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com.eldrix.hermes.core

Provides a terminology service, wrapping the SNOMED store and search implementations as a single unified service.

Provides a terminology service, wrapping the SNOMED store and
search implementations as a single unified service.
raw docstring

active-association-targetsclj

(active-association-targets svc component-id refset-id)

Return the active association targets for a given component.

Return the active association targets for a given component.
sourceraw docstring

all-transitive-synonymsclj

(all-transitive-synonyms svc params)
source

are-any?clj

(are-any? svc concept-ids parent-ids)

Are any of the concept-ids subsumed by any of the parent-ids?

Checks the is-a relationships of the concepts in question against the set of parent identifiers.

Are any of the concept-ids subsumed by any of the parent-ids?

Checks the is-a relationships of the concepts in question against the set of
parent identifiers.
sourceraw docstring

build-search-indexclj

(build-search-index root)
(build-search-index root language-priority-list)
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closeclj

(close svc)
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compactclj

(compact root)
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create-serviceclj

(create-service root import-from)
(create-service root import-from locale-preference-string)

Create a terminology service combining both store and search functionality in a single step. It would be unusual to use this; usually each step would be performed interactively by an end-user.

Create a terminology service combining both store and search functionality
in a single step. It would be unusual to use this; usually each step would be
performed interactively by an end-user.
sourceraw docstring

ecl-contains?clj

(ecl-contains? svc concept-ids ecl)

Do any of the concept-ids satisfy the constraint expression specified? This is an alternative to expanding the valueset and then checking membership.

Do any of the concept-ids satisfy the constraint expression specified?
This is an alternative to expanding the valueset and then checking membership.
sourceraw docstring

expand-eclclj

(expand-ecl svc ecl)

Expand an ECL expression.

Expand an ECL expression.
sourceraw docstring

expand-ecl-historicclj

(expand-ecl-historic svc ecl)

Expand an ECL expression and include historic associations of the results, so that the results will include now inactive/deprecated concept identifiers.

Expand an ECL expression and include historic associations of the results,
so that the results will include now inactive/deprecated concept identifiers.
sourceraw docstring

get-all-childrenclj

(get-all-children svc concept-id)
(get-all-children svc concept-id type-id)
source

get-all-parentsclj

(get-all-parents svc concept-id)
(get-all-parents svc concept-id type-id)
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get-child-relationships-of-typeclj

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

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

Returns a collection of identifiers representing the child relationships of
the specified type of the specified concept.
sourceraw docstring

get-component-refset-itemsclj

(get-component-refset-items svc component-id)
(get-component-refset-items svc component-id refset-id)
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get-conceptclj

(get-concept svc concept-id)
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get-descriptionsclj

(get-descriptions svc concept-id)
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get-extended-conceptclj

(get-extended-concept svc concept-id)
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get-fully-specified-nameclj

(get-fully-specified-name svc concept-id)
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get-installed-reference-setsclj

(get-installed-reference-sets svc)
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get-parent-relationships-of-typeclj

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

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

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

get-preferred-synonymclj

(get-preferred-synonym svc concept-id langs)
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get-reference-setsclj

(get-reference-sets svc component-id)
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get-refset-itemclj

(get-refset-item svc uuid)
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get-release-informationclj

(get-release-information svc)
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get-statusclj

(get-status root
            &
            {:keys [counts? installed-refsets?]
             :or {counts? false installed-refsets? true}})
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get-synonymsclj

(get-synonyms svc concept-id)

Returns a collection of synonyms for the given concept.

Returns a collection of synonyms for the given concept.
sourceraw docstring

historical-associationsclj

(historical-associations svc component-id)

Returns all historical-type associations for the specified component. Result is a map, keyed by the type of association (e.g. SAME-AS) and a sequence of reference set items for that association. Some concepts may be ambiguous and therefore map to multiple targets. Annoyingly, but understandably, the 'moved-to' reference set does not actually reference the new component - but the namespace to which it has moved - so for example an ancient International release may have accidentally including UK specific concepts - so they will have been removed. It is hoped that most MOVED-TO concepts will also have a SAME-AS or POSSIBLY-EQUIVALENT-TO historical association. See https://confluence.ihtsdotools.org/display/DOCRELFMT/5.2.5.1+Historical+Association+Reference+Sets and https://confluence.ihtsdotools.org/display/editorialag/Component+Moved+Elsewhere

Returns all historical-type associations for the specified component.
Result is a map, keyed by the type of association (e.g. SAME-AS) and
a sequence of reference set items for that association. Some concepts
may be ambiguous and therefore map to multiple targets. Annoyingly, but
understandably, the 'moved-to' reference set does not actually reference
the new component - but the namespace to which it has moved - so for example
an ancient International release may have accidentally including UK specific
concepts - so they will have been removed. It is hoped that most MOVED-TO
concepts will also have a SAME-AS or POSSIBLY-EQUIVALENT-TO historical
association.
See https://confluence.ihtsdotools.org/display/DOCRELFMT/5.2.5.1+Historical+Association+Reference+Sets
and https://confluence.ihtsdotools.org/display/editorialag/Component+Moved+Elsewhere
sourceraw docstring

import-snomedclj

(import-snomed root dirs)

Import SNOMED distribution files from the directories dirs specified into the database directory root specified.

Import SNOMED distribution files from the directories `dirs` specified into
the database directory `root` specified.
sourceraw docstring

log-metadataclj

(log-metadata dir)
source

openclj

(open root)

Open a (read-only) SNOMED service from the path root.

Open a (read-only) SNOMED service from the path `root`.
sourceraw docstring

parse-expressionclj

(parse-expression svc s)
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paths-to-rootclj

(paths-to-root svc concept-id)
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reverse-mapclj

(reverse-map svc refset-id code)
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reverse-map-rangeclj

(reverse-map-range svc refset-id prefix)
(reverse-map-range svc refset-id lower-bound upper-bound)
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(search svc params)
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some-indexedclj

(some-indexed pred coll)

Returns index and first logical true value of (pred x) in coll, or nil. e.g. (some-indexed #{64572001} '(385093006 233604007 205237003 363169009 363170005 123946008 64572001 404684003 138875005)) returns: [6 664572001].

Returns index and first logical true value of (pred x) in coll, or nil.
e.g.
(some-indexed #{64572001} '(385093006 233604007 205237003 363169009 363170005 123946008 64572001 404684003 138875005))
returns:
[6 664572001].
sourceraw docstring

source-historicalclj

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

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

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

source-historical-associationsclj

(source-historical-associations svc component-id)

Returns all historical-type associations in which the specified component is the target. For example, searching for 24700007 will result in a map keyed by refset-id (e.g. SAME-AS reference set) and a set of concept identifiers.

Returns all historical-type associations in which the specified component is
the target. For example, searching for 24700007 will result in a map keyed
by refset-id (e.g. SAME-AS reference set) and a set of concept identifiers.
sourceraw docstring

subsumed-by?clj

(subsumed-by? svc concept-id subsumer-concept-id)
source

with-historicalclj

(with-historical svc concept-ids)
(with-historical svc concept-ids assoc-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.

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. 
sourceraw docstring

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