com.eldrix.hermes.importer
Provides import functionality for processing directories of files
Provides import functionality for processing directories of files
all-metadataclj
(all-metadata dir)Returns all release metadata from the directory specified.
Returns all release metadata from the directory specified.
csv-data->mapsclj
(csv-data->maps csv-data)Turn CSV data into maps, assuming first row is the header.
Turn CSV data into maps, assuming first row is the header.
importable-filesclj
(importable-files dir)Return a list of importable files from the directory specified.
Return a list of importable files from the directory specified.
load-snomedclj
(load-snomed dir
&
{:keys [nthreads batch-size] :or {nthreads 4 batch-size 5000}})Imports a SNOMED-CT distribution from the specified directory, returning results on the returned channel which will be closed once all files have been sent through.
Imports a SNOMED-CT distribution from the specified directory, returning results on the returned channel which will be closed once all files have been sent through.
metadata-filesclj
(metadata-files dir)Returns a list of release package information files from the directory.
Each entry returned in the list will be a java.io.File.
These files have been issued since the July 2020 International edition release.
Returns a list of release package information files from the directory. Each entry returned in the list will be a `java.io.File`. These files have been issued since the July 2020 International edition release.
read-metadataclj
(read-metadata f)Reads the metadata from the file specified.
Unfortunately, some UK releases have invalid JSON in their metadata, so we log an error and avoid throwing an exception. Raised as issue #34057 with NHS Digital.
Unfortunately the name of the release is not included currently, but as the metadata file exists at the root of the release, we can guess the name from the parent directory and use that if a 'name' isn't in the metadata. Raised as issue #32991 with Snomed International.
Reads the metadata from the file specified. Unfortunately, some UK releases have invalid JSON in their metadata, so we log an error and avoid throwing an exception. Raised as issue #34057 with NHS Digital. Unfortunately the *name* of the release is not included currently, but as the metadata file exists at the root of the release, we can guess the name from the parent directory and use that if a 'name' isn't in the metadata. Raised as issue #32991 with Snomed International.
snomed-file-seqclj
(snomed-file-seq dir)A tree sequence for SNOMED CT data files, returning a sequence of maps.
Each result is a map of SNOMED information from the filename as per the release file documentation, with
- :path : the path of the file,
- :component the canonical name of the SNOMED component (e.g. 'Concept', 'SimpleRefset')
A tree sequence for SNOMED CT data files, returning a sequence of maps. Each result is a map of SNOMED information from the filename as per the [release file documentation](https://confluence.ihtsdotools.org/display/DOCRELFMT/3.3.2+Release+File+Naming+Convention), with * :path : the path of the file, * :component the canonical name of the SNOMED component (e.g. 'Concept', 'SimpleRefset')
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