75 allow to specify multiple query arguments in df contraints #76
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…, which also explains why mypy was not happy with it
…o-specify-multiple-query-arguments-in-df_contraints
giuliabaldini
deleted the
75-allow-to-specify-multiple-query-arguments-in-df_contraints
branch
giuliabaldini
added a commit
that referenced
this pull request
Mar 17, 2023
* Update to 3.8 because of numpy security update (#64) * Update to 3.8 because of numpy security update * Remove openpyxl because 3.7 is not supported anymore * 33 convert basic bundle collection to generator (#60) * 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 function * 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 * Add history support (#74) * 8 add handling for dataframe functions using (#72) * 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 * Update README.md * Fix Error for Paging when the URL changes from HTTP to HTTPS (#78) * Fix the bug by introducing a new variable that contains the domain * Add forgotten regex group and add test * Update README.md * 75 allow specifying multiple query arguments in df contraints (#76) * 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 * Update README.md * Update README.md * Create CITATION.cff * Update CITATION.cff * Update CITATION.cff * Update README.md * Fix CITATION.cff * Add version attribute to init (#80) * Check for file existance and return a warning and none in fix_mapping_dataframe (#82) * Update pyproject.toml * Update CITATION.cff * Fix readme error due to changes in code * Update CITATION.cff * Update CITATION.cff * 83 allow turning off checks for dicom download (#85) * Add turn of checks option * Make the continue statement depend on the turn_off_checks variable * Add resource name to the TQDM description (#88) * 84 merge trade rows for dataframe and trade rows for dataframe with ref (#89) * Merge trade_rows_for_dataframe and trade_rows_for_dataframe_with_ref * Update version * Modify tests * Update notebooks * 86 allow addition of any column to the trade rows for dataframe result (#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 * Make pre-commit up to date with pyproject * Remove version 3.7 from automatic tests and add 3.10 * 91 add merge on option to steal bundles to dataframe (#92) * Add merge_on to all dataframe functions * Modify mypy command in github workflows * Add directory for mypy check * Fix file after wrong conflict resolving * Fix readme * Fix readme hyperlink * Fix consistency in README * Update CITATION.cff * Update pyproject.toml * Update authors in readme * Update CITATION.cff * Update poetry in github actions * 95 fix docstring for with columns (#98) * 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 * Update version * 100 force read action on (#101) * Force read request for IDs * Update the bundle processing to go through the resources * 96 add format options for dicomdownloader (#99) * Add the possibility to always save in the study folder * Add new formats to store the downloaded data * Update README.md * Update README.md * Convert logging.warn to warnings when appropriate (#105) * Standardize bundles for read and search (#106) * Update CITATION.cff * Update CITATION.cff * 104 smarter caching (#107) * 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 * Update CITATION.cff * 111 make current beta compatible with 010 (#112) * 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 * 94 efficiency problem with merge on (#113) * 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 * Make fhirpathpy input greedy (#116) Co-authored-by: Giulia Baldini <Giulia.Baldini@uk-essen.de> * Update pyproject.toml --------- Co-authored-by: Giulia Baldini <Giulia.Baldini@uk-essen.de>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.