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Update flusurv schema and docs with new age, sex, and race groups (#1287)
* add new columns to flusurv endpoint spec * add new age, sex, race strata, and season to schema * list new signals in documentation * move new season column to end of table * add migration script to add new fields to flusurv table * add field descriptions; reformat table so don't need to match line lengths * point from acquisition script to docs and schema def to deduplicate
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‎docs/api/flusurv.md‎

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@@ -52,22 +52,40 @@ If neither is specified, the current issues are used.
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## Response
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| Field | Description | Type |
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|--------------------------|-----------------------------------------------------------------|------------------|
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| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
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| `epidata` | list of results | array of objects |
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| `epidata[].release_date` | | string |
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| `epidata[].location` | | string |
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| `epidata[].issue` | | integer |
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| `epidata[].epiweek` | | integer |
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| `epidata[].lag` | | integer |
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| `epidata[].rate_age_0` | | float |
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| `epidata[].rate_age_1` | | float |
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| `epidata[].rate_age_2` | | float |
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| `epidata[].rate_age_3` | | float |
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| `epidata[].rate_age_4` | | float |
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| `epidata[].rate_overall` | | float |
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| `message` | `success` or error message | string |
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| Field | Description | Type |
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|---|---|---|
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| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
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| `epidata` | list of results | array of objects |
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| `epidata[].release_date` | the date when this record was first published by the CDC | string |
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| `epidata[].location` | the name of the catchment (e.g. 'network_all', 'CA', 'NY_albany' | string |
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| `epidata[].issue` | the epiweek of publication (e.g. issue 201453 includes epiweeks up to and including 2014w53, but not 2015w01 or following) | integer |
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| `epidata[].epiweek` | the epiweek during which the data was collected | integer |
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| `epidata[].lag` | number of weeks between `epiweek` and `issue` | integer |
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| `epidata[].rate_age_0` | hospitalization rate for ages 0-4 | float |
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| `epidata[].rate_age_1` | hospitalization rate for ages 5-17 | float |
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| `epidata[].rate_age_2` | hospitalization rate for ages 18-49 | float |
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| `epidata[].rate_age_3` | hospitalization rate for ages 50-64 | float |
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| `epidata[].rate_age_4` | hospitalization rate for ages 65+ | float |
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| `epidata[].rate_overall` | overall hospitalization rate | float |
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| `epidata[].rate_age_5` | hospitalization rate for ages 65-74 | float |
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| `epidata[].rate_age_6` | hospitalization rate for ages 75-84 | float |
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| `epidata[].rate_age_7` | hospitalization rate for ages 85+ | float |
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| `epidata[].rate_age_18t29` | hospitalization rate for ages 18 to 29 | float |
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| `epidata[].rate_age_30t39` | hospitalization rate for ages 30 to 39 | float |
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| `epidata[].rate_age_40t49` | hospitalization rate for ages 40 to 49 | float |
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| `epidata[].rate_age_5t11` | hospitalization rate for ages 5 to 11 | float |
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| `epidata[].rate_age_12t17` | hospitalization rate for ages 12 to 17 | float |
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| `epidata[].rate_age_lt18` | hospitalization rate for ages <18 | float |
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| `epidata[].rate_age_gte18` | hospitalization rate for ages >=18 | float |
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| `epidata[].rate_race_white` | hospitalization rate for white people | float |
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| `epidata[].rate_race_black` | hospitalization rate for black people | float |
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| `epidata[].rate_race_hisp` | hospitalization rate for Hispanic/Latino people | float |
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| `epidata[].rate_race_asian` | hospitalization rate for Asian people | float |
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| `epidata[].rate_race_natamer` | hospitalization rate for American Indian/Alaskan Native people | float |
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| `epidata[].rate_sex_male` | hospitalization rate for males | float |
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| `epidata[].rate_sex_female` | hospitalization rate for females | float |
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| `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 |
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| `message` | `success` or error message | string |
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Notes:
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* The `flusurv` age groups are, in general, not the same as the ILINet

‎src/acquisition/flusurv/flusurv_update.py‎

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@@ -19,42 +19,9 @@
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=== Data Dictionary ===
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=======================
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`flusurv` is the table where US flu hospitalization rates are stored.
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+--------------+-------------+------+-----+---------+----------------+
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| Field | Type | Null | Key | Default | Extra |
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+--------------+-------------+------+-----+---------+----------------+
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| id | int(11) | NO | PRI | NULL | auto_increment |
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| release_date | date | NO | MUL | NULL | |
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| issue | int(11) | NO | MUL | NULL | |
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| epiweek | int(11) | NO | MUL | NULL | |
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| location | varchar(32) | NO | MUL | NULL | |
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| lag | int(11) | NO | MUL | NULL | |
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| rate_age_0 | double | YES | | NULL | |
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| rate_age_1 | double | YES | | NULL | |
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| rate_age_2 | double | YES | | NULL | |
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| rate_age_3 | double | YES | | NULL | |
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| rate_age_4 | double | YES | | NULL | |
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| rate_overall | double | YES | | NULL | |
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| rate_age_5 | double | YES | | NULL | |
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| rate_age_6 | double | YES | | NULL | |
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| rate_age_7 | double | YES | | NULL | |
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+--------------+-------------+------+-----+---------+----------------+
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id: unique identifier for each record
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release_date: the date when this record was first published by the CDC
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issue: the epiweek of publication (e.g. issue 201453 includes epiweeks up to
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and including 2014w53, but not 2015w01 or following)
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epiweek: the epiweek during which the data was collected
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location: the name of the catchment (e.g. 'network_all', 'CA', 'NY_albany')
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lag: number of weeks between `epiweek` and `issue`
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rate_age_0: hospitalization rate for ages 0-4
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rate_age_1: hospitalization rate for ages 5-17
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rate_age_2: hospitalization rate for ages 18-49
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rate_age_3: hospitalization rate for ages 50-64
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rate_age_4: hospitalization rate for ages 65+
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rate_overall: overall hospitalization rate
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rate_age_5: hospitalization rate for ages 65-74
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rate_age_6: hospitalization rate for ages 75-84
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rate_age_7: hospitalization rate for ages 85+
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`flusurv` is the table where US flu hospitalization rates are stored. See
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`strc/ddl/fluview.sql` for the `flusurv` schema. See `docs/api/flusurv.md` for
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field descriptions.
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=================
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=== Changelog ===

‎src/ddl/fluview.sql‎

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@@ -329,7 +329,7 @@ CREATE TABLE `fluview_public` (
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) ENGINE=InnoDB DEFAULT CHARSET=utf8;
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/*
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`flusurv` stores FluSurv-NET data (flu hospitaliation rates) as published by
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`flusurv` stores FluSurv-NET data (flu hospitalization rates) as published by
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CDC.
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Data is public.
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particular "catchment" (e.g. 'network_all', 'CA', 'NY_albany') rather than by
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regions and states in general.
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+--------------+-------------+------+-----+---------+----------------+
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| Field | Type | Null | Key | Default | Extra |
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+--------------+-------------+------+-----+---------+----------------+
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| id | int(11) | NO | PRI | NULL | auto_increment |
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| release_date | date | NO | MUL | NULL | |
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| issue | int(11) | NO | MUL | NULL | |
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| epiweek | int(11) | NO | MUL | NULL | |
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| location | varchar(32) | NO | MUL | NULL | |
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| lag | int(11) | NO | MUL | NULL | |
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| rate_age_0 | double | YES | | NULL | |
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| rate_age_1 | double | YES | | NULL | |
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| rate_age_2 | double | YES | | NULL | |
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| rate_age_3 | double | YES | | NULL | |
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| rate_age_4 | double | YES | | NULL | |
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| rate_overall | double | YES | | NULL | |
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| rate_age_5 | double | YES | | NULL | |
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| rate_age_6 | double | YES | | NULL | |
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| rate_age_7 | double | YES | | NULL | |
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+--------------+-------------+------+-----+---------+----------------+
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+-------------------+-------------+------+-----+---------+----------------+
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| Field | Type | Null | Key | Default | Extra |
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+-------------------+-------------+------+-----+---------+----------------+
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| id | int(11) | NO | PRI | NULL | auto_increment |
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| release_date | date | NO | MUL | NULL | |
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| issue | int(11) | NO | MUL | NULL | |
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| epiweek | int(11) | NO | MUL | NULL | |
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| location | varchar(32) | NO | MUL | NULL | |
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| lag | int(11) | NO | MUL | NULL | |
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| rate_age_0 | double | YES | | NULL | |
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| rate_age_1 | double | YES | | NULL | |
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| rate_age_2 | double | YES | | NULL | |
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| rate_age_3 | double | YES | | NULL | |
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| rate_age_4 | double | YES | | NULL | |
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| rate_overall | double | YES | | NULL | |
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| rate_age_5 | double | YES | | NULL | |
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| rate_age_6 | double | YES | | NULL | |
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| rate_age_7 | double | YES | | NULL | |
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| rate_age_18t29 | double | YES | | NULL | |
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| rate_age_30t39 | double | YES | | NULL | |
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| rate_age_40t49 | double | YES | | NULL | |
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| rate_age_5t11 | double | YES | | NULL | |
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| rate_age_12t17 | double | YES | | NULL | |
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| rate_age_lt18 | double | YES | | NULL | |
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| rate_age_gte18 | double | YES | | NULL | |
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| rate_race_white | double | YES | | NULL | |
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| rate_race_black | double | YES | | NULL | |
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| rate_race_hisp | double | YES | | NULL | |
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| rate_race_asian | double | YES | | NULL | |
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| rate_race_natamer | double | YES | | NULL | |
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| rate_sex_male | double | YES | | NULL | |
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| rate_sex_female | double | YES | | NULL | |
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| season | char(7) | YES | | NULL | |
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+-------------------+-------------+------+-----+---------+----------------+
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*/
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CREATE TABLE `flusurv` (
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`rate_age_5` double DEFAULT NULL,
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`rate_age_6` double DEFAULT NULL,
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`rate_age_7` double DEFAULT NULL,
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`rate_age_18t29` double DEFAULT NULL,
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`rate_age_30t39` double DEFAULT NULL,
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`rate_age_40t49` double DEFAULT NULL,
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`rate_age_5t11` double DEFAULT NULL,
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`rate_age_12t17` double DEFAULT NULL,
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`rate_age_lt18` double DEFAULT NULL,
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`rate_age_gte18` double DEFAULT NULL,
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`rate_race_white` double DEFAULT NULL,
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`rate_race_black` double DEFAULT NULL,
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`rate_race_hisp` double DEFAULT NULL,
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`rate_race_asian` double DEFAULT NULL,
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`rate_race_natamer` double DEFAULT NULL,
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`rate_sex_male` double DEFAULT NULL,
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`rate_sex_female` double DEFAULT NULL,
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`season` char(7) DEFAULT NULL,
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PRIMARY KEY (`id`),
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UNIQUE KEY `issue` (`issue`,`epiweek`,`location`),
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KEY `release_date` (`release_date`),

‎src/ddl/migrations/flusurv_age_sex_race_strata.sql‎

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-- Add new age, race, and sex strata, and season descriptor (YYYY-YY format)
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ALTER TABLE `flusurv` ADD (
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`rate_age_18t29` double DEFAULT NULL,
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`rate_age_30t39` double DEFAULT NULL,
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`rate_age_40t49` double DEFAULT NULL,
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`rate_age_5t11` double DEFAULT NULL,
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`rate_age_12t17` double DEFAULT NULL,
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`rate_age_lt18` double DEFAULT NULL,
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`rate_age_gte18` double DEFAULT NULL,
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`rate_race_white` double DEFAULT NULL,
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`rate_race_black` double DEFAULT NULL,
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`rate_race_hisp` double DEFAULT NULL,
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`rate_race_asian` double DEFAULT NULL,
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`rate_race_natamer` double DEFAULT NULL,
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`rate_sex_male` double DEFAULT NULL,
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`rate_sex_female` double DEFAULT NULL,
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`season` char(7) DEFAULT NULL,
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);

‎src/server/endpoints/flusurv.py‎

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# basic query info
2020
q = QueryBuilder("flusurv", "fs")
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fields_string = ["release_date", "location"]
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fields_string = ["release_date", "location", "season"]
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fields_int = ["issue", "epiweek", "lag"]
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fields_float = [
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"rate_age_0",
@@ -28,6 +28,27 @@ def handle():
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"rate_age_3",
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"rate_age_4",
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"rate_overall",
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"rate_age_5",
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"rate_age_6",
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"rate_age_7",
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"rate_age_18t29",
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"rate_age_30t39",
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"rate_age_40t49",
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"rate_age_5t11",
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"rate_age_12t17",
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"rate_age_lt18",
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"rate_age_gte18",
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"rate_race_white",
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"rate_race_black",
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"rate_race_hisp",
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"rate_race_asian",
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"rate_race_natamer",
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"rate_sex_male",
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"rate_sex_female",
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]
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q.set_fields(fields_string, fields_int, fields_float)
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q.set_sort_order("epiweek", "location", "issue")

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