v0.0.7: Expand to all domains (#36)

* added other domains to generate_included_concept_list

* added alias to the join

* added observation and device_exposure to spark_utils

* added cache_events when building NestedCohortBuilder

* used datetime to filter for the ehr records

* fixed the inded datetime for cabg

* fixed index date for atrial_fibrillation.py

* fixed index_date for coronary_artery_disease.py

* fixed the index date for ischemic_stroke.py

* fixed the index date for last_visit_discharged_home.py

* fixed the index date for type_two_diabietes.py

* fixed the person_id reference in the cohort definitions

* fixed the index dates for the patient outcome prediction tasks

* updated the index dates for the disease cohorts by using the condition_start_datetime

* updated the how the records are filtered

* fixed an alias for referencing condition_start_date

* removed filtering

* Revert "removed filtering"

This reverts commit 2dcb9137d49eec8eaf9828faf4e01acb64f42c2c.

* cache all ehr events to the disk for constructing cohorts

* added 0.1 second to the index date before we apply the filter to extract the features from the patient timelines

* updated the type two diabetes index date definition

* added a function to construct artificial visits for the problem list type of data

* added the logic for fixing the visit_occurrence_id in patient_events

* set visit_concept_id to 0 when the visit_occurrence_id is invalidated

* reconstruct visit_occurrence_ids for problem list events

* updated the logic for extracting features

* updated the index dates of the phenotype definitions

* added a timestamp format to to_timestamp

* convert the timestamp from utc to nyc

* removed time zone conversion

* set the index_date to visit_start_date + 23:59:00 for phenotypes if the condition_start_datetime occurred before the corresponding visit_start_datetime

* swtiched from date_add to the sql expression to keep the index_date as timestamp

* updated the test set up

* added optional caching for artificial visits

* Revert "updated the test set up"

This reverts commit e8962a8d4adcce8aeb47993fa5e33f6380c32d49.

* fixed the output of the cohort

* added an option to construct artificial visits for the problem list records that occur years ahead

* restored inpatient_att_type in generate_training_data

* updated the default value for date_filter: