# HEA Server Framework
[Research Informatics Shared Resource](https://risr.hci.utah.edu), [Huntsman Cancer Institute](https://healthcare.utah.edu/huntsmancancerinstitute/), Salt Lake City, UT
The HEA Server Framework contains shared code for creating HEA microservices.
## Version 1.15.0
* Added resource_base parameter to mongoservicelib.post and mongoservicelib.post_dict.
* Docstring enhancements.
* Fixed AttributeError in mockmongo.update_admin.
* Added client_error_code() function to the heaserver.service.db.aws module to centralize what to do to extract the error code out of a boto3 ClientError exception.
* In a Collection+JSON template when there is more than one desktop object in the document, create an object desktop object of the same type and use its attributes to determine which fields to make read-only.
## Version 1.14.1
* Includes opensearch-py sdk the required dependency of OpenSearch.
## Version 1.14.0
* Adds supporting classes for doing search in OpenSearch.
* Added client_error_code() function to the heaserver.service.db.aws module to centralize what to do to extract the error code out of a boto3 ClientError exception.
* In a Collection+JSON template when there is more than one desktop object in the document, create an object desktop object of the same type and use its attributes to determine which fields to make read-only.
## Version 1.14.0
* Added resource_base parameter to mongoservicelib.post and mongoservicelib.post_dict.
* Docstring enhancements.
* Fixed AttributeError in mockmongo.update_admin.
* Added client_error_code() function to the heaserver.service.db.aws module to centralize what to do to extract the error code out of a boto3 ClientError exception.
* In a Collection+JSON template when there is more than one desktop object in the document, create an object desktop object of the same type and use its attributes to determine which fields to make read-only.
## Version 1.13.2
* Fixed handling of id fields in mongo admin non-desktop object upsert and update.
* Properly remove 'id' fields in desktop objects.
## Version 1.13.1
* Cache account owner information for a caching boost.
## Version 1.13
* Removed heaserver.service.aiohttp.StreamResponseFileLikeWrapper.
* Handle iterator-of-tuple header format in heaserver.service.response.status_ok().
## Version 1.12.2
* Made heaserver.service.testcase.microsevicetestcase.MicroserviceTestCase an abstract class with a default constructor
to prevent errors with recent pytest versions. The class was previously documented as abstract but did not inherit from
abc.ABC nor did it have any methods marked as abstract.
* Updated dependencies.
## Version 1.12.1
* Caching optimizations.
## Version 1.12.0
* Support passing the Bearer token in the access_token query parameter as an alternative to the Authorization header.
## Version 1.11.0
* The OIDC claim constants now include more claims.
* Respond with HTTP status code 409 (Conflict) on insertions when there is a conflict.
* Added optional desktop object parameter to heaserver.service.db.mongoservicelib.put.
* Addressed minor bugs in the testing framework.
* The heaserver.service.db.database.DatabaseContextManager.credentials property now does a deep copy of the credential list before returning it.
* Altered parameter validation of heaserver.service.db.aws.S3.get_client() so that the credentials and volume_id parameters can both be None (which delegates credentials to the boto3 library).
* Improved docstrings.
* New functions for improving error messages (s3_object_display_name and http_error_message in heaserver.service.awsservicelib,
and http_error_message in heaserver.service.aiohttp).
## Version 1.10.7
* Updated pymongo dependency
## Version 1.10.6
* Addressed potential interpreter hang at the end of running tests.
## Version 1.10.5
* Fixed bug sometimes preventing role from being assumed.
## Version 1.10.4
* Improved performance generating cloud credentials.
## Version 1.10.3
* Fixed type hints and logging.
* Make mongo insert calls return HTTP Conflict status code when appropriate.
* Resolved a potential issue getting an AWS account.
## Version 1.10.2
* Adds email util
## Version 1.10.1
* Limit the duration of privilege elevation when requesting it from AWS.
## Version 1.10.0
* Added elevate_privileges method to heaserver.service.db.S3.
## Version 1.9.0
* Fixed type hints, requiring mostly minor API changes.
## Version 1.8.3
* Fixed error getting object versions if no prefix is specified.
## Version 1.8.2
* Retry getting temporary credentials when the call to boto3 assume_role_with_web_identity fails.
* Use boto3's built-in paginator everywhere.
## Version 1.8.1
* Prevent failed content downloads from hanging the microservice.
## Version 1.8.0
* Moved CLIENT_ERROR* constants from heaserver.service.db.awsservicelib to the aws module.
* Updated the logic for determining permissions for AWS accounts, buckets, and objects to fallback to full permissions if the user lacks permission in AWS to simulate permissions. Thus, the behavior will fall back to that of version 1.6 or earlier. As before, AWS will still reject requests that the user lacks permissions for. A future version of heaserver will likely attempt to use elevated permissions to perform the simulation.
## Version 1.7.1
* Fixed the order in which multiple exceptions are raised.
## Version 1.7.0
* requirements_dev.txt now sets a minimum version of setuptools to address a security vulnerability. Also updated to a newer version of build.
* Implemented attribute-level permissions.
* Addressed potential performance issue with unarchiving large numbers of AWS S3 objects.
* Addressed potential crash when the server loses its connection to a client while downloading an object's contents, and increased logging during downloads.
* Mapped AWS access policies to HEA permissions so that HEA may present accurate permissions for AWS accounts, S3 buckets, and S3 objects.
## Version 1.6.3
* Upgrading heaobject dependency to get bug fixes.
## Version 1.6.2
* Added ability to toggle aws key duration depending on if system credential manager or any other user.
* Background tasks now pass the aiohttp app object as a parameter of the coroutine added to the queue.
* Added the scheduled_cleanup_ctx manager for scheduling reoccurring tasks with a delay optionally.
* Prevent the id field from appearing in mongodb when a new desktop object is inserted.
## Version 1.6.0
* Improved docstrings.
* New heaobject dependency.
* Removed account_type_names parameters from heaserver.service.db.database.get_volumes and heaserver.service.db.database.Database.get_volumes.
* New heaserver.service.util.now() function.
* Removed file system-related parameters from heaserver.service.heaobjectsupport functions (type_to_resource_url, get_dict, get, get_all, get_component, get_resource_url).
* heaserver.service.client: Made a type passed into type_or_obj not used to create the object instance; new get_all_list() function.
* Use heaobject.util.now() instead of datetime.now() to get the current datetime with a timezone.
* Don't allow creating a new desktop object in MongoDB if the current user and the owner of the object are not the same.
* Set the created and modified attributes of desktop objects in heaserver.service.db.mongo.
* Populate new AWSAccount attributes.
## Version 1.5.3
* When updating AWS temporary credentials, generate new headers rather than pass the headers from the HTTP request,
possibly resulting in a Content-Length header that is shorter than the request body.
* Make heaserver.service.db.aws.get_credentials raise the right exception.
## Version 1.5.2
* Fixed TypeError regression in the heaserver.service.client module.
## Version 1.5.1
* Ensure the Content-Type header is set to application/json in heaserver.service.client put and post calls.
## Version 1.5.0
* Added attribute-level permissions.
* Temporarily restored the role check that was removed in version 1.4.1 in case an AWS credentials object with overly
permissive permissions is altered.
## Version 1.4.2
* Synchronize around getting temporary credentials.
## Version 1.4.1
* Increased the boto3 max connection pool size from the default value (10) to 25.
* Fixed a connection leak in DatabaseContextManager, and fixed the documentation for the connection() method.
* Updated heaobject dependency.
* Removed an unnecessary role check.
## Version 1.4.0
* Added type_display_name attribute to all HEA objects.
## Version 1.3.0
* Performance improvement getting accounts.
* heaserver.service.db.database.DatabaseContextManagers now allow initializing with either a volume id or a Credentials
object.
## Version 1.2.0
* get_volumes() in the database module and Database class can now filter by account ids.
* New heaobject dependency: new heaobject.root.AbstractAssociation base class and heaobject.account.AccountAssociation
implementation, and heaobject.organization.Organization class now has an accounts attribute using AccountAssociation.
## Version 1.1.3
* Fixed permissions setting in mongoservicelib.aggregate().
## Version 1.1.2
* Added resolved permissions for desktop objects in WeSTL and Collection+JSON docs.
## Version 1.1.1
* No longer errors out when accessing account information that the user is unauthorized to see.
## Version 1.1.0
* AWS account objects are now populated with more information.
* New heaobject with new APIs.
## Version 1.0.8
* Performance improvements converting to/from a HEAObject and a dictionary.
## Version 1.0.7
* Prevent a condition where zip file generation resulted in a truncated zip file.
## Version 1.0.6
* Prevent hang while getting HEA object content when the client connection goes away.
## Version 1.0.5
* Backed out boto connections issue.
## Version 1.0.4
* Don't crash when getting the user's AWS account list includes an account that doesn't exist.
* Fixed exceptions while unarchiving objects.
* Better error messaging when trying to move archived files.
* Allow copying and moving unarchived files.
## Version 1.0.3
* Added heaserver.service.response.status_generic_error() function.
* Made heaserver.service.db.awsservicelib.handle_client_error always return an HTTP response object that can be raised
as an exception.
## Version 1.0.2
* Improved performance of heaserver.service.activity.DesktopObjectActionLifecycle context manager.
* Removed unused properties from heaserver.service.activity.DesktopObjectActionLifecycle.
* Implemented input validation for heaserver.service.db.awsservicelib.archive_object().
## Version 1.0.1
* Fixed caching bug affecting mongodb paginated queries.
* Fixed passing one desktop object dict to heaserver.service.wstl.RuntimeWeSTLDocumentBuilder().
## Version 1
Initial release.
## Runtime requirements
* Python 3.10 or 3.11.
## Development environment
### Build requirements
* Any development environment is fine.
* On Windows, you also will need:
* Build Tools for Visual Studio 2019, found at https://visualstudio.microsoft.com/downloads/. Select the C++ tools.
* git, found at https://git-scm.com/download/win.
* On Mac, Xcode or the command line developer tools is required, found in the Apple Store app.
* Python 3.10 or 3.11: Download and install Python 3.10 from https://www.python.org, and select the options to install
for all users and add Python to your environment variables. The install for all users option will help keep you from
accidentally installing packages into your Python installation's site-packages directory instead of to your virtualenv
environment, described below.
* Create a virtualenv environment using the `python -m venv <venv_directory>` command, substituting `<venv_directory>`
with the directory name of your virtual environment. Run `source <venv_directory>/bin/activate` (or `<venv_directory>/Scripts/activate` on Windows) to activate the virtual
environment. You will need to activate the virtualenv every time before starting work, or your IDE may be able to do
this for you automatically. **Note that PyCharm will do this for you, but you have to create a new Terminal panel
after you newly configure a project with your virtualenv.**
* From the project's root directory, and using the activated virtualenv, run `pip install wheel` followed by
`pip install -r requirements_dev.txt`. **Do NOT run `python setup.py develop`. It will break your environment.**
### Running tests
Run tests with the `pytest` command from the project root directory. To improve performance, run tests in multiple
processes with `pytest -n auto`.
### Running integration tests
* Install Docker
* On Windows, install pywin32 version >= 223 from https://github.com/mhammond/pywin32/releases. In your venv, make sure that
`include-system-site-packages` is set to `true`.
### Packaging and releasing this project
See the [RELEASING.md](RELEASING.md) file for details.
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"author": "Research Informatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT",
"author_email": "Andrew.Post@hci.utah.edu",
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"description": "# HEA Server Framework\r\n[Research Informatics Shared Resource](https://risr.hci.utah.edu), [Huntsman Cancer Institute](https://healthcare.utah.edu/huntsmancancerinstitute/), Salt Lake City, UT\r\n\r\nThe HEA Server Framework contains shared code for creating HEA microservices.\r\n\r\n## Version 1.15.0\r\n* Added resource_base parameter to mongoservicelib.post and mongoservicelib.post_dict.\r\n* Docstring enhancements.\r\n* Fixed AttributeError in mockmongo.update_admin.\r\n* Added client_error_code() function to the heaserver.service.db.aws module to centralize what to do to extract the error code out of a boto3 ClientError exception.\r\n* In a Collection+JSON template when there is more than one desktop object in the document, create an object desktop object of the same type and use its attributes to determine which fields to make read-only.\r\n\r\n## Version 1.14.1\r\n* Includes opensearch-py sdk the required dependency of OpenSearch.\r\n\r\n## Version 1.14.0\r\n* Adds supporting classes for doing search in OpenSearch.\r\n* Added client_error_code() function to the heaserver.service.db.aws module to centralize what to do to extract the error code out of a boto3 ClientError exception.\r\n* In a Collection+JSON template when there is more than one desktop object in the document, create an object desktop object of the same type and use its attributes to determine which fields to make read-only.\r\n\r\n## Version 1.14.0\r\n* Added resource_base parameter to mongoservicelib.post and mongoservicelib.post_dict.\r\n* Docstring enhancements.\r\n* Fixed AttributeError in mockmongo.update_admin.\r\n* Added client_error_code() function to the heaserver.service.db.aws module to centralize what to do to extract the error code out of a boto3 ClientError exception.\r\n* In a Collection+JSON template when there is more than one desktop object in the document, create an object desktop object of the same type and use its attributes to determine which fields to make read-only.\r\n\r\n## Version 1.13.2\r\n* Fixed handling of id fields in mongo admin non-desktop object upsert and update.\r\n* Properly remove 'id' fields in desktop objects.\r\n\r\n## Version 1.13.1\r\n* Cache account owner information for a caching boost.\r\n\r\n## Version 1.13\r\n* Removed heaserver.service.aiohttp.StreamResponseFileLikeWrapper.\r\n* Handle iterator-of-tuple header format in heaserver.service.response.status_ok().\r\n\r\n## Version 1.12.2\r\n* Made heaserver.service.testcase.microsevicetestcase.MicroserviceTestCase an abstract class with a default constructor\r\nto prevent errors with recent pytest versions. The class was previously documented as abstract but did not inherit from\r\nabc.ABC nor did it have any methods marked as abstract.\r\n* Updated dependencies.\r\n\r\n## Version 1.12.1\r\n* Caching optimizations.\r\n\r\n## Version 1.12.0\r\n* Support passing the Bearer token in the access_token query parameter as an alternative to the Authorization header.\r\n\r\n## Version 1.11.0\r\n* The OIDC claim constants now include more claims.\r\n* Respond with HTTP status code 409 (Conflict) on insertions when there is a conflict.\r\n* Added optional desktop object parameter to heaserver.service.db.mongoservicelib.put.\r\n* Addressed minor bugs in the testing framework.\r\n* The heaserver.service.db.database.DatabaseContextManager.credentials property now does a deep copy of the credential list before returning it.\r\n* Altered parameter validation of heaserver.service.db.aws.S3.get_client() so that the credentials and volume_id parameters can both be None (which delegates credentials to the boto3 library).\r\n* Improved docstrings.\r\n* New functions for improving error messages (s3_object_display_name and http_error_message in heaserver.service.awsservicelib,\r\nand http_error_message in heaserver.service.aiohttp).\r\n\r\n## Version 1.10.7\r\n* Updated pymongo dependency\r\n\r\n## Version 1.10.6\r\n* Addressed potential interpreter hang at the end of running tests.\r\n\r\n## Version 1.10.5\r\n* Fixed bug sometimes preventing role from being assumed.\r\n\r\n## Version 1.10.4\r\n* Improved performance generating cloud credentials.\r\n\r\n## Version 1.10.3\r\n* Fixed type hints and logging.\r\n* Make mongo insert calls return HTTP Conflict status code when appropriate.\r\n* Resolved a potential issue getting an AWS account.\r\n\r\n## Version 1.10.2\r\n* Adds email util\r\n\r\n## Version 1.10.1\r\n* Limit the duration of privilege elevation when requesting it from AWS.\r\n\r\n## Version 1.10.0\r\n* Added elevate_privileges method to heaserver.service.db.S3.\r\n\r\n## Version 1.9.0\r\n* Fixed type hints, requiring mostly minor API changes.\r\n\r\n## Version 1.8.3\r\n* Fixed error getting object versions if no prefix is specified.\r\n\r\n## Version 1.8.2\r\n* Retry getting temporary credentials when the call to boto3 assume_role_with_web_identity fails.\r\n* Use boto3's built-in paginator everywhere.\r\n\r\n## Version 1.8.1\r\n* Prevent failed content downloads from hanging the microservice.\r\n\r\n## Version 1.8.0\r\n* Moved CLIENT_ERROR* constants from heaserver.service.db.awsservicelib to the aws module.\r\n* Updated the logic for determining permissions for AWS accounts, buckets, and objects to fallback to full permissions if the user lacks permission in AWS to simulate permissions. Thus, the behavior will fall back to that of version 1.6 or earlier. As before, AWS will still reject requests that the user lacks permissions for. A future version of heaserver will likely attempt to use elevated permissions to perform the simulation.\r\n\r\n## Version 1.7.1\r\n* Fixed the order in which multiple exceptions are raised.\r\n\r\n## Version 1.7.0\r\n* requirements_dev.txt now sets a minimum version of setuptools to address a security vulnerability. Also updated to a newer version of build.\r\n* Implemented attribute-level permissions.\r\n* Addressed potential performance issue with unarchiving large numbers of AWS S3 objects.\r\n* Addressed potential crash when the server loses its connection to a client while downloading an object's contents, and increased logging during downloads.\r\n* Mapped AWS access policies to HEA permissions so that HEA may present accurate permissions for AWS accounts, S3 buckets, and S3 objects.\r\n\r\n## Version 1.6.3\r\n* Upgrading heaobject dependency to get bug fixes.\r\n\r\n## Version 1.6.2\r\n* Added ability to toggle aws key duration depending on if system credential manager or any other user.\r\n* Background tasks now pass the aiohttp app object as a parameter of the coroutine added to the queue.\r\n* Added the scheduled_cleanup_ctx manager for scheduling reoccurring tasks with a delay optionally.\r\n* Prevent the id field from appearing in mongodb when a new desktop object is inserted.\r\n\r\n\r\n## Version 1.6.0\r\n* Improved docstrings.\r\n* New heaobject dependency.\r\n* Removed account_type_names parameters from heaserver.service.db.database.get_volumes and heaserver.service.db.database.Database.get_volumes.\r\n* New heaserver.service.util.now() function.\r\n* Removed file system-related parameters from heaserver.service.heaobjectsupport functions (type_to_resource_url, get_dict, get, get_all, get_component, get_resource_url).\r\n* heaserver.service.client: Made a type passed into type_or_obj not used to create the object instance; new get_all_list() function.\r\n* Use heaobject.util.now() instead of datetime.now() to get the current datetime with a timezone.\r\n* Don't allow creating a new desktop object in MongoDB if the current user and the owner of the object are not the same.\r\n* Set the created and modified attributes of desktop objects in heaserver.service.db.mongo.\r\n* Populate new AWSAccount attributes.\r\n\r\n## Version 1.5.3\r\n* When updating AWS temporary credentials, generate new headers rather than pass the headers from the HTTP request,\r\npossibly resulting in a Content-Length header that is shorter than the request body.\r\n* Make heaserver.service.db.aws.get_credentials raise the right exception.\r\n\r\n## Version 1.5.2\r\n* Fixed TypeError regression in the heaserver.service.client module.\r\n\r\n## Version 1.5.1\r\n* Ensure the Content-Type header is set to application/json in heaserver.service.client put and post calls.\r\n\r\n## Version 1.5.0\r\n* Added attribute-level permissions.\r\n* Temporarily restored the role check that was removed in version 1.4.1 in case an AWS credentials object with overly\r\npermissive permissions is altered.\r\n\r\n## Version 1.4.2\r\n* Synchronize around getting temporary credentials.\r\n\r\n## Version 1.4.1\r\n* Increased the boto3 max connection pool size from the default value (10) to 25.\r\n* Fixed a connection leak in DatabaseContextManager, and fixed the documentation for the connection() method.\r\n* Updated heaobject dependency.\r\n* Removed an unnecessary role check.\r\n\r\n## Version 1.4.0\r\n* Added type_display_name attribute to all HEA objects.\r\n\r\n## Version 1.3.0\r\n* Performance improvement getting accounts.\r\n* heaserver.service.db.database.DatabaseContextManagers now allow initializing with either a volume id or a Credentials\r\nobject.\r\n\r\n## Version 1.2.0\r\n* get_volumes() in the database module and Database class can now filter by account ids.\r\n* New heaobject dependency: new heaobject.root.AbstractAssociation base class and heaobject.account.AccountAssociation\r\nimplementation, and heaobject.organization.Organization class now has an accounts attribute using AccountAssociation.\r\n\r\n## Version 1.1.3\r\n* Fixed permissions setting in mongoservicelib.aggregate().\r\n\r\n## Version 1.1.2\r\n* Added resolved permissions for desktop objects in WeSTL and Collection+JSON docs.\r\n\r\n## Version 1.1.1\r\n* No longer errors out when accessing account information that the user is unauthorized to see.\r\n\r\n## Version 1.1.0\r\n* AWS account objects are now populated with more information.\r\n* New heaobject with new APIs.\r\n\r\n## Version 1.0.8\r\n* Performance improvements converting to/from a HEAObject and a dictionary.\r\n\r\n## Version 1.0.7\r\n* Prevent a condition where zip file generation resulted in a truncated zip file.\r\n\r\n## Version 1.0.6\r\n* Prevent hang while getting HEA object content when the client connection goes away.\r\n\r\n## Version 1.0.5\r\n* Backed out boto connections issue.\r\n\r\n## Version 1.0.4\r\n* Don't crash when getting the user's AWS account list includes an account that doesn't exist.\r\n* Fixed exceptions while unarchiving objects.\r\n* Better error messaging when trying to move archived files.\r\n* Allow copying and moving unarchived files.\r\n\r\n## Version 1.0.3\r\n* Added heaserver.service.response.status_generic_error() function.\r\n* Made heaserver.service.db.awsservicelib.handle_client_error always return an HTTP response object that can be raised\r\n as an exception.\r\n\r\n## Version 1.0.2\r\n* Improved performance of heaserver.service.activity.DesktopObjectActionLifecycle context manager.\r\n* Removed unused properties from heaserver.service.activity.DesktopObjectActionLifecycle.\r\n* Implemented input validation for heaserver.service.db.awsservicelib.archive_object().\r\n\r\n## Version 1.0.1\r\n* Fixed caching bug affecting mongodb paginated queries.\r\n* Fixed passing one desktop object dict to heaserver.service.wstl.RuntimeWeSTLDocumentBuilder().\r\n\r\n## Version 1\r\nInitial release.\r\n\r\n## Runtime requirements\r\n* Python 3.10 or 3.11.\r\n\r\n## Development environment\r\n\r\n### Build requirements\r\n* Any development environment is fine.\r\n* On Windows, you also will need:\r\n * Build Tools for Visual Studio 2019, found at https://visualstudio.microsoft.com/downloads/. Select the C++ tools.\r\n * git, found at https://git-scm.com/download/win.\r\n* On Mac, Xcode or the command line developer tools is required, found in the Apple Store app.\r\n* Python 3.10 or 3.11: Download and install Python 3.10 from https://www.python.org, and select the options to install\r\nfor all users and add Python to your environment variables. The install for all users option will help keep you from\r\naccidentally installing packages into your Python installation's site-packages directory instead of to your virtualenv\r\nenvironment, described below.\r\n* Create a virtualenv environment using the `python -m venv <venv_directory>` command, substituting `<venv_directory>`\r\nwith the directory name of your virtual environment. Run `source <venv_directory>/bin/activate` (or `<venv_directory>/Scripts/activate` on Windows) to activate the virtual\r\nenvironment. You will need to activate the virtualenv every time before starting work, or your IDE may be able to do\r\nthis for you automatically. **Note that PyCharm will do this for you, but you have to create a new Terminal panel\r\nafter you newly configure a project with your virtualenv.**\r\n* From the project's root directory, and using the activated virtualenv, run `pip install wheel` followed by\r\n `pip install -r requirements_dev.txt`. **Do NOT run `python setup.py develop`. It will break your environment.**\r\n\r\n### Running tests\r\nRun tests with the `pytest` command from the project root directory. To improve performance, run tests in multiple\r\nprocesses with `pytest -n auto`.\r\n\r\n### Running integration tests\r\n* Install Docker\r\n* On Windows, install pywin32 version >= 223 from https://github.com/mhammond/pywin32/releases. In your venv, make sure that\r\n`include-system-site-packages` is set to `true`.\r\n\r\n### Packaging and releasing this project\r\nSee the [RELEASING.md](RELEASING.md) file for details.\r\n",
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