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109 support for custom certificates needed #119

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merged 55 commits into from
Mar 17, 2023

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giuliabaldini and others added 30 commits August 3, 2022 11:13
* Update to 3.8 because of numpy security update

* Remove openpyxl because 3.7 is not supported anymore
* Convert functions to return generators

* Update readme

* Add more tests

* Remove pyrohealth from tests because it is currently not working

* Add another type ignore for cuntion

* Remove all fhirpathpy import tries

* Update example 4

* Change functions used in public tests

* Fix problems with trade_rows_for_dataframe_with_ref and mypy issues

* Update example 2

* Update example 1

* Fix tqdm text name

* Update example 2&4

* Update example 3

* Re-add none case to reset empty lists in fhirpaths
* Remove initial reference name in df_constraints if the search parameter is _id

* Add error if there are None values in a DF constraint column

* Bump up version because of incompatibility

* Add pipe for system only if the first element of the df_contraints is a URL
* Fix the bug by introducing a new variable that contains the domain

* Add forgotten regex group and add test
* Add option to have multiple values for df_contraints keys

* Working now, I did not remember the structure that should be expected, which also explains why mypy was not happy with it

* Fix error for history, since it always expected a string instead of a list of strings

* Add conversion to string when adding identifiers

* Add more tests

* Make tests less time consuming
* Add turn of checks option

* Make the continue statement depend on the turn_off_checks variable
…ef (#89)

* Merge trade_rows_for_dataframe and trade_rows_for_dataframe_with_ref

* Update version

* Modify tests

* Update notebooks
#90)

* Update version

* Add the option of adding to the output DF of trade_rows_for_dataframe any input column

* Add the option of renaming the columns

* Add space in warning

* Remove blank lines
* Add merge_on to all dataframe functions

* Modify mypy command in github workflows

* Add directory for mypy check

* Fix file after wrong conflict resolving
giuliabaldini and others added 25 commits September 23, 2022 13:47
* Fix link to part of readme

* Add docstring about with_columns

* Improve spacing in docstring

* Test for mypy

* Check if the error depends on 3.10

* Update packages and try again with 3.10

* Set 3.10.6 as py version

* Add type ignores

* Add type ignores
* Force read request for IDs

* Update the bundle processing to go through the resources
* Add the possibility to always save in the study folder

* Add new formats to store the downloaded data
* First draft of http caching

* Improve docstrings

* Add a couple of todos

* Add retry option and custom create_key parameter for caching

* Sort request params to ensure same order for caching
* Bump up version

* Add query_to_dataframe function to ensure compatibility with v0.1.0

* Fix text in examples

* Fix parameter inconsistency in query_to_dataframe§

* Update tests with query_to_dataframe

* Adjust tests
* Remove the merge on parameter and return one dataframe per resource

* Filter out none values directly from the returned records

* Modify bundle_to_dataframe to take the union of all processed bundles per resource

* Adjust tests

* Different outputs for query_to_dataframe

* Remove always return dict overwrite, that may kill everything

* Update pyproject.toml
Co-authored-by: Giulia Baldini <Giulia.Baldini@uk-essen.de>
@giuliabaldini giuliabaldini linked an issue Mar 17, 2023 that may be closed by this pull request
@giuliabaldini giuliabaldini merged commit 004036b into main Mar 17, 2023
@giuliabaldini giuliabaldini deleted the 109-support-for-custom-certificates-needed branch March 17, 2023 09:42
giuliabaldini added a commit that referenced this pull request Jun 29, 2023
* Add custom session object option 

Resolves #119
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Support for custom certificates needed
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