update tapipy requirements

setup.cfg

@@ -29,9 +29,9 @@ install_requires =
     pytz
     requests
     simplejson
-    tapipy ==1.0.7
+    tapipy>=1.6
     Jinja2
-    jsonschema ==3.2.0
+    jsonschema
 
 [options.packages.find]
 where = src

src/vbr/api/logistics.py

@@ -216,7 +216,7 @@ def relocate_measurement(
         """Move a Measurement to a Container."""
         orig_measurement_container = measurement.container
         measurement.container = container.container_id
-        container = self.vbr_client.update_row(measurement)
+        measurement = self.vbr_client.update_row(measurement)
         DataEventApi.create_and_link(
             self,
             comment="Relocated to container {0}".format(container.local_id),

src/vbr/api/measurement.py

@@ -36,6 +36,7 @@ def create_measurement(
         status_id: int,
         volume: float = DEFAULT_VOLUME_ML,
         creation_timestr: str = None,
+        redcap_repeat_instance: int = None,
     ) -> Measurement:
         """Create a new Measurement."""
         # TODO - data_event
@@ -49,6 +50,7 @@ def create_measurement(
             status=status_id,
             volume=volume,
             creation_time=creation_timestr,
+            redcap_repeat_instance=redcap_repeat_instance,
         )
         try:
             return self.vbr_client.create_row(bs)[0]
@@ -66,6 +68,7 @@ def create_or_get_measurement_by_tracking_id(
         status_id: int,
         volume: float,
         creation_timestr: str = None,
+        redcap_repeat_instance: int = None,
     ) -> Measurement:
         """Create a Measurement or return existing with specified tracking_id."""
         try:
@@ -79,6 +82,7 @@ def create_or_get_measurement_by_tracking_id(
                 status_id,
                 volume,
                 creation_timestr,
+                redcap_repeat_instance
             )
         except Exception:
             return self.get_measurement_by_tracking_id(tracking_id)
@@ -154,9 +158,17 @@ def get_measurements_in_container(self, container: Container) -> List[Measuremen
             root_url="measurement", query=query, limit=1000000
         )
 
-    def get_measurements_in_biosample(self, biosample: Biosample) -> List[Measurement]:
+    def get_measurements_in_biosample(self, biosample: Biosample, redcap_repeat_instance) -> List[Measurement]:
         """Retrieve Measurements in a Biosample."""
-        query = {"biosample": {"operator": "=", "value": biosample.biosample_id}}
+        # PgREST doesn't handle =None queries well, patch:
+        if redcap_repeat_instance is not None:
+            query = {
+                    "biosample": {"operator": "=", "value": biosample.biosample_id},
+                    "redcap_repeat_instance": {"operator": "=", "value": redcap_repeat_instance}
+                    }
+        else:
+            query = {
+                "biosample": {"operator": "=", "value": biosample.biosample_id}}
         return self.vbr_client.query_rows(
             root_url="measurement", query=query, limit=1000000
         )

src/vbr/api/redcap.py

@@ -45,6 +45,17 @@ def get_redcap_record_by_biosample_and_instance(
 
         return self._get_row_from_table_with_query(redcap_form_name, query=query)
 
+    def get_redcap_record_by_subject_and_protocol(
+        self, redcap_form_name: str, subject_id: str, protocol_id: str
+        ) -> RcapTable:
+        """Retrieve a Biosample by subject and protocol IDs."""
+        redcap_form_name = 'rcap_'+redcap_form_name
+        query = {
+            "subject_id": {"operator": "=", "value": subject_id},
+            "protocol_id": {"operator": "=", "value": protocol_id}
+            }
+        return self._get_row_from_table_with_query(redcap_form_name, query=query)
+
     def update_redcap_record(
         self, redcap_form_name: str, redcap_record: RcapTable, rcap_row: RcapTable
         ) -> RcapTable:

src/vbr/tableclasses/__init__.py

@@ -14,6 +14,12 @@
         RcapConsentedParticipantInformation,
         RcapPatientDemographicsBaselineV03DemographicsI,
         RcapPatientDemographicsFullPart2V03Demographics,
+        RcapImagingItemsV01,
+        RcapImagingItemsV11,
+        RcapImagingMcc1V09,
+        RcapImagingMcc2V01,
+        RcapQstMcc1V03,
+        RcapPostconsentStudyPlanCrfV06
     )
 except ImportError:
     from .redcap.autogenerated import *

src/vbr/tableclasses/redcap/autogenerated/__init__.py

@@ -2,107 +2,60 @@
 """
 from .consented_participant_information import RcapConsentedParticipantInformation
 from .postconsent_study_plan_crf_v06 import RcapPostconsentStudyPlanCrfV06
-from .patient_demographics_baseline_v03_demographics_i import (
-    RcapPatientDemographicsBaselineV03DemographicsI,
-)
-from .other_pain_treatments_v3_other_treatments import (
-    RcapOtherPainTreatmentsV3OtherTreatments,
-)
+from .patient_demographics_baseline_v03_demographics_i import RcapPatientDemographicsBaselineV03DemographicsI
+from .other_pain_treatments_v3_other_treatments import RcapOtherPainTreatmentsV3OtherTreatments
 from .other_medical_surgical_treatments_ii import RcapOtherMedicalSurgicalTreatmentsIi
-from .patient_global_impression_of_change_pgic import (
-    RcapPatientGlobalImpressionOfChangePgic,
-)
-from .bpisf_the_brief_pain_inventory_v23_short_form_bpi import (
-    RcapBpisfTheBriefPainInventoryV23ShortFormBpi,
-)
+from .patient_global_impression_of_change_pgic import RcapPatientGlobalImpressionOfChangePgic
+from .bpisf_the_brief_pain_inventory_v23_short_form_bpi import RcapBpisfTheBriefPainInventoryV23ShortFormBpi
 from .symptom_severity_index_v10_ssi import RcapSymptomSeverityIndexV10Ssi
 from .pain_detect_questionnaire_pdq import RcapPainDetectQuestionnairePdq
-from .knee_injury_osteoarthritis_outcome_score_koos12 import (
-    RcapKneeInjuryOsteoarthritisOutcomeScoreKoos12,
-)
+from .danish_thoracic_surgery_questionnaire_v02 import RcapDanishThoracicSurgeryQuestionnaireV02
+from .deep_breathing_and_coughing_v02 import RcapDeepBreathingAndCoughingV02
 from .promis_sf_v12_physical_function_8b import RcapPromisSfV12PhysicalFunction8B
-from .promis_sf_v10_sleep_disturbance_6a_sleep_i import (
-    RcapPromisSfV10SleepDisturbance6ASleepI,
-)
+from .promis_sf_v10_sleep_disturbance_6a_sleep_i import RcapPromisSfV10SleepDisturbance6ASleepI
 from .painsleep_duration_sleep_ii import RcapPainsleepDurationSleepIi
 from .promis_sf_v10_fatigue_7a import RcapPromisSfV10Fatigue7A
-from .generalized_anxiety_disorder_7_item_gad7_scale_sco import (
-    RcapGeneralizedAnxietyDisorder7ItemGad7ScaleSco,
-)
-from .patient_health_questionnaire_depression_scale_phq import (
-    RcapPatientHealthQuestionnaireDepressionScalePhq,
-)
-from .pain_catastrophizing_questionnaire_pcs6 import (
-    RcapPainCatastrophizingQuestionnairePcs6,
-)
-from .fearavoidance_beliefs_questionnaire_v03_fabq import (
-    RcapFearavoidanceBeliefsQuestionnaireV03Fabq,
-)
+from .generalized_anxiety_disorder_7_item_gad7_scale_sco import RcapGeneralizedAnxietyDisorder7ItemGad7ScaleSco
+from .patient_health_questionnaire_depression_scale_phq import RcapPatientHealthQuestionnaireDepressionScalePhq
+from .pain_catastrophizing_questionnaire_pcs6 import RcapPainCatastrophizingQuestionnairePcs6
+from .fearavoidance_beliefs_questionnaire_v03_fabq import RcapFearavoidanceBeliefsQuestionnaireV03Fabq
 from .pain_resilience_scale_prs import RcapPainResilienceScalePrs
 from .promis_sf_v20_emotional_support_6a import RcapPromisSfV20EmotionalSupport6A
-from .promis_sf_v20_informational_support_6a import (
-    RcapPromisSfV20InformationalSupport6A,
-)
-from .multidimensional_inventory_of_subjective_cognitive import (
-    RcapMultidimensionalInventoryOfSubjectiveCognitive,
-)
-from .adverse_childhood_experience_questionnaire_ace import (
-    RcapAdverseChildhoodExperienceQuestionnaireAce,
-)
+from .promis_sf_v20_informational_support_6a import RcapPromisSfV20InformationalSupport6A
+from .multidimensional_inventory_of_subjective_cognitive import RcapMultidimensionalInventoryOfSubjectiveCognitive
+from .adverse_childhood_experience_questionnaire_ace import RcapAdverseChildhoodExperienceQuestionnaireAce
 from .taps1 import RcapTaps1
 from .taps2 import RcapTaps2
 from .opioid_use_baseline_v10_opioid_use_i import RcapOpioidUseBaselineV10OpioidUseI
-from .opioid_use_acute_followup_v10_opioid_use_ii import (
-    RcapOpioidUseAcuteFollowupV10OpioidUseIi,
-)
-from .opioid_use_longterm_followup_v10_opioid_use_iii import (
-    RcapOpioidUseLongtermFollowupV10OpioidUseIii,
-)
-from .opioid_side_effects_and_likeability_v03_side_effec import (
-    RcapOpioidSideEffectsAndLikeabilityV03SideEffec,
-)
-from .opioid_and_pain_control_satisfaction_v02_satisfact import (
-    RcapOpioidAndPainControlSatisfactionV02Satisfact,
-)
+from .opioid_use_acute_followup_v10_opioid_use_ii import RcapOpioidUseAcuteFollowupV10OpioidUseIi
+from .opioid_use_longterm_followup_v10_opioid_use_iii import RcapOpioidUseLongtermFollowupV10OpioidUseIii
+from .opioid_side_effects_and_likeability_v03_side_effec import RcapOpioidSideEffectsAndLikeabilityV03SideEffec
+from .opioid_and_pain_control_satisfaction_v02_satisfact import RcapOpioidAndPainControlSatisfactionV02Satisfact
 from .current_opioid_misuse_v02_comm import RcapCurrentOpioidMisuseV02Comm
-from .rapid_assessment_of_physical_activity_v10_rapa import (
-    RcapRapidAssessmentOfPhysicalActivityV10Rapa,
-)
+from .rapid_assessment_of_physical_activity_v10_rapa import RcapRapidAssessmentOfPhysicalActivityV10Rapa
 from .general_sensory_sensitivity_v02_gss8 import RcapGeneralSensorySensitivityV02Gss8
 from .the_big_five_inventory_bfi2s import RcapTheBigFiveInventoryBfi2S
-from .patient_demographics_full_part_2_v03_demographics import (
-    RcapPatientDemographicsFullPart2V03Demographics,
-)
-from .selfadministered_comorbidity_questionnaire_v4_scq import (
-    RcapSelfadministeredComorbidityQuestionnaireV4Scq,
-)
+from .patient_demographics_full_part_2_v03_demographics import RcapPatientDemographicsFullPart2V03Demographics
+from .selfadministered_comorbidity_questionnaire_v4_scq import RcapSelfadministeredComorbidityQuestionnaireV4Scq
 from .expectation_items_v12 import RcapExpectationItemsV12
-from .acute_phase_trajectory_items_v05_acute_daily import (
-    RcapAcutePhaseTrajectoryItemsV05AcuteDaily,
-)
-from .daily_items_6_mo_v03_6month_daily import RcapDailyItems6MoV036MonthDaily
-from .month_remote_followup_v20_12month_followup import (
-    RcapMonthRemoteFollowupV2012MonthFollowup,
-)
-from .functional_testing import RcapFunctionalTesting
+from .acute_phase_trajectory_items_v05_acute_daily import RcapAcutePhaseTrajectoryItemsV05AcuteDaily
+from .acute_phase_trajectory_items_v01_6month_daily import RcapAcutePhaseTrajectoryItemsV016MonthDaily
+from .month_remote_followup_v20_12month_followup import RcapMonthRemoteFollowupV2012MonthFollowup
+from .functional_testing_mcc2_v01 import RcapFunctionalTestingMcc2V01
 from .qst_mcc1_v03 import RcapQstMcc1V03
 from .current_medications_v02 import RcapCurrentMedicationsV02
-from .blood_sample_collection_and_processing_crf import (
-    RcapBloodSampleCollectionAndProcessingCrf,
-)
-from .imaging_items_v11 import RcapImagingItemsV11
-from .imaging_mcc1_v09 import RcapImagingMcc1V09
+from .blood_sample_collection_and_processing_crf import RcapBloodSampleCollectionAndProcessingCrf
+from .imaging_items_v01 import RcapImagingItemsV01
+from .imaging_mcc2_v01 import RcapImagingMcc2V01
+from .baseline_visit_reset import RcapBaselineVisitReset
 from .study_visit_feedback_v03 import RcapStudyVisitFeedbackV03
+from .form_uploads import RcapFormUploads
 from .patient_encounters import RcapPatientEncounters
 from .reportable_eventdeviation_v03 import RcapReportableEventdeviationV03
 from .early_withdrawal_v04 import RcapEarlyWithdrawalV04
-from .danish_thoracic_surgery_questionnaire_v02 import (
-    RcapDanishThoracicSurgeryQuestionnaireV02,
-)
-from .deep_breathing_and_coughing_v02 import RcapDeepBreathingAndCoughingV02
-from .acute_phase_trajectory_items_v01_6month_daily import (
-    RcapAcutePhaseTrajectoryItemsV016MonthDaily,
-)
-from .functional_testing_mcc2_v01 import RcapFunctionalTestingMcc2V01
-from .imaging_items_v01 import RcapImagingItemsV01
-from .imaging_mcc2_v01 import RcapImagingMcc2V01
+from .knee_injury_osteoarthritis_outcome_score_koos12 import RcapKneeInjuryOsteoarthritisOutcomeScoreKoos12
+from .daily_items_6_mo_v03_6month_daily import RcapDailyItems6MoV036MonthDaily
+from .functional_testing import RcapFunctionalTesting
+from .imaging_items_v11 import RcapImagingItemsV11
+from .imaging_mcc1_v09 import RcapImagingMcc1V09
+from .visit_reset_archive import RcapVisitResetArchive

src/vbr/tableclasses/redcap/autogenerated/acute_phase_trajectory_items_v01_6month_daily.py

@@ -1,4 +1,4 @@
-"""Autogenerated 2021-11-16T11:37:36.593350 by redcap_classfiles.py
+"""Autogenerated 2024-09-18T10:32:28.909725 by redcap_classfiles.py
 """
 
 from ....pgrest import *
@@ -7,19 +7,16 @@
 
 from ..rcaptable import RcapTable
 
-__all__ = ["RcapAcutePhaseTrajectoryItemsV016MonthDaily"]
+__all__ = ['RcapAcutePhaseTrajectoryItemsV016MonthDaily']
 
 
 class RcapAcutePhaseTrajectoryItemsV016MonthDaily(RcapTable):
-    """Acute Phase Trajectory Items V01 6Month Daily"""
-
-    __redcap_form_name = "acute_phase_trajectory_items_v01_6month_daily"
-    acute_phase_trajectory_items_v01_6month_daily_id = (
-        Constants.SERIAL_PRIMARY_KEY_COLUMN
-    )
+    """Acute Phase Trajectory Items V01 6Month Daily
+    """
+    __redcap_form_name = 'acute_phase_trajectory_items_v01_6month_daily'
+    acute_phase_trajectory_items_v01_6month_daily_id = Constants.SERIAL_PRIMARY_KEY_COLUMN
     acute_phase_trajectory_items_v01_6month_daily_complete = Column(
-        Integer, ForeignKey("status.status_id")
-    )
+        Integer, ForeignKey('status.status_id'))
     # Date entered
     # Field Type: text
     # Choices: N/A
@@ -48,11 +45,15 @@ class RcapAcutePhaseTrajectoryItemsV016MonthDaily(RcapTable):
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj24medyn = Column(Boolean, nullable=True, comments=None)
-    # 1. Over-the-counter pain relievers (e.g., acetaminophen Tylen...
+    # 1. Acetaminophen (Tylenol)
+    # Field Type: radio
+    # Choices: Y, Yes | N, No
+    traj24medlist1tylenol = Column(Boolean, nullable=True, comments=None)
+    # 2. Over-the-counter or prescription non‐steroidal pain reliev...
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj24medlist1otc = Column(Boolean, nullable=True, comments=None)
-    # 2. Opioid pain relievers (e.g., oxycodone, Percocet, Nucynta,...
+    # 3. Opioid pain relievers (e.g., oxycodone, Percocet, Nucynta,...
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj24medlist2opioid = Column(Boolean, nullable=True, comments=None)
@@ -64,7 +65,7 @@ class RcapAcutePhaseTrajectoryItemsV016MonthDaily(RcapTable):
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj24medlist4gaba = Column(Boolean, nullable=True, comments=None)
-    # Duloxetine (Cymbalta) or venlafaxine (Wellbutrin)
+    # Duloxetine (Cymbalta) or venlafaxine (Effexor)
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj24medlist5dulox = Column(Boolean, nullable=True, comments=None)

src/vbr/tableclasses/redcap/autogenerated/acute_phase_trajectory_items_v05_acute_daily.py

@@ -1,4 +1,4 @@
-"""Autogenerated 2021-11-16T11:37:36.538059 by redcap_classfiles.py
+"""Autogenerated 2024-09-18T10:32:28.908211 by redcap_classfiles.py
 """
 
 from ....pgrest import *
@@ -7,32 +7,29 @@
 
 from ..rcaptable import RcapTable
 
-__all__ = ["RcapAcutePhaseTrajectoryItemsV05AcuteDaily"]
+__all__ = ['RcapAcutePhaseTrajectoryItemsV05AcuteDaily']
 
 
 class RcapAcutePhaseTrajectoryItemsV05AcuteDaily(RcapTable):
-    """Acute Phase Trajectory Items V05 Acute Daily"""
-
-    __redcap_form_name = "acute_phase_trajectory_items_v05_acute_daily"
-    acute_phase_trajectory_items_v05_acute_daily_id = (
-        Constants.SERIAL_PRIMARY_KEY_COLUMN
-    )
+    """Acute Phase Trajectory Items V05 Acute Daily
+    """
+    __redcap_form_name = 'acute_phase_trajectory_items_v05_acute_daily'
+    acute_phase_trajectory_items_v05_acute_daily_id = Constants.SERIAL_PRIMARY_KEY_COLUMN
     acute_phase_trajectory_items_v05_acute_daily_complete = Column(
-        Integer, ForeignKey("status.status_id")
-    )
-    # Ignored multiline Field Name in Data Dictionary
+        Integer, ForeignKey('status.status_id'))
+    # Date entered
     # Field Type: text
     # Choices: N/A
     traj04wkenterdate = Column(String, nullable=True, comments=None)
-    # 1. Please rate your chest pain by choosing the number that be...
+    # 1. Please rate your knee pain by choosing the number that bes...
     # Field Type: radio
     # Choices: 0, 0 No pain | 1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5 | 6, 6 | 7, 7 | 8, 8 | 9, 9 | 10, 10 Pain as bad as you can imagine
     traj04worstpainscl = Column(Integer, nullable=True, comments=None)
-    # 2. Please rate your chest pain by choosing the number that be...
+    # 2. Please rate your knee pain by choosing the number that bes...
     # Field Type: radio
     # Choices: 0, 0 No pain | 1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5 | 6, 6 | 7, 7 | 8, 8 | 9, 9 | 10, 10 Pain as bad as you can imagine
     traj04avgpainscl = Column(Integer, nullable=True, comments=None)
-    # 3. Please rate how much your chest pain has interfered with y...
+    # 3. Please rate how much your knee pain has interfered with yo...
     # Field Type: radio
     # Choices: 0, 0 Did not interfere | 1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5 | 6, 6 | 7, 7 | 8, 8 | 9, 9 | 10, 10 Completely interfered
     traj04painintfactivscl = Column(Integer, nullable=True, comments=None)
@@ -60,7 +57,11 @@ class RcapAcutePhaseTrajectoryItemsV05AcuteDaily(RcapTable):
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj04medyn = Column(Boolean, nullable=True, comments=None)
-    # Over-the-counter pain relievers (e.g., acetaminophen Tylenol,...
+    # Acetaminophen (Tylenol)
+    # Field Type: radio
+    # Choices: Y, Yes | N, No
+    traj04medlisttylenol = Column(Boolean, nullable=True, comments=None)
+    # Over-the-counter or prescription non‐steroidal pain relievers...
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj04medlist1otc = Column(Boolean, nullable=True, comments=None)
@@ -76,7 +77,7 @@ class RcapAcutePhaseTrajectoryItemsV05AcuteDaily(RcapTable):
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj04medlist4gaba = Column(Boolean, nullable=True, comments=None)
-    # Duloxetine (Cymbalta) or venlafaxine (Wellbutrin)
+    # Duloxetine (Cymbalta) or venlafaxine (Effexor)
     # Field Type: radio
     # Choices: Y, Yes | N, No
     traj04medlist5dulox = Column(Boolean, nullable=True, comments=None)