i have mapped around 20 fields from the sample data. All of them come under Observation category. I have a field/Label which we created to denote each patient.
"PatientLabel" : 0
I understand FHIR is all about fixed set of items. But, is there a way to include this in FHIR Json. i would need this information while processing.
"extension": [
{
"name": "PatientLabel",
"value": 0
}
tried the above one.. FHIR validator is throwing error
Extensions don't have a 'name', they have a 'url'. Also, 'value' is a polymorphic type, so you'd need "valueInteger" or "valueDecimal". That said, "0" seems an unusual value for something titled "patient label". Normally, the Patient would be in the Observation.subject. If you just have a label and not a reference, you could use subject.display and not need an extension at all...
Related
I can't work out how to use the $orderby with SODA on an id field (such as created or lastModified. I'm using SODA for REST directly and not the other projects.
Sort syntax is:
{
$orderby: {
path: 'created',
datatype: 'date',
order: 'desc'
}
}
And I've also tried:
{
"$orderby": {
"$fields": [{
"path": "created",
"datatype": "date",
"order": "desc"
}],
"$scalarRequired": true
}
}
And replacing the path with $id: 'created' (as you can use that in a filter specification to access non-document metadata. But nothing works to order properly.
Short of putting the created field into my object when I create them (which defeats the purpose of having those fields) how can I use orderby on a metadata field?
Max here from the SODA dev team. I am not 100% sure what you mean by an "id field". Looks like you mean the "created on" and "last modified" document components automatically maintained by SODA, right? If so, we don't support orderbys on these (though it could be added as an enhancement).
As of now, as you mentioned in your post, best option is to create a field in your JSON documents' content and set it to ISO8601 format timestamp value (e.g. 2020-10-13T07:01:01). You can then do an orderby on such a field (with datatype "datetime"). Please let me know if more details on this are needed.
In SODA REST, when you're listing collection contents, you could specify since=timestamp and until=timestamp query parameters. That'll give you all documents with last modified timestamp greater than the "since" one, and less than or equal to the "until" one.
Example:
http://host:port/ords/scott/soda/latest/myColl?since=2020:01:01T00:00:00&until=2021:01:01T00:00:00
As part of this operation, SODA automatically adds an orderby on "last modified". Not sure if that's useful to you though, since that's just for listing all documents in the collection (i.e. you can't combine it with a QBE, for example). So if this doesn't meet your needs, best option right now is to explicitly add something like a "modified' field to the document content, and do an orderby on that.
I am trying to use the metricbeat http module to monitor F5 pools.
I make a request to the f5 api and bring back json, which is saved to kibana. But the json contains an array of pool members and I want to count the number which are up.
The advice seems to be that this can be done with a scripted field. However, I can't get the script to retrieve the array. eg
doc['http.f5pools.items.monitor'].value.length()
returns in the preview results with the same 'Additional Field' added for comparison:
[
{
"_id": "rT7wdGsBXQSGm_pQoH6Y",
"http": {
"f5pools": {
"items": [
{
"monitor": "default"
},
{
"monitor": "default"
}
]
}
},
"pool.MemberCount": [
7
]
},
If I try
doc['http.f5pools.items']
Or similar I just get an error:
"reason": "No field found for [http.f5pools.items] in mapping with types []"
Googling suggests that the doc construct does not contain arrays?
Is it possible to make a scripted field which can access the set of values? ie is my code or the way I'm indexing the data wrong.
If not is there an alternative approach within metricbeats? I don't want to have to make a whole new api to do the calculation and add a separate field
-- update.
Weirdly it seems that the number values in the array do return the expected results. ie.
doc['http.f5pools.items.ratio']
returns
{
"_id": "BT6WdWsBXQSGm_pQBbCa",
"pool.MemberCount": [
1,
1
]
},
-- update 2
Ok, so if the strings in the field have different values then you get all the values. if they are the same you just get one. wtf?
I'm adding another answer instead of deleting my previous one which is not the actual question but still may be helpful for someone else in future.
I found a hint in the same documentation:
Doc values are a columnar field value store
Upon googling this further I found this Doc Value Intro which says that the doc values are essentially "uninverted index" useful for operations like sorting; my hypotheses is while sorting you essentially dont want same values repeated and hence the data structure they use removes those duplicates. That still did not answer as to why it works different for string than number. Numbers are preserved but strings are filters into unique.
This “uninverted” structure is often called a “column-store” in other
systems. Essentially, it stores all the values for a single field
together in a single column of data, which makes it very efficient for
operations like sorting.
In Elasticsearch, this column-store is known as doc values, and is
enabled by default. Doc values are created at index-time: when a field
is indexed, Elasticsearch adds the tokens to the inverted index for
search. But it also extracts the terms and adds them to the columnar
doc values.
Some more deep-dive into doc values revealed it a compression technique which actually de-deuplicates the values for efficient and memory-friendly operations.
Here's a NOTE given on the link above which answers the question:
You may be thinking "Well that’s great for numbers, but what about
strings?" Strings are encoded similarly, with the help of an ordinal
table. The strings are de-duplicated and sorted into a table, assigned
an ID, and then those ID’s are used as numeric doc values. Which means
strings enjoy many of the same compression benefits that numerics do.
The ordinal table itself has some compression tricks, such as using
fixed, variable or prefix-encoded strings.
Also, if you dont want this behavior then you can disable doc-values
OK, solved it.
https://discuss.elastic.co/t/problem-looping-through-array-in-each-doc-with-painless/90648
So as I discovered arrays are prefiltered to only return distinct values (except in the case of ints apparently?)
The solution is to use params._source instead of doc[]
The answer for why doc doesnt work
Quoting below:
Doc values are a columnar field value store, enabled by default on all
fields except for analyzed text fields.
Doc-values can only return "simple" field values like numbers, dates,
geo- points, terms, etc, or arrays of these values if the field is
multi-valued. It cannot return JSON objects
Also, important to add a null check as mentioned below:
Missing fields
The doc['field'] will throw an error if field is
missing from the mappings. In painless, a check can first be done with
doc.containsKey('field')* to guard accessing the doc map.
Unfortunately, there is no way to check for the existence of the field
in mappings in an expression script.
Also, here is why _source works
Quoting below:
The document _source, which is really just a special stored field, can
be accessed using the _source.field_name syntax. The _source is loaded
as a map-of-maps, so properties within object fields can be accessed
as, for example, _source.name.first.
.
Responding to your comment with an example:
The kyeword here is: It cannot return JSON objects. The field doc['http.f5pools.items'] is a JSON object
Try running below and see the mapping it creates:
PUT t5/doc/2
{
"items": [
{
"monitor": "default"
},
{
"monitor": "default"
}
]
}
GET t5/_mapping
{
"t5" : {
"mappings" : {
"doc" : {
"properties" : {
"items" : {
"properties" : {
"monitor" : { <-- monitor is a property of items property(Object)
"type" : "text",
"fields" : {
"keyword" : {
"type" : "keyword",
"ignore_above" : 256
}
}
}
}
}
}
}
}
}
}
If I want to update the "amount" field within a particular element inside "f_units" collection in the below resource (protocol buffer), how will the FieldMask look like to update the amount field? Does the field mask operate on array index for collections?
{
"f_sel": {
"f_units": [
{
"id": "1",
"amount": {
"coefficient": 1000,
"exponent": -2
}
},
{
"id": "2",
"amount": {
"coefficient": 2000,
"exponent": -2
}
}
]
}
}
Will it be "f_sel.f_units.0.amount" ? How can I update the amount using FieldMask?
As far as I know, there is no way to replace individual elements of a repeated field with an index in a FieldMask.
Instead, you'd update the amount field for the element within f_units you wish to change and set the FieldMask to
"f_sel.f_units"
It would be slightly more efficient to only have to send a delta to the original list, but it would be hard to prevent bugs. For example, what if the proto was modified in the meantime and the specified index (presuming there was a way to specify one) for the repeated field was no longer in range?
As an aside, Google does propose the concept of MergeOptions which defines semantics for how repeated fields are to be handled when merging. Currently, it appears they intend for you either to replace the repeated field in its entirety or append to the end of the destination field. Both of these merging strategies avoid the aforementioned bug that could be caused by specifying an invalid index.
I need a field, here score, to be a number, and other times a string. Like:
{
"name": "Joe"
"score": 32.5
}
{
"name": "Sue"
"score": "NOT_AVAILABLE"
}
How can I express this in this in the index settings in Elastic Search?
I basically want "dynamic typing" on the field. The code may not make sense to you (like: why not split it into 2 different fields), but it's necessary to be this way on my end (for consistency reasons).
I don't need/want the property to be indexed/"searchable" btw. I just need the data to be in the json response. I need something like "any object will fit here".
Finally figured it out. All I had to do was to set enabled to false, and elastic search will not attempt to do anything with the data - but it's still present in the json response.
Like so:
"score": {
"enabled": false
}
Just define "score" field to be of type "string" in your mapping. That's it. Make sure you do define the mapping before indexing any document though. Otherwise if you let the mapping be created dynamically and the type of value of "score" field is anything but string in the first document you index, you won't be able to index any document next in which "score" holds a string.
I am using Codeigniter and Alex Bilbie's MongoDB library.
In my API that I am developing users can upload images and other users can comment on them.
I have chosen to include the comments as sub documents to the images.
Each comment contains:
Fullname (of author)
Comment
Created_at
So in other words. The users full name is "hard coded" into each comment so if they
later decides to change their names I have a problem.
I read that I can use atomic updates to update all occurrences of the name (like in comments) but how can I do this using Alex´s library? Can I update all places where the name is wrong?
UPDATE
This is how the image document looks like with the comments.
I think that it is pretty strange that MongoDB encourage the use of subdocuments but then does not include a way to update multiple items in an array.
{
"_id": ObjectId("4e9ead773dc793dc01020000"),
"description": "An image",
"category": "accident",
"comments": [
{
"id": ObjectId("4e96bd063dc7937202000000"),
"fullname": "James Bond",
"comment": "This is a comment.",
"created_at": "2011-10-19 13:02:40"
}
],
"created_at": "2011-10-19 12:59:03"
}
Thankful for all help!
I am not familiar with codeignitor, but mb mongodb shell syntax will help you:
db.comments.update( {"Fullname":"Andrew Orsich"},
{ $set : { Fullname: "New name"} }, false, true )
Last true flag indicate that you want update multiple documents. So it is possible to update all comments in one update operation.
BTW: denormalazing (not 'hard coding') data in mongodb and nosql in general is usual operation. Also operation that require update a lot of documents usually work async. But it is up to you.
Update:
db.comments.update( {"comments.Fullname":"Andrew Orsich"},
{ $set : { comments.$.Fullname: "New name"} }, false, true )
But, above query will update full name in first comment on nested array. If you need to affect changes to more than one array element you will need to use multiple update statements.