🤝 Resolve conflicts

.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

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
 

docs/api_reference/repeating.md

@@ -0,0 +1,5 @@
+# Repeating
+
+::: redcap.methods.repeating
+    selection:
+      inherited_members: true

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

pyproject.toml

@@ -45,7 +45,6 @@ mkdocs = "^1.2.3"
 mkdocs-material = "^8.1.3"
 mkdocstrings = "^0.17.0"
 pytest-doctestplus = "^0.11.2"
-typing-extensions = "^4.0.1"
 
 [tool.poetry.extras]
 data_science = ["pandas"]

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

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

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)

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

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
@@ -359,15 +362,15 @@ 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}
         """
         payload = self._initialize_import_payload(
             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

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

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,