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fix: fix HTTP calls with raw text input for the R client
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Lines changed: 94 additions & 39 deletions

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‎README.md‎

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Original file line numberDiff line numberDiff line change
@@ -1,11 +1,60 @@
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# CMS Client
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This repo contains SDKs for interacting with the [Cogstack ModelServe](https://github.com/cogstack/CogStack-ModelServe) (CMS) APIs.
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CMS is a model serving and governance system for CogStack NLP solutions. The client SDKs in this repo are generated from the OpenAPI specification to provide type-safe, language-native ways to interact with the CMS APIs from your own applications. These cover authentication, NER annotation, streaming and real-time entity extraction and redaction, text embedding, model training and evaluation, annotation statistics and rendering, free text or structured output generation, and other auxiliary functionalities related to model serving and fine-tuning. The following languages are supported:
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[![Java](https://img.shields.io/badge/Java-SDK-blue?logo=java)](src/gen/java/README.md)
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[![Python](https://img.shields.io/badge/Python-SDK-blue?logo=python)](src/gen/python/README.md)
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[![R](https://img.shields.io/badge/R-SDK-blue?logo=r)](src/gen/r/README.md)
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This repo contains SDKs for interacting with the [Cogstack ModelServe](https://github.com/cogstack/CogStack-ModelServe) (CMS) APIs.
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CMS is a model serving and governance system for CogStack NLP solutions. The client SDKs in this repo are generated from the OpenAPI specification to provide type-safe, language-native ways to interact with the CMS APIs from your own applications. These cover authentication, NER annotation, streaming and real-time entity extraction and redaction, text embedding, model training and evaluation, annotation statistics and rendering, free text or structured output generation, and other auxiliary functionalities related to model serving and fine-tuning.
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## Usage
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To use one of these SDKs, navigate to the specific language directory above and follow the installation instructions provided in the README file.
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* [Java](https://github.com/cogstack/cms-client/blob/main/src/gen/java/README.md)
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* [Python](https://github.com/cogstack/cms-client/blob/main/src/gen/python/README.md)
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* [R](https://github.com/cogstack/cms-client/blob/main/src/gen/r/README.md)
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## Usage
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## Examples
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### Entity extraction
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Java:
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```java
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import org.cms.client.ApiClient;
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import org.cms.client.api.AnnotationsApi;
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String cmsBaseUrl = "http://localhost:8000";
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ApiClient client = new ApiClient();
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client.setBasePath(cmsBaseUrl);
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AnnotationsApi api = new AnnotationsApi(client);
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String text = "John had been diagnosed with acute Kidney Failure the week beforel";
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var response = api.getEntitiesFromText(text);
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System.out.println(response);
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```1
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Python:
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```python
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import cms_client
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cms_base_url = "http://localhost:8000"
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configuration = cms_client.Configuration(host=cms_base_url)
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with cms_client.ApiClient(configuration) as api_client:
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api_instance = cms_client.AnnotationsApi(api_client)
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text = "John had been diagnosed with acute Kidney Failure the week before."
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response = api_instance.get_entities_from_text(text)
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print(response)
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```
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R:
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```r
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library(cmsClient)
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To use one of these SDKs, navigate to the specific language directory above and follow the installation instructions provided in the README file.
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cms_base_url <- "http://localhost:8000"
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api_instance <- AnnotationsApi$new()
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api_instance$api_client$base_path <- cms_base_url
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text <- "John had been diagnosed with acute Kidney Failure the week before."
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response <- api_instance$GetEntitiesFromText(text)
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print(response)
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```

‎src/gen/r/R/annotations_api.R‎

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Original file line numberDiff line numberDiff line change
@@ -525,7 +525,13 @@ AnnotationsApi <- R6::R6Class(
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}
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if (!is.null(`body`)) {
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local_var_body <- `body`$toJSONString()
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if (is.character(`body`)) {
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local_var_body <- `body`
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} else if (!is.null(`body`$toJSONString)) {
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local_var_body <- `body`$toJSONString()
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} else {
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local_var_body <- jsonlite::toJSON(`body`, auto_unbox = TRUE, null = "null")
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}
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} else {
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local_var_body <- NULL
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}

‎src/gen/r/R/api_client.R‎

Lines changed: 34 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -216,7 +216,14 @@ ApiClient <- R6::R6Class(
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form_params, file_params,
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accepts, content_types,
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body, stream_callback = NULL, ...) {
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headers <- httr::add_headers(c(header_params, self$default_headers))
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headers <- character()
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if (!is.null(header_params) && length(header_params) > 0) {
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headers <- c(headers, unlist(header_params, use.names = TRUE))
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}
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if (!is.null(self$default_headers) && length(self$default_headers) > 0) {
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headers <- c(headers, unlist(self$default_headers, use.names = TRUE))
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}
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headers <- as.character(headers)
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http_timeout <- NULL
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if (!is.null(self$timeout)) {
@@ -226,63 +233,56 @@ ApiClient <- R6::R6Class(
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# set HTTP accept header
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accept = self$select_header(accepts)
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if (!is.null(accept)) {
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headers['Accept'] = accept
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headers <- c(headers, "Accept" = accept)
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}
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# set HTTP content-type header
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content_type = self$select_header(content_types)
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if (!is.null(content_type)) {
235-
headers['Content-Type'] = content_type
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headers <- c(headers, "Content-Type" = content_type)
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}
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request_config <- list()
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if (length(headers) > 0) {
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request_config[[length(request_config) + 1]] <- httr::add_headers(.headers = headers)
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}
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if (!is.null(http_timeout)) {
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request_config[[length(request_config) + 1]] <- http_timeout
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}
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if (!is.null(self$`user_agent`)) {
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request_config[[length(request_config) + 1]] <- httr::user_agent(self$`user_agent`)
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}
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if (typeof(stream_callback) == "closure") { # stream data
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if (method == "GET") {
240-
httr::GET(url, query = query_params, headers, http_timeout,
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httr::user_agent(self$`user_agent`), write_stream(stream_callback), ...)
258+
httr_response <- do.call(httr::GET, c(list(url = url, query = query_params), request_config, list(...)))
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} else if (method == "POST") {
243-
httr::POST(url, query = query_params, headers, body = body,
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httr::content_type("application/json"), http_timeout,
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httr::user_agent(self$`user_agent`), write_stream(stream_callback), ...)
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httr_response <- do.call(httr::POST, c(list(url = url, query = query_params, body = body, encode = "raw"), request_config, list(...)))
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} else if (method == "PUT") {
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httr::PUT(url, query = query_params, headers, body = body,
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httr::content_type("application/json"), http_timeout,
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http_timeout, httr::user_agent(self$`user_agent`), write_stream(stream_callback), ...)
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httr_response <- do.call(httr::PUT, c(list(url = url, query = query_params, body = body, encode = "raw"), request_config, list(...)))
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} else if (method == "PATCH") {
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httr::PATCH(url, query = query_params, headers, body = body,
252-
httr::content_type("application/json"), http_timeout,
253-
http_timeout, httr::user_agent(self$`user_agent`), write_stream(stream_callback), ...)
264+
httr_response <- do.call(httr::PATCH, c(list(url = url, query = query_params, body = body, encode = "raw"), request_config, list(...)))
254265
} else if (method == "HEAD") {
255-
httr::HEAD(url, query = query_params, headers, http_timeout,
256-
http_timeout, httr::user_agent(self$`user_agent`), write_stream(stream_callback), ...)
266+
httr_response <- do.call(httr::HEAD, c(list(url = url, query = query_params), request_config, list(...)))
257267
} else if (method == "DELETE") {
258-
httr::DELETE(url, query = query_params, headers, http_timeout,
259-
http_timeout, httr::user_agent(self$`user_agent`), write_stream(stream_callback), ...)
268+
httr_response <- do.call(httr::DELETE, c(list(url = url, query = query_params), request_config, list(...)))
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} else {
261270
err_msg <- "Http method must be `GET`, `HEAD`, `OPTIONS`, `POST`, `PATCH`, `PUT` or `DELETE`."
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stop(err_msg)
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}
264273
} else { # no streaming
265274
if (method == "GET") {
266-
httr_response <- httr::GET(url, query = query_params, headers, http_timeout,
267-
httr::user_agent(self$`user_agent`), ...)
275+
httr_response <- do.call(httr::GET, c(list(url = url, query = query_params), request_config, list(...)))
268276
} else if (method == "POST") {
269-
httr_response <- httr::POST(url, query = query_params, headers, body = body,
270-
httr::content_type("application/json"), http_timeout,
271-
httr::user_agent(self$`user_agent`), ...)
277+
httr_response <- do.call(httr::POST, c(list(url = url, query = query_params, body = body, encode = "raw"), request_config, list(...)))
272278
} else if (method == "PUT") {
273-
httr_response <- httr::PUT(url, query = query_params, headers, body = body,
274-
httr::content_type("application/json"), http_timeout,
275-
http_timeout, httr::user_agent(self$`user_agent`), ...)
279+
httr_response <- do.call(httr::PUT, c(list(url = url, query = query_params, body = body, encode = "raw"), request_config, list(...)))
276280
} else if (method == "PATCH") {
277-
httr_response <- httr::PATCH(url, query = query_params, headers, body = body,
278-
httr::content_type("application/json"), http_timeout,
279-
http_timeout, httr::user_agent(self$`user_agent`), ...)
281+
httr_response <- do.call(httr::PATCH, c(list(url = url, query = query_params, body = body, encode = "raw"), request_config, list(...)))
280282
} else if (method == "HEAD") {
281-
httr_response <- httr::HEAD(url, query = query_params, headers, http_timeout,
282-
http_timeout, httr::user_agent(self$`user_agent`), ...)
283+
httr_response <- do.call(httr::HEAD, c(list(url = url, query = query_params), request_config, list(...)))
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} else if (method == "DELETE") {
284-
httr_response <- httr::DELETE(url, query = query_params, headers, http_timeout,
285-
http_timeout, httr::user_agent(self$`user_agent`), ...)
285+
httr_response <- do.call(httr::DELETE, c(list(url = url, query = query_params), request_config, list(...)))
286286
} else {
287287
err_msg <- "Http method must be `GET`, `HEAD`, `OPTIONS`, `POST`, `PATCH`, `PUT` or `DELETE`."
288288
stop(err_msg)
@@ -412,7 +412,7 @@ ApiClient <- R6::R6Class(
412412
}
413413

414414
# not json mime type, simply return the first one
415-
return(headers[1])
415+
return(headers[[1]])
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}
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},
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