hl7 / utg

Unified Terminology Governance

UTG

Unified Terminology Governance

utg's Issues

SimpleWorkerContext.fromClassPath results in "Stream closed" IOException

I try to create a SimpleWorkerContext given a zip file on the classpath:

SimpleWorkerContext.fromClassPath(CORE_R4_FHIR_RESOURCES_FILENAME);

This results in a IOException: Stream closed.

The reason is, my zip file (the Core R4 Profile) contains Json files, and the JsonParser closes the stream after parsing each zip entry, although more entries are available on the zip stream.

Explanation:

This method is looping through the entries in the zip file (which is perfectly fine):
SimpleWorkerContext:

private void loadFromStream(InputStream stream, IContextResourceLoader loader) throws IOException, FHIRException {
  ZipInputStream zip = new ZipInputStream(stream);
  ZipEntry ze;
  while ((ze = zip.getNextEntry()) != null) {
      loadDefinitionItem(ze.getName(), zip, loader);
    zip.closeEntry();
  }
zip.close();
}

The loadDefinitions() calls the JsonParser, which in turn calls this:
TextFile:

  public static String streamToString(InputStream input) throws IOException  {
    InputStreamReader sr = new InputStreamReader(input, "UTF-8");    
    StringBuilder b = new StringBuilder();
    //while (sr.ready()) { Commented out by Claude Nanjo (1/14/2014) - sr.ready() always returns false - please remove if change does not impact other areas of codebase
    int i = -1;
    while((i = sr.read()) > -1) {
      char c = (char) i;
      b.append(c);
    }
    sr.close();
    
    return  b.toString().replace("\uFEFF", ""); 
  }

This closes the InputStream, which causes the entire zip stream to be closed, causing everything to fail.

Also, reading a file byte for byte seems horribly inefficient!

Improve documentation: how does terminology.hl7.org relate to tx.fhir.org and the hl7-terminology Node package?

I've been trying to figure out how terminology.hl7.org (which appears to be generated by the code in this repository) relates to https://tx.fhir.org and the hl7-terminology Node package. I have run the ./runonce.sh script from this repo in Java 11 and successfully generated the documentation I see at https://terminology.hl7.org/, including the NPM packages on the download page at https://terminology.hl7.org/downloads.html. However, based on the output from that shell script, this code appears to access both tx.fhir.org ("Connect to Terminology Server at http://tx.fhir.org", "-tx: Connect to http://tx.fhir.org/r4") and possibly hl7-terminology ("Installing hl7.terminology#3.0.0 to the package cache", which I haven’t figured out where that is yet).

I would really appreciate some documentation on:

1. How does this repository use tx.fhir.org? Does it only use terminologies from there, or does it compare the CodeSystems stored locally (e.g. https://github.com/HL7/UTG/blob/master/input/sourceOfTruth/external/v3/codeSystems/cs-v3-snomed-CT.xml) with those stored on tx.fhir.org?
2. Is this the repository that generates the hl7-terminology Node package? If so, does it use tx.fhir.org, the CodeSystems mentioned above, or some other source for the CodeSystem/NamingSystem information?
3. If this is not the repository that generates the hl7-terminology Node package, could you please point me to the documentation on how that package is generated?

The reason I'm poking around with this is because I'd like to propose that FHIR CodeSystems and NamingSystems store the prefixes we need to convert a FHIR Coding (e.g. system: http://hl7.org/fhir/sid/icd-10, code: G44.1) to a concept URL (e.g. http://purl.bioontology.org/ontology/ICD10/G44.1) and vice versa. I'm doing this to solve a problem relating to FHIR RDF generation (see my latest comment on that issue here: w3c/hcls-fhir-rdf#94 (comment)), for which I'd like to be able to modify the hl7.terminology NPM package to add a "prefix" field for a few CodingSystem/NodeSystem entries as an example.

Thanks so much for your help!

Incorrect property code in UTG/input/sourceOfTruth/v2/v2-tables.xml

For all concept entries for "tables" that are actually v3 CodeSystems, the property code v2cs-uri is used. The correct code is v2-cs-uri.

Example:

  <concept>
    <code value="0719"/>
    <display value="Access Restriction Reason Code"/>
    <definition value="Table of codes specifying the reason for the restricted access.  Note these codes are maintained within HL7, but outside of Version 2."/>
    ...
    <property>
      <code value="v2cs-uri"/>
      <valueString value="http://terminology.hl7.org/CodeSystem/v3-ActCode"/>
    </property>
     ...
  </concept>