Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add ETL timestamp to completion table, make it non-unique #353

Merged
merged 1 commit into from
Oct 28, 2024
Merged

Add ETL timestamp to completion table, make it non-unique #353

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 7 additions & 1 deletion cumulus_etl/completion/schema.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,11 @@ def completion_format_args() -> dict:
"""Returns kwargs to pass to the Format class initializer of your choice"""
return {
"dbname": COMPLETION_TABLE,
"uniqueness_fields": {"table_name", "group_name"},
# These fields altogether basically guarantee that we never collide.
# (i.e. that every 'merge' is really an 'insert')
# That's intentional - we want this table to be a bit of a historical log.
# (We couldn't have no uniqueness fields -- delta lake doesn't like that.)
"uniqueness_fields": {"table_name", "group_name", "export_time", "etl_time"},
Comment on lines -16 to +20
Copy link
Contributor Author

@mikix mikix Oct 28, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is the change I was most interested in making. Some considerations:

  • Growth of this table - I don't think it's too bad? This will be one entry per FHIR ETL'd resource every run. At BCH, we have about 120 groups, across 12 resources (1440 entries assuming we never ETL'd something twice, which i'm sure we did a bit). But point is, this table will always be quite small and definitely smaller than the source tables. I think the debugging history is worth it. (We already kept some of this info in JSON log files in S3, but this is now much easier to inspect)
    • In fact, I just checked and our Cerner output folder has 1632 JobConfig entries (which is how many times the ETL has been run) - but usually for a single resource, so that's probably a close count to how big this table would be.
  • Can the Library side handle this change already? Yes - I looked at the code and did a quick test. Its existing completion tracking code handles these rows not being table-group unique.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

just confirming - for everything before this change, we basically have one big group?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Naw more like we only kept records of each group & resource combo once. Like if I ETL patients from group Cohort1 yesterday, then I do a new export and ETL Cohort1 again with new data, we'd only keep track of the latest one.

}


Expand Down Expand Up @@ -47,6 +51,8 @@ def completion_schema() -> pyarrow.Schema:
pyarrow.field("export_time", pyarrow.string()),
pyarrow.field("export_url", pyarrow.string()),
pyarrow.field("etl_version", pyarrow.string()),
# See note above for why this isn't a pyarrow.timestamp() field.
pyarrow.field("etl_time", pyarrow.string()),
]
)

Expand Down
5 changes: 3 additions & 2 deletions cumulus_etl/etl/config.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ def __init__(
self._output_format = output_format
self.dir_errors = dir_errors
self.client = client
self.timestamp = common.timestamp_filename(timestamp)
self.timestamp = timestamp
self.hostname = gethostname()
self.comment = comment or ""
self.batch_size = batch_size
Expand All @@ -67,7 +67,8 @@ def path_config(self) -> str:
return os.path.join(self.dir_job_config(), "job_config.json")

def dir_job_config(self) -> str:
path = self._output_root.joinpath(f"JobConfig/{self.timestamp}")
timestamp_dir = common.timestamp_filename(self.timestamp)
path = self._output_root.joinpath(f"JobConfig/{timestamp_dir}")
self._output_root.makedirs(path)
return path

Expand Down
1 change: 1 addition & 0 deletions cumulus_etl/etl/tasks/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -272,6 +272,7 @@ def _update_completion_table(self) -> None:
"export_time": self.task_config.export_datetime.isoformat(),
"export_url": self.task_config.export_url,
"etl_version": cumulus_etl.__version__,
"etl_time": self.task_config.timestamp.isoformat(),
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

What time to use here was a small choice. I initially had "whatever time it is right now as we're writing this completion entry" - but then I switched it to the global ETL timestamp, which gets set early in the ETL run. This means that the timestamp is a little less accurate to the exact time the entries get uploaded to Athena, but... we gain the ability to check which resources have the same timestamp (i.e. were in the same run) and we gain the ability to go look up the log files in S3 because they use the same global timestamp in their filename.

}
for output in self.outputs
if not output.get_name(self).startswith("etl__")
Expand Down
2 changes: 1 addition & 1 deletion tests/data/covid/output/etl__completion/etl__completion.000.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "covid_symptom__nlp_results", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "covid_symptom__nlp_results", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/covid/term-exists/etl__completion/etl__completion.000.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "covid_symptom__nlp_results_term_exists", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "covid_symptom__nlp_results_term_exists", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/hftest/output/etl__completion/etl__completion.000.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "hftest__summary", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "hftest__summary", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/i2b2/output/etl__completion/etl__completion.000.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "encounter", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "encounter", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/i2b2/output/etl__completion/etl__completion.001.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "patient", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "patient", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/i2b2/output/etl__completion/etl__completion.002.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "condition", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "condition", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/i2b2/output/etl__completion/etl__completion.003.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "documentreference", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "documentreference", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
4 changes: 2 additions & 2 deletions tests/data/i2b2/output/etl__completion/etl__completion.004.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
{"table_name": "medication", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "medicationrequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "medication", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
{"table_name": "medicationrequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/i2b2/output/etl__completion/etl__completion.005.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "observation", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "observation", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/batched-output/etl__completion/etl__completion.000.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "encounter", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "encounter", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/batched-output/etl__completion/etl__completion.001.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "patient", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "patient", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/batched-output/etl__completion/etl__completion.002.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "condition", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "condition", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/batched-output/etl__completion/etl__completion.003.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "documentreference", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "documentreference", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
4 changes: 2 additions & 2 deletions tests/data/simple/batched-output/etl__completion/etl__completion.004.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
{"table_name": "medication", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "medicationrequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "medication", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
{"table_name": "medicationrequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/batched-output/etl__completion/etl__completion.005.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "observation", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "observation", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/batched-output/etl__completion/etl__completion.006.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "procedure", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "procedure", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/batched-output/etl__completion/etl__completion.007.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "servicerequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "servicerequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.000.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "encounter", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "encounter", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.001.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "patient", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "patient", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.002.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "allergyintolerance", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "allergyintolerance", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.003.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "condition", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "condition", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.004.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "device", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "device", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.005.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "diagnosticreport", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "diagnosticreport", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.006.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "documentreference", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "documentreference", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.007.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "immunization", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "immunization", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
4 changes: 2 additions & 2 deletions tests/data/simple/output/etl__completion/etl__completion.008.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
{"table_name": "medication", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "medicationrequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "medication", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
{"table_name": "medicationrequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.009.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "observation", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "observation", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.010.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "procedure", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "procedure", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
2 changes: 1 addition & 1 deletion tests/data/simple/output/etl__completion/etl__completion.011.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"table_name": "servicerequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test"}
{"table_name": "servicerequest", "group_name": "test-group", "export_time": "2020-10-13T12:00:20-05:00", "etl_version": "1.0.0+test", "etl_time": "2021-09-14T21:23:45+00:00"}
1 change: 1 addition & 0 deletions tests/etl/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,7 @@ def setUp(self) -> None:
"ndjson",
"ndjson",
client,
timestamp=common.datetime_now(),
batch_size=5,
dir_errors=self.errors_dir,
export_group_name="test-group",
Expand Down
13 changes: 11 additions & 2 deletions tests/etl/test_tasks.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,9 @@ async def test_encounter_completion(self):
self.assertFalse(comp_enc_format.update_existing)

self.assertEqual("etl__completion", comp_format.dbname)
self.assertEqual({"table_name", "group_name"}, comp_format.uniqueness_fields)
self.assertEqual(
{"table_name", "group_name", "export_time", "etl_time"}, comp_format.uniqueness_fields
)
self.assertTrue(comp_format.update_existing)

self.assertEqual(2, comp_enc_format.write_records.call_count)
Expand Down Expand Up @@ -240,6 +242,7 @@ async def test_encounter_completion(self):
"export_time": "2012-10-10T05:30:12+00:00",
"export_url": self.export_url,
"etl_version": "1.0.0+test",
"etl_time": "2021-09-14T21:23:45+00:00",
}
],
comp_batch.rows,
Expand Down Expand Up @@ -276,13 +279,15 @@ async def test_medication_completion(self):
"export_time": "2012-10-10T05:30:12+00:00",
"export_url": self.export_url,
"etl_version": "1.0.0+test",
"etl_time": "2021-09-14T21:23:45+00:00",
},
{
"table_name": "medicationrequest",
"group_name": "test-group",
"export_time": "2012-10-10T05:30:12+00:00",
"export_url": self.export_url,
"etl_version": "1.0.0+test",
"etl_time": "2021-09-14T21:23:45+00:00",
},
],
comp_batch.rows,
Expand Down Expand Up @@ -330,6 +335,7 @@ async def test_allow_empty_group(self):
"export_time": "2012-10-10T05:30:12+00:00",
"export_url": self.export_url,
"etl_version": "1.0.0+test",
"etl_time": "2021-09-14T21:23:45+00:00",
}
],
comp_format.write_records.call_args[0][0].rows,
Expand Down Expand Up @@ -420,7 +426,10 @@ async def test_external_medications(self, mock_download):
uniqueness_fields=None,
update_existing=True,
),
mock.call(dbname="etl__completion", uniqueness_fields={"group_name", "table_name"}),
mock.call(
dbname="etl__completion",
uniqueness_fields={"group_name", "table_name", "export_time", "etl_time"},
),
],
self.create_formatter_mock.call_args_list,
)
Expand Down
1 change: 1 addition & 0 deletions tests/loaders/ndjson/test_bulk_export.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -922,6 +922,7 @@ async def test_successful_etl_bulk_export(self):
"export_time": "2015-02-07T13:28:17+02:00",
"export_url": f"{self.fhir_url}/$export?_type=Patient",
"etl_version": "1.0.0+test",
"etl_time": "2021-09-14T21:23:45+00:00",
},
common.read_json(f"{tmpdir}/output/etl__completion/etl__completion.000.ndjson"),
)
Expand Down