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Revert "Update flusurv schema and docs with new age, sex, and race groups" #1426

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May 8, 2024
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Revert "Update flusurv schema and docs with new age, sex, and race groups" #1426

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50 changes: 16 additions & 34 deletions docs/api/flusurv.md
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Expand Up @@ -52,40 +52,22 @@ If neither is specified, the current issues are used.

## Response

| Field | Description | Type |
|---|---|---|
| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
| `epidata` | list of results | array of objects |
| `epidata[].release_date` | the date when this record was first published by the CDC | string |
| `epidata[].location` | the name of the catchment (e.g. 'network_all', 'CA', 'NY_albany' | string |
| `epidata[].issue` | the epiweek of publication (e.g. issue 201453 includes epiweeks up to and including 2014w53, but not 2015w01 or following) | integer |
| `epidata[].epiweek` | the epiweek during which the data was collected | integer |
| `epidata[].lag` | number of weeks between `epiweek` and `issue` | integer |
| `epidata[].rate_age_0` | hospitalization rate for ages 0-4 | float |
| `epidata[].rate_age_1` | hospitalization rate for ages 5-17 | float |
| `epidata[].rate_age_2` | hospitalization rate for ages 18-49 | float |
| `epidata[].rate_age_3` | hospitalization rate for ages 50-64 | float |
| `epidata[].rate_age_4` | hospitalization rate for ages 65+ | float |
| `epidata[].rate_overall` | overall hospitalization rate | float |
| `epidata[].rate_age_5` | hospitalization rate for ages 65-74 | float |
| `epidata[].rate_age_6` | hospitalization rate for ages 75-84 | float |
| `epidata[].rate_age_7` | hospitalization rate for ages 85+ | float |
| `epidata[].rate_age_18t29` | hospitalization rate for ages 18 to 29 | float |
| `epidata[].rate_age_30t39` | hospitalization rate for ages 30 to 39 | float |
| `epidata[].rate_age_40t49` | hospitalization rate for ages 40 to 49 | float |
| `epidata[].rate_age_5t11` | hospitalization rate for ages 5 to 11 | float |
| `epidata[].rate_age_12t17` | hospitalization rate for ages 12 to 17 | float |
| `epidata[].rate_age_lt18` | hospitalization rate for ages <18 | float |
| `epidata[].rate_age_gte18` | hospitalization rate for ages >=18 | float |
| `epidata[].rate_race_white` | hospitalization rate for white people | float |
| `epidata[].rate_race_black` | hospitalization rate for black people | float |
| `epidata[].rate_race_hisp` | hospitalization rate for Hispanic/Latino people | float |
| `epidata[].rate_race_asian` | hospitalization rate for Asian people | float |
| `epidata[].rate_race_natamer` | hospitalization rate for American Indian/Alaskan Native people | float |
| `epidata[].rate_sex_male` | hospitalization rate for males | float |
| `epidata[].rate_sex_female` | hospitalization rate for females | float |
| `epidata[].season` | indicates the start and end years of the winter flu season in the format YYYY-YY (e.g. 2022-23 indicates the flu season running late 2022 through early 2023) | string |
| `message` | `success` or error message | string |
| Field | Description | Type |
|--------------------------|-----------------------------------------------------------------|------------------|
| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
| `epidata` | list of results | array of objects |
| `epidata[].release_date` | | string |
| `epidata[].location` | | string |
| `epidata[].issue` | | integer |
| `epidata[].epiweek` | | integer |
| `epidata[].lag` | | integer |
| `epidata[].rate_age_0` | | float |
| `epidata[].rate_age_1` | | float |
| `epidata[].rate_age_2` | | float |
| `epidata[].rate_age_3` | | float |
| `epidata[].rate_age_4` | | float |
| `epidata[].rate_overall` | | float |
| `message` | `success` or error message | string |

Notes:
* The `flusurv` age groups are, in general, not the same as the ILINet
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39 changes: 36 additions & 3 deletions src/acquisition/flusurv/flusurv_update.py
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Expand Up @@ -19,9 +19,42 @@
=== Data Dictionary ===
=======================

`flusurv` is the table where US flu hospitalization rates are stored. See
`strc/ddl/fluview.sql` for the `flusurv` schema. See `docs/api/flusurv.md` for
field descriptions.
`flusurv` is the table where US flu hospitalization rates are stored.
+--------------+-------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+--------------+-------------+------+-----+---------+----------------+
| id | int(11) | NO | PRI | NULL | auto_increment |
| release_date | date | NO | MUL | NULL | |
| issue | int(11) | NO | MUL | NULL | |
| epiweek | int(11) | NO | MUL | NULL | |
| location | varchar(32) | NO | MUL | NULL | |
| lag | int(11) | NO | MUL | NULL | |
| rate_age_0 | double | YES | | NULL | |
| rate_age_1 | double | YES | | NULL | |
| rate_age_2 | double | YES | | NULL | |
| rate_age_3 | double | YES | | NULL | |
| rate_age_4 | double | YES | | NULL | |
| rate_overall | double | YES | | NULL | |
| rate_age_5 | double | YES | | NULL | |
| rate_age_6 | double | YES | | NULL | |
| rate_age_7 | double | YES | | NULL | |
+--------------+-------------+------+-----+---------+----------------+
id: unique identifier for each record
release_date: the date when this record was first published by the CDC
issue: the epiweek of publication (e.g. issue 201453 includes epiweeks up to
and including 2014w53, but not 2015w01 or following)
epiweek: the epiweek during which the data was collected
location: the name of the catchment (e.g. 'network_all', 'CA', 'NY_albany')
lag: number of weeks between `epiweek` and `issue`
rate_age_0: hospitalization rate for ages 0-4
rate_age_1: hospitalization rate for ages 5-17
rate_age_2: hospitalization rate for ages 18-49
rate_age_3: hospitalization rate for ages 50-64
rate_age_4: hospitalization rate for ages 65+
rate_overall: overall hospitalization rate
rate_age_5: hospitalization rate for ages 65-74
rate_age_6: hospitalization rate for ages 75-84
rate_age_7: hospitalization rate for ages 85+

=================
=== Changelog ===
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70 changes: 20 additions & 50 deletions src/ddl/fluview.sql
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Expand Up @@ -329,7 +329,7 @@ CREATE TABLE `fluview_public` (
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

/*
`flusurv` stores FluSurv-NET data (flu hospitalization rates) as published by
`flusurv` stores FluSurv-NET data (flu hospitaliation rates) as published by
CDC.

Data is public.
Expand All @@ -345,40 +345,25 @@ Note that the flusurv age groups are, in general, not the same as the ILINet
particular "catchment" (e.g. 'network_all', 'CA', 'NY_albany') rather than by
regions and states in general.

+-------------------+-------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+-------------------+-------------+------+-----+---------+----------------+
| id | int(11) | NO | PRI | NULL | auto_increment |
| release_date | date | NO | MUL | NULL | |
| issue | int(11) | NO | MUL | NULL | |
| epiweek | int(11) | NO | MUL | NULL | |
| location | varchar(32) | NO | MUL | NULL | |
| lag | int(11) | NO | MUL | NULL | |
| rate_age_0 | double | YES | | NULL | |
| rate_age_1 | double | YES | | NULL | |
| rate_age_2 | double | YES | | NULL | |
| rate_age_3 | double | YES | | NULL | |
| rate_age_4 | double | YES | | NULL | |
| rate_overall | double | YES | | NULL | |
| rate_age_5 | double | YES | | NULL | |
| rate_age_6 | double | YES | | NULL | |
| rate_age_7 | double | YES | | NULL | |
| rate_age_18t29 | double | YES | | NULL | |
| rate_age_30t39 | double | YES | | NULL | |
| rate_age_40t49 | double | YES | | NULL | |
| rate_age_5t11 | double | YES | | NULL | |
| rate_age_12t17 | double | YES | | NULL | |
| rate_age_lt18 | double | YES | | NULL | |
| rate_age_gte18 | double | YES | | NULL | |
| rate_race_white | double | YES | | NULL | |
| rate_race_black | double | YES | | NULL | |
| rate_race_hisp | double | YES | | NULL | |
| rate_race_asian | double | YES | | NULL | |
| rate_race_natamer | double | YES | | NULL | |
| rate_sex_male | double | YES | | NULL | |
| rate_sex_female | double | YES | | NULL | |
| season | char(7) | YES | | NULL | |
+-------------------+-------------+------+-----+---------+----------------+
+--------------+-------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+--------------+-------------+------+-----+---------+----------------+
| id | int(11) | NO | PRI | NULL | auto_increment |
| release_date | date | NO | MUL | NULL | |
| issue | int(11) | NO | MUL | NULL | |
| epiweek | int(11) | NO | MUL | NULL | |
| location | varchar(32) | NO | MUL | NULL | |
| lag | int(11) | NO | MUL | NULL | |
| rate_age_0 | double | YES | | NULL | |
| rate_age_1 | double | YES | | NULL | |
| rate_age_2 | double | YES | | NULL | |
| rate_age_3 | double | YES | | NULL | |
| rate_age_4 | double | YES | | NULL | |
| rate_overall | double | YES | | NULL | |
| rate_age_5 | double | YES | | NULL | |
| rate_age_6 | double | YES | | NULL | |
| rate_age_7 | double | YES | | NULL | |
+--------------+-------------+------+-----+---------+----------------+
*/

CREATE TABLE `flusurv` (
Expand All @@ -397,21 +382,6 @@ CREATE TABLE `flusurv` (
`rate_age_5` double DEFAULT NULL,
`rate_age_6` double DEFAULT NULL,
`rate_age_7` double DEFAULT NULL,
`rate_age_18t29` double DEFAULT NULL,
`rate_age_30t39` double DEFAULT NULL,
`rate_age_40t49` double DEFAULT NULL,
`rate_age_5t11` double DEFAULT NULL,
`rate_age_12t17` double DEFAULT NULL,
`rate_age_lt18` double DEFAULT NULL,
`rate_age_gte18` double DEFAULT NULL,
`rate_race_white` double DEFAULT NULL,
`rate_race_black` double DEFAULT NULL,
`rate_race_hisp` double DEFAULT NULL,
`rate_race_asian` double DEFAULT NULL,
`rate_race_natamer` double DEFAULT NULL,
`rate_sex_male` double DEFAULT NULL,
`rate_sex_female` double DEFAULT NULL,
`season` char(7) DEFAULT NULL,
PRIMARY KEY (`id`),
UNIQUE KEY `issue` (`issue`,`epiweek`,`location`),
KEY `release_date` (`release_date`),
Expand Down
18 changes: 0 additions & 18 deletions src/ddl/migrations/flusurv_age_sex_race_strata.sql
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This file was deleted.

23 changes: 1 addition & 22 deletions src/server/endpoints/flusurv.py
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Expand Up @@ -19,7 +19,7 @@ def handle():
# basic query info
q = QueryBuilder("flusurv", "fs")

fields_string = ["release_date", "location", "season"]
fields_string = ["release_date", "location"]
fields_int = ["issue", "epiweek", "lag"]
fields_float = [
"rate_age_0",
Expand All @@ -28,27 +28,6 @@ def handle():
"rate_age_3",
"rate_age_4",
"rate_overall",

"rate_age_5",
"rate_age_6",
"rate_age_7",

"rate_age_18t29",
"rate_age_30t39",
"rate_age_40t49",
"rate_age_5t11",
"rate_age_12t17",
"rate_age_lt18",
"rate_age_gte18",

"rate_race_white",
"rate_race_black",
"rate_race_hisp",
"rate_race_asian",
"rate_race_natamer",

"rate_sex_male",
"rate_sex_female",
]
q.set_fields(fields_string, fields_int, fields_float)
q.set_sort_order("epiweek", "location", "issue")
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