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‎Authentication.md

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# Authentication
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The whcs-python-sdk project supports the following types of authentication:
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- Identity and Access Management (IAM)
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The apikey for your service can be found by clicking the service instance of the resources list in the IBM Cloud dashboard.
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## programming examples
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```python
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import watson_health_cognitive_services as whys
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Service = whcs.AnnotatorForClinicalDataV1('my_service_url', 'my_apikey', 'api_version')
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```
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```python
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import watson_health_cognitive_services as whys
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Service = whcs.InsightsFOrMedicalLiteratureServiceV1('my_service_url', 'my_apikey', 'api_version')
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```

‎CONTRIBUTING.md

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# Questions
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If you are having difficulties using the APIs or have a question about the IBM Cloud and Services,
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please ask a question on [dW Answers][dw] or [Stack Overflow][stackoverflow].
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# Issues
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If you encounter an issue with the Python Core SDK, you are welcome to submit a [bug report](https://github.com/IBM/whcs-python-sdk/issues).
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Before that, please search for similar issues. It's possible somebody has encountered this issue already.
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# Code
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## Commit Messages
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Commit messages should follow the [Angular Commit Message Guidelines](https://github.com/angular/angular/blob/master/CONTRIBUTING.md#-commit-message-guidelines).
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This is because our release tool - [semantic-release](https://github.com/semantic-release/semantic-release) -
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uses this format for determining release versions and generating changelogs.
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Tools such as [commitizen](https://github.com/commitizen/cz-cli) or [commitlint](https://github.com/conventional-changelog/commitlint)
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can be used to help contributors and enforce commit messages.
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Here are some examples of acceptable commit messages, along with the release type that would be done based on the commit message:
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| Commit message | Release type |
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|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------|
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| `fix(Returns Model) Passages serialization error.` | Patch Release |
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| `feat(Repository Messages): add support for returning repository responses.` | ~~Minor~~ Feature Release |
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# Pull Requests
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If you want to contribute to the repository, here's a quick guide:
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1. Fork the repository
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1. Install `virtualenv` and `tox`
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1. Develop and test your code changes with [pytest].
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* Respect the original code [style guide][styleguide].
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* Only use spaces for indentation.
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* Create minimal diffs - disable on save actions like reformat source code or organize imports. If you feel the source code should be reformatted create a separate PR for this change.
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* Check for unnecessary whitespace with `git diff --check` before committing.
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* Make sure your code supports Python 3.5, 3.6, and 3.7. You can use `pyenv` and `tox` for this
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1. Make the test pass
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1. Check code coverage. Add tests for all new functionality and ensure overall coverage does not decrease.
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1. Commit your changes
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* Commits should follow the [Angular commit message guidelines](https://github.com/angular/angular/blob/master/CONTRIBUTING.md#-commit-message-guidelines). This is because our release tool uses this format for determining release versions and generating changelogs. To make this easier, we recommend using the [Commitizen CLI](https://github.com/commitizen/cz-cli) with the `cz-conventional-changelog` adapter.
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1. Push to your fork and submit a pull request to the `dev` branch
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# Running the tests
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You probably want to set up a [virtualenv].
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1. Clone this repository:
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```sh
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git clone [email protected]/IBM/python-sdk-core.git
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```
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1. Install the SDK as an editable package using the current source:
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```sh
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pip3 install --editable .
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```
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1. Install the test dependencies with:
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```sh
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pip3 install -r requirements-dev.txt
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```
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1. Run the test cases with:
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The test cases make use of configuration files to provide API input.
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Each module in the SDK has a config.ini file in the test folder with
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default values for a provisioned Standard plan instance of the service.
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Populate the missing elements from the settings section so a connection
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to your service instance can be generated. From the module directory
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For your provisioned service run the following command:
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```sh
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Python -m pytest tests/functional
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```
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NOTE: If you have provisioned a Custom plan instance of Insights for Medical Literature
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The Tests will fail until enriched content has been added to the instance. All default
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Values may need to be updated to reflect your level of enrichment.
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# Developer's Certificate of Origin 1.1
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By making a contribution to this project, I certify that:
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(a) The contribution was created in whole or in part by me and I
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have the right to submit it under the open source license
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indicated in the file; or
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(b) The contribution is based upon previous work that, to the best
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of my knowledge, is covered under an appropriate open source
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license and I have the right under that license to submit that
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work with modifications, whether created in whole or in part
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by me, under the same open source license (unless I am
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permitted to submit under a different license), as indicated
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in the file; or
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(c) The contribution was provided directly to me by some other
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person who certified (a), (b) or (c) and I have not modified
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it.
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(d) I understand and agree that this project and the contribution
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are public and that a record of the contribution (including all
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personal information I submit with it, including my sign-off) is
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maintained indefinitely and may be redistributed consistent with
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this project or the open source license(s) involved.
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# Additional Resources
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* [General GitHub documentation](https://help.github.com/)
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* [GitHub pull request documentation](https://help.github.com/send-pull-requests/)
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[IBM Watson Health Support](https://ibmwatsonhealth.force.com/mysupport/s/)
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[styleguide]: http://google.github.io/styleguide/pyguide.html
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[pytest]: http://pytest.org/latest/
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[virtualenv]: http://virtualenv.readthedocs.org/en/latest/index.html

‎LICENSE ‎LICENSE.md

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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.
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limitations under the License.

‎README.md

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# whcs-python-sdk
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Watson Health Cognitive Services Python SDK
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[![Build Status](https://travis.ibm.com/ibmcloud/platform-services-java-sdk.svg?token=eW5FVD71iyte6tTby8gr&branch=master)](https://travis.ibm.com/ibmcloud/platform-services-java-sdk)
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[![semantic-release](https://img.shields.io/badge/%20%20%F0%9F%93%A6%F0%9F%9A%80-semantic--release-e10079.svg)](https://github.com/semantic-release/semantic-release)
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# Watson Health Cognitive Services Python SDK Version 0.0.1
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The IBM Watson Health Cognitive Services (WHCS) Python SDK allows developers to programmaticlly interact with the following WHCS services:
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| Service Name | Artifact Id |
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|--------------|-------------|
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| [Annotator for Clinical data](https://cloud.ibm.com/apidocs/wh-acd) | annotator_for_clinical_data |
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| [Insights for Medical Literature](https://cloud.ibm.com/apidocs/wh-iml) | insights_for_medical_literature |
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## Prerequisites
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[ibm-cloud-onboarding]: https://cloud.ibm.com/registration?target=%2Fdeveloper%2Fwatson&
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An [IBM CLoud](ibm-cloud-onboarding) account.
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An IAM API key to allow the SDK to access your provisioned service instance.
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Python 3.5 or above
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## Installation
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To install, use `pip`
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```bash
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pip install --upgrade whys-python-sdk
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```
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## Authentication
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The whcs-python-sdk project supports the following types of authentication:
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- Identity and Access Management (IAM)
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For more information about how to use authentication with your services click [here](Authentication.md)
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## Using the SDK
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For general SDK usage information, please see [this link](https://github.com/IBM/ibm-cloud-sdk-common/blob/master/README.md)
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## Examples
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For SDK usage examples, please see the service API documentation. There are code examples and sample responses for each service API
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- [Annotator for Clinical data](https://cloud.ibm.com/apidocs/wh-acd)
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- [Insights for Medical Literature](https://cloud.ibm.com/apidocs/wh-iml)
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## Questions
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If you are having difficulties using this SDK or have a question about the IBM Cloud services,
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please ask a question at [IBM Watson Health Support](https://ibmwatsonhealth.force.com/mysupport/s/).
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## Issues
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If you encounter an issue with the project, you are welcome to submit a
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[bug report](https://github.com/IBM/whcs-python-sdk>/issues).
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Before that, please search for similar issues. It's possible that someone has already reported the problem.
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## Logging
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### Enable logging
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```python
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import logging
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logging.basicConfig(level=logging.DEBUG)
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```
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This would show output of the form:
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```
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DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): iam.cloud.ibm.com:443
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DEBUG:urllib3.connectionpool:https://iam.cloud.ibm.com:443 "POST /identity/token HTTP/1.1" 200 1809
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DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): gateway.watsonplatform.net:443
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DEBUG:urllib3.connectionpool:https://gateway.watsonplatform.net:443 "POST /assistant/api/v1/workspaces?version=2018-07-10 HTTP/1.1" 201 None
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DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): gateway.watsonplatform.net:443
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DEBUG:urllib3.connectionpool:https://gateway.watsonplatform.net:443 "GET /assistant/api/v1/workspaces/883a2a44-eb5f-4b1a-96b0-32a90b475ea8?version=2018-07-10&export=true HTTP/1.1" 200 None
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DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): gateway.watsonplatform.net:443
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DEBUG:urllib3.connectionpool:https://gateway.watsonplatform.net:443 "DELETE /assistant/api/v1/workspaces/883a2a44-eb5f-4b1a-96b0-32a90b475ea8?version=2018-07-10 HTTP/1.1" 200 28
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```
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### Low level request and response dump
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To get low level information of the requests/ responses:
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```python
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from http.client import HTTPConnection
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HTTPConnection.debuglevel = 1
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```
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## Open source @ IBM
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Find more open source projects on the [IBM Github Page](http://ibm.github.io/)
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## Contributing
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See [CONTRIBUTING](CONTRIBUTING.md).
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## License
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The IBM Cloud MySDK Java SDK is released under the Apache 2.0 license.
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The license's full text can be found in [LICENSE](LICENSE).

‎__init__.py

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# Copyright 2018 IBM All Rights Reserved.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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from .version import __version__

‎annotator_for_clinical_data/__init__.py

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# Copyright 2018 IBM All Rights Reserved.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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from .annotator_for_clinical_data_v1 import AnnotatorForClinicalDataV1
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from .annotator_for_clinical_data_v1 import AcdFlow
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from .annotator_for_clinical_data_v1 import AcdProfile
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from .annotator_for_clinical_data_v1 import AllergyMedication
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from .annotator_for_clinical_data_v1 import Annotation
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from .annotator_for_clinical_data_v1 import Annotator
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from .annotator_for_clinical_data_v1 import AnnotatorFlow
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from .annotator_for_clinical_data_v1 import AssistanceAnnotation
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from .annotator_for_clinical_data_v1 import AttributeValueAnnotation
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from .annotator_for_clinical_data_v1 import AttributeValueEntry
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from .annotator_for_clinical_data_v1 import CancerDiagnosis
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from .annotator_for_clinical_data_v1 import Concept
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from .annotator_for_clinical_data_v1 import ConceptValue
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from .annotator_for_clinical_data_v1 import ConfigurationEntity
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from .annotator_for_clinical_data_v1 import ContainerAnnotation
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from .annotator_for_clinical_data_v1 import ContainerGroup
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from .annotator_for_clinical_data_v1 import Disambiguation
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from .annotator_for_clinical_data_v1 import EjectionFractionAnnotation
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from .annotator_for_clinical_data_v1 import Flow
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from .annotator_for_clinical_data_v1 import FlowEntry
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from .annotator_for_clinical_data_v1 import LabValueAnnotation
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from .annotator_for_clinical_data_v1 import ListStringWrapper
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from .annotator_for_clinical_data_v1 import MedicationAnnotation
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from .annotator_for_clinical_data_v1 import Name
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from .annotator_for_clinical_data_v1 import NegatedSpan
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from .annotator_for_clinical_data_v1 import NluEntities
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from .annotator_for_clinical_data_v1 import Node
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from .annotator_for_clinical_data_v1 import Procedure
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from .annotator_for_clinical_data_v1 import Relations
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from .annotator_for_clinical_data_v1 import RequestContainer
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from .annotator_for_clinical_data_v1 import Section
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from .annotator_for_clinical_data_v1 import SectionTrigger
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from .annotator_for_clinical_data_v1 import Smoking
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from .annotator_for_clinical_data_v1 import SpellCorrectedText
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from .annotator_for_clinical_data_v1 import SpellingCorrection
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from .annotator_for_clinical_data_v1 import Suggestion
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from .annotator_for_clinical_data_v1 import SymptomDisease
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from .annotator_for_clinical_data_v1 import UnstructuredContainer
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from .annotator_for_clinical_data_v1 import ACDException
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#from .util import CustomDeserializer
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#from .util import CustomCollection

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