I am trying to read & parse HL7 messages and have a question about how they're physically stored in a file.
Can a file contain multiple HL7 messages or will a file only contain single message?
HL7 message files have mostly the extension *.hl7.
There are the FHS (file header), FTS (file trailer) and BHS (batch header), BTS (batch trailer) segments to envelope multiple HL7-messages in one message file.
I recommend to search for "hl7 fhs bhs" in Google.
from HL7eu 2.3.6 HL7 Batch Protocol
[FHS] (file header segment)
{ [BHS] (batch header segment)
{ MSH (one or more HL7 messages)
....
....
....
}
[BTS] (batch trailer segment)
}
[FTS] (file trailer segment)
There is no such a concept in HL7 protocol as "File".
You choose whether to store the message in file or save it in database or elsewhere.
You create a file if you need.
You choose its extension as ".hl7" or ".txt" or else.
You choose whether there should be single message in a file or multiple.
HL7 message when transferred on socket needs to be enclosed in MLLP blocks. You can learn more about it here and here. Here, of-course it matters that you enclose each message separately in MLLP block.
Note that, even though you store the message in file, there is no "file header". So, to summarize it all -- "Its up to you".
I was not aware about FHS (file header) and BHS (batch header) feature (2.3.6 HL7 Batch Protocol) in HL7. I learned it from other answer from #sqlab on this question.
Yes; it is a feature for batching the messages.
But I still do not think the FHS and BHS is "file header" the way we have header for JPEG or many other file types where we can read just header and validate file type.
If there is no FHS segment in message file, we cannot say it is not a HL7 message.
Not sure though, one may have multiple "batches" in single file.
IMO, this more behaves like "batching the messages" than a "file header".
About extension ".hl7"; yes, many organizations use this extension commonly for HL7 files.
But it is not standard or mandatory or forced per say (not mentioned in Specifications).
Just making the extension ".txt" does not make it invalid HL7 file; though some third party applications may not work with it, but that is different problem.
Related
Do I have to specify a MIME type if the uploaded file has no extension?
In other words is there a default general MIME type?
You can use application/octet-stream for unknown types.
RFC 2046 states in section 4.5.1:
The "octet-stream" subtype is used to
indicate that a body contains
arbitrary binary data.
RFC resources:
We should use RFC-7231 (HTTP/1.1 Semantics and Content) as reference instead of RFC-2046 (Media Types) because question was clearly about HTTP Content-Type.
Also RFC-2046 does not clearly define unknown types but RFC-7231 does.
Short answer:
Do not send MIME type for unknown data.
To be more clear: Do not use Content-Type header at all.
References:
RFC-7231Hypertext Transfer Protocol (HTTP/1.1): Semantics and Content3.1.1.5. Content-Type
A sender that generates a message containing a payload body SHOULD
generate a Content-Type header field in that message unless the
intended media type of the enclosed representation is unknown to the
sender.
That section clearly tells you to leave it out if you don't know it for sure.
It also tells that receiver could assume that type is application/octet-stream but thing is that it might also be something else.
What's different then?
RFC-20464.5.1. Octet-Stream Subtype
The recommended action for an implementation that receives an
"application/octet-stream" entity is to simply offer to put the data
in a file, with any Content-Transfer-Encoding undone, or perhaps to
use it as input to a user-specified process.
And, as already stated above:
RFC-72313.1.1.5. Content-Type
If a Content-Type header field is not present, the recipient
MAY either assume a media type of "application/octet-stream"
([RFC2046], Section 4.5.1) or examine the data to determine its type.
Conclusion:
If you define it as "application/octet-stream" then you are telling that you know that it is "application/octet-stream".
If you don't define it then you are telling that you don't know what it is and leave decision to receiver and receiver could then check if it walks like duck and...
I prefer application/unknown, but result will be surely the same as application/octet-stream
I use MWeb to write markdown documents. Recently I met a problem when I publish markdown document to Evernote, this is the error code:
Error Domain=com.evernote.sdk Code=11
"Content of submitted note was malformed"
UserInfo={NSLocalizedDescription=Content of submitted note was malformed, parameter=Element type "row" must be declared.}
mweb-error
Root cause:
I used "Raw" in the doc, I think word "Raw" maybe a keyword in Evernote API. So if I add "Raw" in the doc, a raw definition must be declared.
My solution
surrounding the word "Raw" with ``. For example:
change "Java API, users need to use Dataset to represent a DataFrame." to "Java API, users need to use `Dataset` to represent a DataFrame."
Within a Mirth Connect installation (version 3.5.1), I have setup a channel TCP (LLP) that receive a message HL7 and send an XML with the data of the PID segment (plus some of other useful informations about the HL7 message) to an external site.
I want to validate the message (if contains an error) and filtering the message according to some rules for the data of the segment PID (no name, no surname, etc).
To accompish this requirement, I have write a simple javascript filter and set in the channel (from Summary tab) the strict validation.
But I have this behavior.
If I don't use the strict validation option for the messages, I get all the data of the segment PID within tags like PID.1, PID.2 etc (e.g. for the name I have the following XML structure <PID.5><PID.5.1>XXX</PID.5.1>....</PID.5>).
Instead, if I use the strict validation option the message (in the filter) became different and other tags are present (e.g. for the name I have the following XML structure <PID.5><XPN.1><FN.1>XXX</FN.1></XPN.1>....</PID.5>).
Someone know the why I have this behavior? It is caused by some misconfiguration? Or it is the normal behavior?
Thanks at all for the support.
UPDATE
I realized only now that the structures were not visible.
Now, yes.
Thanks again at all for the support.
This is normal behavior. The default parser is implemented in the mirth hl7v2 datatype itself. When you use the strict parser, it uses the HAPI parser which produces the alternate xml you are seeing that actually conforms to the hl7 specification.
there exist some sample code for an Http Server in the Dart:io section.
Now I will distribute images with this server. To achieve this, I read the requested image file and send its content to the client via request.response.write().
The problem is the format of the read data:
Either I read the image file as 16bit-String or as Byte Array. Neither of them is compatible to a raw 8-bit array, which I have to send to the client.
May someone help me?
There exist several kinds of write-methods in the response class.
write
writeCharCode
add
While "write" writes the data 'as seen', "writeCharCode" transforms the data back to raw-format. However, writeCharCode prepends some "magic byte" (C2) at the beginning, so it corrupts the data.
Another function, called add( List < int > ) processes the readAsBytes-result as desired.
Best regards,
Alex
I download an N-Triple file from dbpedia,but when I wanted to read it in to Jena model,some exceptions throw out.Below is a part of this file:
<http://dbpedia.org/resource/Jacky_Cheung>
<http://dbpedia.org/resource/Template:%E8%97%9D%E4%BA%BA> "\u9AD4\u91CD"#zh .
<http://dbpedia.org/resource/Jacky_Cheung> <http://dbpedia.org/resource/Template:%E8%97%9D%E4%BA%BA> "\u8EAB\u9AD8"#zh .
<http://dbpedia.org/resource/Jacky_Cheung> <http://dbpedia.org/resource/Template:%E8%97%9D%E4%BA%BA> "\u8840\u578B"#zh .
<http://dbpedia.org/resource/Jacky_Cheung> <http://dbpedia.org/resource/Template:%E8%97%9D%E4%BA%BA> "\u8A9E\u8A00"#zh .
The exception throws out is:
Exception in thread "main" com.hp.hpl.jena.shared.InvalidPropertyURIException: http://dbpedia.org/resource/Template:%E8%97%9D%E4%BA%BA
at com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.splitTag(BaseXMLWriter.java:393)
at com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.startElementTag(BaseXMLWriter.java:368)
at com.hp.hpl.jena.xmloutput.impl.Unparser$3.wTypeStart(Unparser.java:671)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wPropertyEltValueString(Unparser.java:488)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wPropertyEltValue(Unparser.java:473)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wPropertyElt(Unparser.java:339)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wPropertyEltStar(Unparser.java:811)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wTypedNodeOrDescriptionLong(Unparser.java:797)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wTypedNodeOrDescription(Unparser.java:727)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wDescription(Unparser.java:686)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wObj(Unparser.java:642)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wObjStar(Unparser.java:317)
at com.hp.hpl.jena.xmloutput.impl.Unparser.wRDF(Unparser.java:298)
at com.hp.hpl.jena.xmloutput.impl.Unparser.write(Unparser.java:200)
at com.hp.hpl.jena.xmloutput.impl.Abbreviated.writeBody(Abbreviated.java:143)
at com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.writeXMLBody(BaseXMLWriter.java:500)
at com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:472)
at com.hp.hpl.jena.xmloutput.impl.Abbreviated.write(Abbreviated.java:128)
at com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:458)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.write(ModelCom.java:277)
at jena.ReadRDF.main(ReadRDF.java:45)
Java Result: 1
The problem is caused by "%E8%97%9D%E4%BA%BA",when use URIref.decode() to decode URI with this string,"%E8%97%9D%E4%BA%BA" represents tow Chinese characters.
But when I use Sesame to read this N-Triple file,it is OK without any problem.
My questions are that whether any way to solve this problem in Jena,and why dbpedia choose N-Triple to be the default RDF syntax?.It works bad with Non-ASCII languages.
Also ,I want to know that,if I want to publish my RDF data as Linked data,but the URIs of resources come with some Chinese and Japanese,should I decode the URIs at first?
Well, your question isn't completely clear because you asked about "reading in a Jena model" but the stacktrace you quoted actually starts with a call to the writer.
Jena, in general, tries very hard to conform to the relevant RDF recommendations from W3C and IETF. In particular, it tries to not generate any URI's which do not conform to the rules for valid URI's. This is compounded in the case of writing XML, because most RDF identifiers are not legal XML element ID's, meaning that you have to split the URI somewhere and use XML namespaces to make the full identifier. Not all RDF toolkits are as particular as Jena is about conforming to some of the rules in the standards.
Things you can try:
do you need to call Model.write() as part of your loading process? You should be able to load and process a model, without the check for legal URI's being invoked.
try writing the output using Turtle format, rather than XML. Turtle doesn't have the same restrictions as XML, and it's a heck of a lot easier for humans to read as well.
if there are particular ill-formed URI's in the data you are loading, look to see if there is a newer version of the data. Illegal URI's in dbpedia has been an issue in the past. If the illegal URI's are still there in the latest version, notify the dbpedia team about them.
try pre-processing your data to remove triples containing illegal URI's before they enter your processing chain.
As for URI's containing Chinese and Japanese characters, Jena conforms to the IRI spec, so as long as your URI's conform to that you should be OK.