diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 49cb7d8..6ed0812 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -37,9 +37,9 @@ jobs: poetry install -E data_science - name: Run doctests # Forks can't run doctests, requires super user token - if: github.repository == 'redcap-tools/PyCap' + if: github.actor == 'pwildenhain' run: | - poetry run pytest --doctest-only + poetry run pytest --doctest-only --doctest-plus - name: Run tests run: | poetry run pytest diff --git a/README.md b/README.md index be5a81c..4bbd9cc 100644 --- a/README.md +++ b/README.md @@ -43,6 +43,7 @@ Currently, these API calls are available: * Field names * Instrument-event mapping +* Repeating instruments and events * File * Metadata * Project Info @@ -57,6 +58,7 @@ Currently, these API calls are available: * File * Metadata * Records +* Repeating instruments and events ### Delete diff --git a/docs/api_reference/repeating.md b/docs/api_reference/repeating.md new file mode 100644 index 0000000..8cdd89b --- /dev/null +++ b/docs/api_reference/repeating.md @@ -0,0 +1,5 @@ +# Repeating + +::: redcap.methods.repeating + selection: + inherited_members: true diff --git a/mkdocs.yml b/mkdocs.yml index 437ded9..0f03e14 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -15,6 +15,7 @@ nav: - Instruments: api_reference/instruments.md - Metadata: api_reference/metadata.md - Project Info: api_reference/project_info.md + - Repeating: api_reference/repeating.md - Records: api_reference/records.md - Reports: api_reference/reports.md - Surveys: api_reference/surveys.md diff --git a/poetry.lock b/poetry.lock index d586b81..735701a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -46,28 +46,24 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (> [[package]] name = "black" -version = "21.12b0" +version = "22.1.0" description = "The uncompromising code formatter." category = "dev" optional = false python-versions = ">=3.6.2" [package.dependencies] -click = ">=7.1.2" +click = ">=8.0.0" mypy-extensions = ">=0.4.3" -pathspec = ">=0.9.0,<1" +pathspec = ">=0.9.0" platformdirs = ">=2" -tomli = ">=0.2.6,<2.0.0" -typing-extensions = [ - {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}, - {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""}, -] +tomli = ">=1.1.0" +typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""} [package.extras] colorama = ["colorama (>=0.4.3)"] d = ["aiohttp (>=3.7.4)"] jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] -python2 = ["typed-ast (>=1.4.3)"] uvloop = ["uvloop (>=0.15.2)"] [[package]] @@ -80,7 +76,7 @@ python-versions = "*" [[package]] name = "charset-normalizer" -version = "2.0.10" +version = "2.0.12" description = "The Real First Universal Charset Detector. 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-typing-extensions = "^4.0.1" [tool.poetry.extras] data_science = ["pandas"] diff --git a/pytest.ini b/pytest.ini index 9163fed..742cccc 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,6 +1,5 @@ [pytest] doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS FAIL_FAST REPORT_NDIFF -doctest_plus = enabled addopts = -rsxX -l --tb=short --strict --pylint --black --cov=redcap --cov-report=xml markers = integration: test connects to redcapdemo.vanderbilt.edu server diff --git a/redcap/methods/__init__.py b/redcap/methods/__init__.py index a23605b..3ac00f7 100644 --- a/redcap/methods/__init__.py +++ b/redcap/methods/__init__.py @@ -6,6 +6,7 @@ import redcap.methods.metadata import redcap.methods.project_info import redcap.methods.records +import redcap.methods.repeating import redcap.methods.reports import redcap.methods.surveys import redcap.methods.users diff --git a/redcap/methods/base.py b/redcap/methods/base.py index 28a06c6..42a63a0 100644 --- a/redcap/methods/base.py +++ b/redcap/methods/base.py @@ -255,7 +255,7 @@ def _initialize_import_payload( to_import: List[dict], import_format: Literal["json"], return_format_type: Literal["json", "csv", "xml"], - data_type: Literal["record", "metadata"], + content: str, ) -> Dict[str, Any]: ... @@ -265,7 +265,7 @@ def _initialize_import_payload( to_import: str, import_format: Literal["csv", "xml"], return_format_type: Literal["json", "csv", "xml"], - data_type: Literal["record", "metadata"], + content: str, ) -> Dict[str, Any]: ... @@ -275,7 +275,7 @@ def _initialize_import_payload( to_import: "pd.DataFrame", import_format: Literal["df"], return_format_type: Literal["json", "csv", "xml"], - data_type: Literal["record", "metadata"], + content: str, ) -> Dict[str, Any]: ... @@ -284,32 +284,27 @@ def _initialize_import_payload( to_import: Union[List[dict], str, "pd.DataFrame"], import_format: Literal["json", "csv", "xml", "df"], return_format_type: Literal["json", "csv", "xml"], - data_type: Literal["record", "metadata"], + content: str, ): """Standardize the data to be imported and add it to the payload Args: to_import: array of dicts, csv/xml string, ``pandas.DataFrame`` - import_format: Format of incoming data. - data_type: The kind of data that are imported + import_format: Format of incoming data + return_format_type: Format of outgoing (returned) data + content: The kind of data that are imported Returns: payload: The initialized payload dictionary and updated format """ payload = self._initialize_payload( - content=data_type, return_format_type=return_format_type + content=content, return_format_type=return_format_type ) if import_format == "df": buf = StringIO() - if data_type == "record": - if self.is_longitudinal: - csv_kwargs = {"index_label": [self.def_field, "redcap_event_name"]} - else: - csv_kwargs = {"index_label": self.def_field} - elif data_type == "metadata": - csv_kwargs = {"index_label": "field_name"} - to_import.to_csv(buf, **csv_kwargs) + has_named_index = to_import.index.name is not None + to_import.to_csv(buf, index=has_named_index) payload["data"] = buf.getvalue() buf.close() import_format = "csv" @@ -425,10 +420,7 @@ def _return_data( return response if not df_kwargs: - if ( - content in ["formEventMapping", "participantList", "project", "user"] - or record_type == "eav" - ): + if record_type == "eav": df_kwargs = {} elif content == "exportFieldNames": df_kwargs = {"index_col": "original_field_name"} @@ -439,6 +431,9 @@ def _return_data( df_kwargs = {"index_col": [self.def_field, "redcap_event_name"]} else: df_kwargs = {"index_col": self.def_field} + # catchall for other endpoints + else: + df_kwargs = {} buf = StringIO(response) dataframe = self._read_csv(buf, **df_kwargs) diff --git a/redcap/methods/metadata.py b/redcap/methods/metadata.py index efc0c75..53926e1 100644 --- a/redcap/methods/metadata.py +++ b/redcap/methods/metadata.py @@ -126,7 +126,7 @@ def import_metadata( to_import: array of dicts, csv/xml string, `pandas.DataFrame` Note: If you pass a csv or xml string, you should use the - `format` parameter appropriately. + `import_format` parameter appropriately. return_format_type: Response format. By default, response will be json-decoded. import_format: @@ -150,7 +150,7 @@ def import_metadata( to_import=to_import, import_format=import_format, return_format_type=return_format_type, - data_type="metadata", + content="metadata", ) # pylint: disable=unsupported-assignment-operation diff --git a/redcap/methods/records.py b/redcap/methods/records.py index 3c7e191..155b454 100644 --- a/redcap/methods/records.py +++ b/redcap/methods/records.py @@ -165,15 +165,18 @@ def export_records( Examples: >>> proj.export_records() - [{'record_id': '1', 'redcap_event_name': 'event_1_arm_1', 'field_1': '1', + [{'record_id': '1', 'redcap_event_name': 'event_1_arm_1', 'redcap_repeat_instrument': '', + 'redcap_repeat_instance': 1, 'field_1': '1', 'checkbox_field___1': '0', 'checkbox_field___2': '1', 'upload_field': 'test_upload.txt', 'form_1_complete': '2'}, - {'record_id': '2', 'redcap_event_name': 'event_1_arm_1', 'field_1': '0', + {'record_id': '2', 'redcap_event_name': 'event_1_arm_1', 'redcap_repeat_instrument': '', + 'redcap_repeat_instance': 1, 'field_1': '0', 'checkbox_field___1': '0', 'checkbox_field___2': '0', 'upload_field': 'myupload.txt', 'form_1_complete': '0'}] >>> proj.export_records(filter_logic="[field_1] = 1") - [{'record_id': '1', 'redcap_event_name': 'event_1_arm_1', 'field_1': '1', + [{'record_id': '1', 'redcap_event_name': 'event_1_arm_1', 'redcap_repeat_instrument': '', + 'redcap_repeat_instance': 1, 'field_1': '1', 'checkbox_field___1': '0', 'checkbox_field___2': '1', 'upload_field': 'test_upload.txt', 'form_1_complete': '2'}] @@ -187,10 +190,10 @@ def export_records( >>> import pandas as pd >>> pd.set_option("display.max_columns", 3) >>> proj.export_records(format_type="df") - field_1 ... form_1_complete - record_id redcap_event_name ... - 1 event_1_arm_1 1 ... 2 - 2 event_1_arm_1 0 ... 0 + redcap_repeat_instrument ... form_1_complete + record_id redcap_event_name ... + 1 event_1_arm_1 NaN ... 2 + 2 event_1_arm_1 NaN ... 0 ... """ # pylint: enable=line-too-long @@ -322,7 +325,7 @@ def import_records( to_import: Note: If you pass a df, csv, or xml string, you should use the - `format` parameter appropriately. + `import_format` parameter appropriately. Note: Keys of the dictionaries should be subset of project's, fields, but this isn't a requirement. If you provide keys @@ -359,7 +362,7 @@ def import_records( Union[Dict, str]: response from REDCap API, json-decoded if `return_format` == `'json'` Examples: - >>> new_record = [{"record_id": 3, "field_1": 1}] + >>> new_record = [{"record_id": 3, "redcap_repeat_instance": 1, "field_1": 1}] >>> proj.import_records(new_record) {'count': 1} """ @@ -367,7 +370,7 @@ def import_records( to_import=to_import, import_format=import_format, return_format_type=return_format_type, - data_type="record", + content="record", ) # pylint: disable=unsupported-assignment-operation @@ -413,8 +416,11 @@ def delete_records( Union[int, str]: Number of records deleted Examples: - >>> new_record = [{"record_id": 3, "field_1": 1}, {"record_id": 4}] - >>> proj.import_records(new_record) + >>> new_records = [ + ... {"record_id": 3, "redcap_repeat_instance": 1, "field_1": 1}, + ... {"record_id": 4, "redcap_repeat_instance": 1} + ... ] + >>> proj.import_records(new_records) {'count': 2} >>> proj.delete_records(["3", "4"]) 2 diff --git a/redcap/methods/repeating.py b/redcap/methods/repeating.py new file mode 100644 index 0000000..6122350 --- /dev/null +++ b/redcap/methods/repeating.py @@ -0,0 +1,92 @@ +"""REDCap API methods for Project repeating instruments""" +from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union, Literal + +from redcap.methods.base import Base + +if TYPE_CHECKING: + import pandas as pd + + +class Repeating(Base): + """Responsible for all API methods under 'Repeating Instruments and Events' + in the API Playground + """ + + def export_repeating_instruments_events( + self, + format_type: Literal["json", "csv", "xml", "df"] = "json", + df_kwargs: Optional[Dict[str, Any]] = None, + ): + """ + Export the project's repeating instruments and events settings + + Args: + format_type: + Return the repeating instruments and events in native objects, + csv or xml, `'df''` will return a `pandas.DataFrame` + df_kwargs: + Passed to pandas.read_csv to control construction of + returned DataFrame + + Returns: + Union[str, List[Dict[str, Any]], pd.DataFrame]: Repeating instruments and events + for the project + + Examples: + >>> proj.export_repeating_instruments_events() + [{'event_name': 'event_1_arm_1', 'form_name': '', 'custom_form_label': ''}] + """ + payload = self._initialize_payload( + content="repeatingFormsEvents", format_type=format_type + ) + + return_type = self._lookup_return_type(format_type, request_type="export") + response = self._call_api(payload, return_type) + + return self._return_data( + response=response, + content="repeatingFormsEvents", + format_type=format_type, + df_kwargs=df_kwargs, + ) + + def import_repeating_instruments_events( + self, + to_import: Union[str, List[Dict[str, Any]], "pd.DataFrame"], + return_format_type: Literal["json", "csv", "xml"] = "json", + import_format: Literal["json", "csv", "xml", "df"] = "json", + ): + """ + Import repeating instrument and event settings into the REDCap Project + + Args: + to_import: array of dicts, csv/xml string, `pandas.DataFrame` + Note: + If you pass a csv or xml string, you should use the + `import format` parameter appropriately. + return_format_type: + Response format. By default, response will be json-decoded. + import_format: + Format of incoming data. By default, to_import will be json-encoded + + Returns: + Union[int, str]: The number of repeated instruments activated + + Examples: + >>> rep_instruments = proj.export_repeating_instruments_events(format_type="csv") + >>> proj.import_repeating_instruments_events(rep_instruments, import_format="csv") + 1 + """ + payload = self._initialize_import_payload( + to_import=to_import, + import_format=import_format, + return_format_type=return_format_type, + content="repeatingFormsEvents", + ) + + return_type = self._lookup_return_type( + format_type=return_format_type, request_type="import" + ) + response = self._call_api(payload, return_type) + + return response diff --git a/redcap/project.py b/redcap/project.py index 252b8dd..145f4a3 100755 --- a/redcap/project.py +++ b/redcap/project.py @@ -25,6 +25,7 @@ class Project( methods.metadata.Metadata, methods.project_info.ProjectInfo, methods.records.Records, + methods.repeating.Repeating, methods.reports.Reports, methods.surveys.Surveys, methods.users.Users, diff --git a/tests/data/doctest_project.xml b/tests/data/doctest_project.xml index 55e2fb3..fddba25 100644 --- a/tests/data/doctest_project.xml +++ b/tests/data/doctest_project.xml @@ -27,16 +27,19 @@ ALL + + + +<p>Have a nice day!</p>" stop_action_acknowledgement="" stop_action_delete_response="0" question_by_section="0" display_page_number="0" question_auto_numbering="1" survey_enabled="1" save_and_return="0" save_and_return_code_bypass="0" logo="" hide_title="0" view_results="0" min_responses_view_results="10" check_diversity_view_results="0" end_survey_redirect_url="" survey_expiration="" promis_skip_question="0" survey_auth_enabled_single="0" edit_completed_response="0" hide_back_button="0" show_required_field_text="1" confirmation_email_subject="" confirmation_email_content="" confirmation_email_from="" confirmation_email_from_display="" confirmation_email_attach_pdf="0" confirmation_email_attachment="" text_to_speech="0" text_to_speech_language="en" end_survey_redirect_next_survey="0" end_survey_redirect_next_survey_logic="" theme="" text_size="1" font_family="16" theme_text_buttons="" theme_bg_page="" theme_text_title="" theme_bg_title="" theme_text_sectionheader="" theme_bg_sectionheader="" theme_text_question="" theme_bg_question="" enhanced_choices="0" repeat_survey_enabled="0" repeat_survey_btn_text="" repeat_survey_btn_location="HIDDEN" response_limit="" response_limit_include_partials="1" response_limit_custom_text="<p>Thank you for your interest; however, the survey is closed because the maximum number of responses has been reached.</p>" survey_time_limit_days="" survey_time_limit_hours="" survey_time_limit_minutes="" email_participant_field="" end_of_survey_pdf_download="0" pdf_save_to_field="" pdf_save_to_event_id="" pdf_auto_archive="0" pdf_econsent_version="" pdf_econsent_type="" pdf_econsent_firstname_field="" pdf_econsent_firstname_event_id="" pdf_econsent_lastname_field="" pdf_econsent_lastname_event_id="" pdf_econsent_dob_field="" pdf_econsent_dob_event_id="" pdf_econsent_allow_edit="1" pdf_econsent_signature_field1="" pdf_econsent_signature_field2="" pdf_econsent_signature_field3="" pdf_econsent_signature_field4="" pdf_econsent_signature_field5=""/> - + - + diff --git a/tests/data/test_long_project.xml b/tests/data/test_long_project.xml index d44a526..3f1b778 100644 --- a/tests/data/test_long_project.xml +++ b/tests/data/test_long_project.xml @@ -27,16 +27,21 @@ ALL + + + + + - - + - + @@ -1212,14 +1217,6 @@ - - - - - - - - @@ -1407,6 +1404,16 @@ + + + + + + + + + + diff --git a/tests/integration/test_long_project.py b/tests/integration/test_long_project.py index 0041647..79715f4 100644 --- a/tests/integration/test_long_project.py +++ b/tests/integration/test_long_project.py @@ -42,3 +42,23 @@ def test_users_export(long_project): def test_records_export_labeled_headers(long_project): data = long_project.export_records(format_type="csv", raw_or_label_headers="label") assert "Study ID" in data + + +def test_repeating_export(long_project): + rep = long_project.export_repeating_instruments_events(format_type="json") + + assert isinstance(rep, list) + + +def test_repeating_export_strictly_enfores_format(long_project): + with pytest.raises(ValueError): + long_project.export_repeating_instruments_events(format_type="unsupported") + + +def test_import_export_repeating_forms(long_project): + for format_type in ["xml", "json", "csv", "df"]: + rep = long_project.export_repeating_instruments_events(format_type=format_type) + res = long_project.import_repeating_instruments_events( + to_import=rep, import_format=format_type + ) + assert res == 1 diff --git a/tests/integration/test_simple_project.py b/tests/integration/test_simple_project.py index cc5e2a8..94de96f 100644 --- a/tests/integration/test_simple_project.py +++ b/tests/integration/test_simple_project.py @@ -57,6 +57,18 @@ def test_import_and_delete_records(simple_project): assert res == 3 +@pytest.mark.integration +def test_import_df_no_index(simple_project): + # declare df_kwargs without specifying index, which returns a df with no index + proj_records_export = simple_project.export_records( + format_type="df", df_kwargs={"sep": ","} + ).convert_dtypes() + + res = simple_project.import_records(proj_records_export, import_format="df") + + assert res["count"] == 3 + + @pytest.mark.integration def test_export_version(simple_project): version = simple_project.export_version() diff --git a/tests/unit/callback_utils.py b/tests/unit/callback_utils.py index 08bbd62..ebb078c 100644 --- a/tests/unit/callback_utils.py +++ b/tests/unit/callback_utils.py @@ -97,6 +97,22 @@ def handle_long_project_form_event_mapping_request(**kwargs) -> MockResponse: return (201, headers, json.dumps(resp)) +def handle_long_project_repeating_form_request(**kwargs) -> MockResponse: + """Give back list of repeating instruments for long project""" + headers = kwargs["headers"] + data = kwargs["data"] + resp = None + # import (JSON only) + if "data" in data: + repeat_forms = json.loads(data["data"][0]) + resp = len(repeat_forms) + # export (JSON only) + else: + resp = [{"form_name": "testform", "custom_form_label": ""}] + + return (201, headers, json.dumps(resp)) + + def handle_simple_project_file_request(**kwargs) -> MockResponse: """Handle file import/export requests""" data = kwargs["data"] @@ -484,6 +500,7 @@ def get_long_project_request_handler(request_type: str) -> Callable: "arm": handle_long_project_arms_request, "file": handle_long_project_file_request, "formEventMapping": handle_long_project_form_event_mapping_request, + "repeatingFormsEvents": handle_long_project_repeating_form_request, "metadata": handle_long_project_metadata_request, "participantList": handle_long_project_survey_participants_request, "record": handle_long_project_records_request, diff --git a/tests/unit/test_long_project.py b/tests/unit/test_long_project.py index 8752adf..1f718bd 100644 --- a/tests/unit/test_long_project.py +++ b/tests/unit/test_long_project.py @@ -124,3 +124,17 @@ def test_reports_df_export(long_project): report = long_project.export_report(report_id="1", format_type="df") assert isinstance(report, pd.DataFrame) + + +def test_repeating_export(long_project): + rep = long_project.export_repeating_instruments_events(format_type="json") + + assert isinstance(rep, list) + + +def test_import_export_repeating_forms(long_project): + rep = long_project.export_repeating_instruments_events(format_type="json") + res = long_project.import_repeating_instruments_events( + to_import=rep, import_format="json" + ) + assert res == 1 diff --git a/tests/unit/test_simple_project.py b/tests/unit/test_simple_project.py index 7a2f288..0c9b66b 100644 --- a/tests/unit/test_simple_project.py +++ b/tests/unit/test_simple_project.py @@ -413,6 +413,9 @@ def test_export_methods_handle_empty_data_error(simple_project, mocker): dataframe = simple_project.export_instrument_event_mappings(format_type="df") assert dataframe.empty + dataframe = simple_project.export_repeating_instruments_events(format_type="df") + assert dataframe.empty + dataframe = simple_project.export_metadata(format_type="df") assert dataframe.empty