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feat: add min_issue to covidcast meta data #236

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feat: add min_issue to covidcast meta data #236

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f723beb
feat: add min_issue to covidcast meta data
sgratzl Oct 7, 2020
f177818
Merge remote-tracking branch 'origin/main' into sgratzl/min_issue
sgratzl Oct 12, 2020
6f01aa5
fix: update min issue computation
sgratzl Oct 12, 2020
b2fce76
fix: python client test
sgratzl Oct 12, 2020
a581f0b
refactor: simpliy lookup
sgratzl Oct 15, 2020
06aab57
fix: test
sgratzl Oct 15, 2020
a85adbb
Merge remote-tracking branch 'origin/main' into sgratzl/min_issue
sgratzl Oct 21, 2020
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1 change: 1 addition & 0 deletions docs/api/covidcast_meta.md
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ None required.
| `epidata[].max_value` | maximum value | float |
| `epidata[].mean_value` | mean of value | float |
| `epidata[].stdev_value` | standard deviation of value | float |
| `epidata[].min_issue` | earliest date data was issued (e.g., 20200710) | integer |
| `epidata[].max_issue` | most recent date data was issued (e.g., 20200710) | integer |
| `epidata[].min_lag` | smallest lag from observation to issue, in `time_type` units | integer |
| `epidata[].max_lag` | largest lag from observation to issue, in `time_type` units | integer |
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1 change: 1 addition & 0 deletions integrations/acquisition/covidcast/test_covidcast_meta_caching.py
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Expand Up @@ -99,6 +99,7 @@ def test_caching(self):
'max_value': 1,
'mean_value': 1,
'stdev_value': 0,
'min_issue': 20200423,
'max_issue': 20200423,
'min_lag': 0,
'max_lag': 1,
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5 changes: 3 additions & 2 deletions integrations/client/test_delphi_epidata.py
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Expand Up @@ -46,7 +46,7 @@ def tearDown(self):
def test_covidcast(self):
"""Test that the covidcast endpoint returns expected data."""
self.maxDiff=None

# insert dummy data
self.cur.execute('''
insert into covidcast values
Expand Down Expand Up @@ -123,7 +123,7 @@ def test_covidcast(self):
}],
'message': 'success',
})

# fetch data, without specifying issue or lag
response_1 = Epidata.covidcast(
'src', 'sig', 'day', 'county', 20200414, '01234')
Expand Down Expand Up @@ -258,6 +258,7 @@ def test_covidcast_meta(self):
'mean_value': 6.5,
'stdev_value': 0.5,
'last_update': 345,
'min_issue': 20200416,
'max_issue': 20200416,
'min_lag': 1,
'max_lag': 2,
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3 changes: 3 additions & 0 deletions integrations/server/test_covidcast_meta.py
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Expand Up @@ -67,6 +67,7 @@ def test_round_trip(self):
'mean_value': 15,
'stdev_value': 5,
'last_update': 123,
'min_issue': 2,
'max_issue': 2,
'min_lag': 0,
'max_lag': 0,
Expand Down Expand Up @@ -116,6 +117,7 @@ def test_filter(self):
'mean_value': 15,
'stdev_value': 5,
'last_update': 123,
'min_issue': 2,
'max_issue': 2,
'min_lag': 0,
'max_lag': 0,
Expand Down Expand Up @@ -235,6 +237,7 @@ def test_suppress_work_in_progress(self):
'mean_value': 15,
'stdev_value': 5,
'last_update': 123,
'min_issue': 2,
'max_issue': 2,
'min_lag': 0,
'max_lag': 0,
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11 changes: 6 additions & 5 deletions src/acquisition/covidcast/database.py
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Expand Up @@ -162,12 +162,12 @@ def insert_or_update_batch(self, cc_rows, batch_size=2**20, commit_partial=False
SET `is_latest_issue`=0
'''
set_is_latest_issue_sql = f'''
UPDATE
UPDATE
(
SELECT `source`, `signal`, `time_type`, `geo_type`, `time_value`, `geo_value`, MAX(`issue`) AS `issue`
FROM
(
SELECT DISTINCT `source`, `signal`, `time_type`, `geo_type`, `time_value`, `geo_value`
SELECT DISTINCT `source`, `signal`, `time_type`, `geo_type`, `time_value`, `geo_value`
FROM `{tmp_table_name}`
) AS TMP
LEFT JOIN `covidcast`
Expand All @@ -176,7 +176,7 @@ def insert_or_update_batch(self, cc_rows, batch_size=2**20, commit_partial=False
) AS TMP
LEFT JOIN `covidcast`
USING (`source`, `signal`, `time_type`, `geo_type`, `time_value`, `geo_value`, `issue`)
SET `is_latest_issue`=1
SET `is_latest_issue`=1
'''

# TODO: ^ do we want to reset `direction_updated_timestamp` and `direction` in the duplicate key case?
Expand Down Expand Up @@ -333,7 +333,7 @@ def get_all_record_values_of_timeseries_with_potentially_stale_direction(self, t
# A query that selects all rows from `covidcast` that have latest issue-date
# for any (time-series-key, time_value) with time_type='day'.
latest_issues_sql = f'''
SELECT
SELECT
`id`,
`source`,
`signal`,
Expand Down Expand Up @@ -576,6 +576,7 @@ def get_covidcast_meta(self):
ROUND(AVG(`value`),7) AS `mean_value`,
ROUND(STD(`value`),7) AS `stdev_value`,
MAX(`value_updated_timestamp`) AS `last_update`,
MIN(`issue`) as `min_issue`,
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i believe this is not going to work as intended, and instead will show the issue date of the least-recently-updated of the issues in a group, which i would argue is meaningless (plz correct me if im wrong). i think it will require a MIN(issue) inside the sub-SELECT and appropriate handling outside of that.

also, some non-trivial test cases would be nice, with different issue values.

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true, I will think about it how to fix it. Moreover, we can think of using the is_latest_issue to find the max issue

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@melange396 can you take a look at the new statements. I split it into two, since I couldn't think of a fast way to handle both cases at the same time. Moreover, I switched the nested statement to the is_latest_issue flag. It is not that easy to test for me, since I don't have access to the real database but just local test data

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i suppose this will work, but the old SQL query would have done the trick if you added min(issue) min_issue`` to the nested select... i think that would be preferable to adding a bunch of extra lines unless you can think of another benefit that justifies the extra complexity

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yes but I think this version should be more efficient using is_latest_issue instead of a join

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after wrestling with and waiting for long-duration queries for the past week, i think it might be wise to test the performance of the one-query vs two-query approaches on the staging server. i can certainly help do this if necessary.

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Apologies for being so late to this conversation.

The use case for min_issue is briefly described in the source issue for this PR, but the jist is this: A researcher is constructing as_of queries and wants to know the earliest date they can pass in and still expect a non-nil result. This means that min_issue must not be restricted to rows with is_latest_issue=1, since that would hide issues which are not the most recent but nevertheless accessible using as_of.

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i will go ahead and try this and other variants out on the staging copy of the database to check performance and runtimes

MAX(`issue`) as `max_issue`,
MIN(`lag`) as `min_lag`,
MAX(`lag`) as `max_lag`
Expand Down Expand Up @@ -621,7 +622,7 @@ def get_covidcast_meta(self):
meta.extend(list(dict(zip(self._cursor.column_names,x)) for x in self._cursor))

return meta

def update_covidcast_meta_cache(self, metadata):
"""Updates the `covidcast_meta_cache` table."""

Expand Down