-zero keys. There is no other intrinsic meaning to the group identifier.

e.g. for lamotrigine:

(properties store 1231295007)
=>
{0 {116680003 #{779653004}, 411116001 #{385060002}, 763032000 #{732936001},
    766939001 #{773862006}, 1142139005 #{"#1"}},
 1 {732943007 #{387562000}, 732945000 #{258684004}, 732947008 #{732936001},
    762949000 #{387562000}, 1142135004 #{"#250"}, 1142136003 #{"#1"}}}

See https://confluence.ihtsdotools.org/display/DOCRELFMT/4.2.3+Relationship+File+Specification "The relationshipGroup field is used to group relationships with the same sourceId field into one or more logical sets. A relationship with a relationshipGroup field value of '0' is considered not to be grouped. All relationships with the same sourceId and non-zero relationshipGroup are considered to be logically grouped.".

Note: All values are returned as sets. It is only through access to the MRCM that cardinality rules could be applied safely, but that requires support for ECL, which is not available at this low level of the library.

properties-by-group clj

(properties-by-group store concept-id)

Returns a concept's properties as a map of group-id to a map of type-id to a set of target identifiers. Results do not include concrete values. e.g.

(properties-by-group store 24700007)
=>
{0 {116680003 #{6118003 414029004 39367000}},
 1 {116676008 #{32693004}, 363698007 #{21483005}, 370135005 #{769247005}},
 2 {116676008 #{409774005}, 363698007 #{21483005}, 370135005 #{769247005}}}

properties-by-group-expanded clj

(properties-by-group-expanded store concept-id)

properties-by-type clj

(properties-by-type store concept-id)

Return a concept's properties as a map of type-id to a map of group-id to a set of target-ids. e.g.

(properties-by-type store 24700007)
=>
{116676008 {1 #{32693004}, 2 #{409774005}},
 116680003 {0 #{6118003 414029004 39367000}},
 363698007 {1 #{21483005}, 2 #{21483005}},
 370135005 {1 #{769247005}, 2 #{769247005}}}

properties-expanded clj

(properties-expanded store concept-id)

Return all properties grouped by relationship group, with results containing concept identifiers expanded to include transitive relationships.

proximal-parent-ids clj

(proximal-parent-ids store concept-id)

(proximal-parent-ids store concept-id type-concept-id)

Returns a sequence of identifiers for the proximal parents of the given type, defaulting to the 'IS-A' relationship if no type is given.

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 %
 ```.

refset-descriptor-attribute-ids clj

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

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

refset-descriptors clj

(refset-descriptors store refset-id)

refset-field-names clj

refset-item clj

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.

relationship clj

release-information clj

(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

source-association-referenced-components clj

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 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 active 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:

• store - SNOMED CT store implementation
• batch - a map containing :type, :headings and :data keys. The implementation will be chosen via the :type of the batch.

write-batch-one-by-one clj

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

Write out a batch one item at a time.

write-batch-with-fallback clj

(write-batch-with-fallback store batch)

Write a batch of data to the store. If there is an error, the write is retried one-by-one so that the parsing error can be identified down to an individual item.