diff --git a/deploy.json b/deploy.json index 45b45883e..c2c798b56 100644 --- a/deploy.json +++ b/deploy.json @@ -65,11 +65,6 @@ "dst": "[[package]]/acquisition/cdcp/", "match": "^.*\\.(py)$", "add-header-comment": true - },{ - "type": "move", - "src": "src/acquisition/cdcp/cdc_upload.php", - "dst": "[[auto_web]]/cdc_upload/index.php", - "add-header-comment": true }, "// acquisition - ght", @@ -107,16 +102,6 @@ "dst": "[[package]]/acquisition/wiki/", "match": "^.*\\.(py)$", "add-header-comment": true - },{ - "type": "move", - "src": "src/acquisition/wiki/master.php", - "dst": "[[auto_web]]/wiki/master.php", - "add-header-comment": true - },{ - "type": "move", - "src": "src/acquisition/wiki/dashboard.php", - "dst": "[[auto_web]]/wiki/index.php", - "add-header-comment": true }, "// acquisition - flusurv", diff --git a/dev/docker/web/epidata/Dockerfile b/dev/docker/web/epidata/Dockerfile deleted file mode 100644 index fa6d503a4..000000000 --- a/dev/docker/web/epidata/Dockerfile +++ /dev/null @@ -1,11 +0,0 @@ -# start with the `delphi_web` image -FROM delphi_web - -# deploy the Epidata API (see `delphi-epidata/deploy.json`) -COPY repos/delphi/delphi-epidata/src/server/*.html /var/www/html/epidata/ -COPY repos/delphi/delphi-epidata/src/server/*.php /var/www/html/epidata/ - -# point to the development database (overwrites the production config) -COPY repos/delphi/delphi-epidata/dev/docker/web/epidata/assets/database_config.php /var/www/html/epidata/ - -RUN chmod o+r /var/www/html/epidata/* diff --git a/dev/docker/web/epidata/README.md b/dev/docker/web/epidata/README.md deleted file mode 100644 index 8656f3e66..000000000 --- a/dev/docker/web/epidata/README.md +++ /dev/null @@ -1,22 +0,0 @@ -# `delphi_web_epidata` - -This image starts with Delphi's web server and adds the sources necessary for -hosting the Epidata API. - -This image includes the file -[`database_config.php`](assets/database_config.php), which points to a local -container running the -[`delphi_database_epidata` image](../../database/epidata/README.md). - -To start a container from this image, run: - -```bash -docker run --rm -p 10080:80 \ - --network delphi-net --name delphi_web_epidata \ - delphi_web_epidata -``` - -You should be able to call the API by setting your base URL to -`http://localhost:10080/epidata/api.php`. To verify that the container is alive -and serving, visit in a web browser (or `curl`) -http://localhost:10080/epidata/. diff --git a/dev/docker/web/epidata/assets/database_config.php b/dev/docker/web/epidata/assets/database_config.php deleted file mode 100644 index 7c7402f47..000000000 --- a/dev/docker/web/epidata/assets/database_config.php +++ /dev/null @@ -1,7 +0,0 @@ - 'delphi_database_epidata', - 'port' => 3306, -); -?> diff --git a/docs/epidata_development.md b/docs/epidata_development.md index 44d13a348..a2f0b7e8e 100644 --- a/docs/epidata_development.md +++ b/docs/epidata_development.md @@ -116,7 +116,7 @@ above. The base images are built first, followed by the derived `epidata`-specific images. - The [`delphi_web_epidata` image](https://github.com/cmu-delphi/delphi-epidata/blob/main/dev/docker/web/epidata/README.md) adds - the Epidata API to the `delphi_web` image. + the Epidata API to the `delphi_web_epidata` image. - The [`delphi_database_epidata` image](https://github.com/cmu-delphi/delphi-epidata/blob/main/dev/docker/database/epidata/README.md) adds user accounts, `epidata` & other appropriate databases, and relevant tables @@ -125,14 +125,8 @@ above. The base images are built first, followed by the derived From the root of your workspace, all of the images can be built as follows: ```bash -docker build -t delphi_web \ - -f repos/delphi/operations/dev/docker/web/Dockerfile . - -docker build -t delphi_web_epidata \ - -f repos/delphi/delphi-epidata/dev/docker/web/epidata/Dockerfile . - -docker build -t delphi_database \ - -f repos/delphi/operations/dev/docker/database/Dockerfile . +docker build -t delphi_web_epidata\ + -f ./devops/Dockerfile .;\ docker build -t delphi_database_epidata \ -f repos/delphi/delphi-epidata/dev/docker/database/epidata/Dockerfile . @@ -394,33 +388,3 @@ The command above maps two local directories into the container: - `/repos/delphi/delphi-epidata/src`: Just the source code, which forms the container's `delphi.epidata` python package. -### server code - -Local web sources (e.g. PHP files) can be bind-mounted into a -`delphi_web_epidata` container as follows: - -```bash -docker run --rm -p 127.0.0.1:10080:80 \ - --mount type=bind,source="$(pwd)"/repos/delphi/delphi-epidata/src/server/api.php,target=/var/www/html/epidata/api.php,readonly \ - --mount type=bind,source="$(pwd)"/repos/delphi/delphi-epidata/src/server/api_helpers.php,target=/var/www/html/epidata/api_helpers.php,readonly \ - --network delphi-net --name delphi_web_epidata \ - delphi_web_epidata -``` - -The command above mounts two specific files into the image. It may be tempting -to bind mount the `src/server` directory rather than specific files, however -that is currently problematic for a couple of reasons: - -1. `server/.htaccess` [from the local repository](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/server/.htaccess) uses - the `Header` directive. However, the webserver in the container doesn't have - the corresponding module enabled. This causes the server to deny access to - the API. -2. `server/database_config.php` - [in the image](https://github.com/cmu-delphi/delphi-epidata/blob/main/dev/docker/web/epidata/assets/database_config.php) contains - database credentials for use in conjunction with the - `delphi_database_epidata` container during development. However, the same - file from [the local repository](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/server/database_config.php) only - contains placeholder values. This prevents communication with the database. - -There is currently no benefit to bind-mounting sources into the database -container because schema changes require restarting the container anyway. diff --git a/docs/new_endpoint_tutorial.md b/docs/new_endpoint_tutorial.md index bd5634c9e..436b89908 100644 --- a/docs/new_endpoint_tutorial.md +++ b/docs/new_endpoint_tutorial.md @@ -273,10 +273,8 @@ already built the `delphi_python` image above: ```bash # build web and database images for epidata -docker build -t delphi_web \ - -f repos/delphi/operations/dev/docker/web/Dockerfile . -docker build -t delphi_web_epidata \ - -f repos/delphi/delphi-epidata/dev/docker/web/epidata/Dockerfile . +docker build -t delphi_web_epidata\ + -f ./devops/Dockerfile .;\ docker build -t delphi_database_epidata \ -f repos/delphi/delphi-epidata/dev/docker/database/epidata/Dockerfile . diff --git a/src/acquisition/cdcp/cdc_upload.php b/src/acquisition/cdcp/cdc_upload.php deleted file mode 100644 index 3dfcb38f3..000000000 --- a/src/acquisition/cdcp/cdc_upload.php +++ /dev/null @@ -1,101 +0,0 @@ - - - - CDC Page Stats - - - - -
-
- -

Upload Result

- 0) { - printf('Error: upload failed (%d)', intval($_FILES['zip_file']['error'])); - } else if($fileType != 'zip') { - printf('Error: expected *.zip, got *.%s', $fileType); - } else { - $template = 'openssl dgst -sha256 -hmac "%s" "%s" | cut -d " " -f 2'; - $command = sprintf($template, $hmacSecret, $_FILES['zip_file']['tmp_name']); - $hmac = trim(shell_exec($command)); - // todo - constant time comparison - if($hmac === $_REQUEST['hmac']) { - $target_dir = '/common/cdc_stage/'; - $target_file = $target_dir . time() . '_' . $fileName; - if (move_uploaded_file($_FILES['zip_file']['tmp_name'], $target_file)) { - mysql_query('CALL automation.RunStep(46)'); // Process CDCP Data - printf('Success, thanks!'); - } else { - printf('Error: something is wrong with file permissions.'); - } - } else { - $expected = substr($hmac, 0, 8) . '...'; - printf("Error: HMAC mismatch, expected [{$expected}]."); - sleep(5); - } - } - } else { - ?> -

Upload zip file

-

- - (We have data through .) -

-
-
-
- -
- -
-
- To compute the hmac of your file, run [ openssl dgst -sha256 -hmac "<secret>" "<filename>" ]. The hmac should be a 64 character string of hex digits (32 bytes, 256 bits). -
-
- - diff --git a/src/acquisition/wiki/dashboard.php b/src/acquisition/wiki/dashboard.php deleted file mode 100644 index 09ae0e9d8..000000000 --- a/src/acquisition/wiki/dashboard.php +++ /dev/null @@ -1,182 +0,0 @@ - - - - - - Wiki Status - - - - - -

Workers

- - - = date_sub(now(), interval 1 hour) order by max(datetime)"); - $num = 0; - while($row = mysql_fetch_array($result)) { - printf("", floatval($row['dl'])); - $num++; - } - ?> -
WorkerDownload (GB)Num JobsLast Job Finished (sec)
{$row['worker']}%.1f{$row['jobs']}{$row['seen']}
-

-

Jobs

- - - "); - } - ?> -
StatusNum JobsDescription
{$row['status']}{$row['num']}{$desc}
-
- 0) { - print(" curr"); - } - print("\">"); - $st_1 = intval($row['st_1']); - $st0 = intval($row['st0']); - $st1 = intval($row['st1']); - $st2 = intval($row['st2']); - $st3 = intval($row['st3']); - $total = $st_1 + $st0 + $st1 + $st2 + $st3; - if($st3 == $total) { - print("
"); - } else { - printf("
", (100 * $st_1 / $total)); - printf("
", (100 * $st0 / $total)); - printf("
", (100 * $st1 / $total)); - printf("
", (100 * $st2 / $total)); - printf("
", (100 * $st3 / $total)); - } - print(""); - } - ?> - - diff --git a/src/acquisition/wiki/master.php b/src/acquisition/wiki/master.php deleted file mode 100644 index 99ace0cd4..000000000 --- a/src/acquisition/wiki/master.php +++ /dev/null @@ -1,53 +0,0 @@ -{'size'}), mysql_real_escape_string($obj->{'worker'}), floatval($obj->{'elapsed'}), mysql_real_escape_string($obj->{'data'}), intval($obj->{'id'}))); - echo 'ok'; - } else { - sleep(5); - http_response_code(400); - echo 'wrong hmac'; - } -} else { - http_response_code(400); - echo 'bad request'; -} -?> diff --git a/src/server/api.php b/src/server/api.php deleted file mode 100644 index 404bd80c2..000000000 --- a/src/server/api.php +++ /dev/null @@ -1,2232 +0,0 @@ - Secrets::$api['twitter'], - 'ght' => Secrets::$api['ght'], - 'fluview' => Secrets::$api['fluview'], - 'cdc' => Secrets::$api['cdc'], - 'sensors' => Secrets::$api['sensors'], - 'sensor_subsets' => Secrets::$api['sensor_subsets'], - 'quidel' => Secrets::$api['quidel'], - 'norostat' => Secrets::$api['norostat'], - 'afhsb' => Secrets::$api['afhsb'] -); -// begin sensor query authentication configuration -// A multimap of sensor names to the "granular" auth tokens that can be used to access them; excludes the "global" sensor auth key that works for all sensors: -$GRANULAR_SENSOR_AUTH_TOKENS = array( - 'twtr' => array($AUTH['sensor_subsets']['twtr_sensor']), - 'gft' => array($AUTH['sensor_subsets']['gft_sensor']), - 'ght' => array($AUTH['sensor_subsets']['ght_sensors']), - 'ghtj' => array($AUTH['sensor_subsets']['ght_sensors']), - 'cdc' => array($AUTH['sensor_subsets']['cdc_sensor']), - 'quid' => array($AUTH['sensor_subsets']['quid_sensor']), - 'wiki' => array($AUTH['sensor_subsets']['wiki_sensor']), -); -// A set of sensors that do not require an auth key to access: -$OPEN_SENSORS = array( - 'sar3', - 'epic', - 'arch', -); -// Limits on the number of effective auth token equality checks performed per sensor query; generate auth tokens with appropriate levels of entropy according to the limits below: -$MAX_GLOBAL_AUTH_CHECKS_PER_SENSOR_QUERY = 1; // (but imagine is larger to futureproof) -$MAX_GRANULAR_AUTH_CHECKS_PER_SENSOR_QUERY = 30; // (but imagine is larger to futureproof) -// A (currently redundant) limit on the number of auth tokens that can be provided: -$MAX_AUTH_KEYS_PROVIDED_PER_SENSOR_QUERY = 1; -// end sensor query authentication configuration - -// result limit, ~10 years of daily data -$MAX_RESULTS = 3650; - -// queries the `fluview` and `fluview_imputed` tables -// $epiweeks (required): array of epiweek values/ranges -// $regions (required): array of region names -// $issues (optional): array of epiweek values/ranges -// overrides $lag -// default: most recent issue -// $lag (optional): number of weeks between each epiweek and its issue -// overridden by $issues -// default: most recent issue -// $authorized: determines whether private data (i.e. `fluview_imputed`) is -// included in the result -function get_fluview($epiweeks, $regions, $issues, $lag, $authorized) { - $epidata = array(); - // public data - $table = '`fluview` fv'; - $fields = "fv.`release_date`, fv.`issue`, fv.`epiweek`, fv.`region`, fv.`lag`, fv.`num_ili`, fv.`num_patients`, fv.`num_providers`, fv.`wili`, fv.`ili`, fv.`num_age_0`, fv.`num_age_1`, fv.`num_age_2`, fv.`num_age_3`, fv.`num_age_4`, fv.`num_age_5`"; - _get_fluview_by_table($epidata, $epiweeks, $regions, $issues, $lag, $table, $fields); - if(!$authorized) { - // Make a special exception for New York. It is a (weighted) sum of two - // constituent locations -- "ny_minus_jfk" and "jfk" -- both of which are - // publicly available. - if(in_array('ny', array_map('strtolower', $regions))) { - $regions = array('ny'); - $authorized = true; - } - } - if($authorized) { - // private data (no release date, no age groups, and wili is equal to ili) - $table = '`fluview_imputed` fv'; - $fields = "NULL `release_date`, fv.`issue`, fv.`epiweek`, fv.`region`, fv.`lag`, fv.`num_ili`, fv.`num_patients`, fv.`num_providers`, fv.`ili` `wili`, fv.`ili`, NULL `num_age_0`, NULL `num_age_1`, NULL `num_age_2`, NULL `num_age_3`, NULL `num_age_4`, NULL `num_age_5`"; - _get_fluview_by_table($epidata, $epiweeks, $regions, $issues, $lag, $table, $fields); - } - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// a helper function to query `fluview` and `fluview_imputed` individually -// parameters -function _get_fluview_by_table(&$epidata, $epiweeks, $regions, $issues, $lag, $table, $fields) { - // basic query info - $order = "fv.`epiweek` ASC, fv.`region` ASC, fv.`issue` ASC"; - // build the epiweek filter - $condition_epiweek = filter_integers('fv.`epiweek`', $epiweeks); - // build the region filter - $condition_region = filter_strings('fv.`region`', $regions); - if($issues !== null) { - // build the issue filter - $condition_issue = filter_integers('fv.`issue`', $issues); - // final query using specific issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_issue}) ORDER BY {$order}"; - } else if($lag !== null) { - // build the lag filter - $condition_lag = "(fv.`lag` = {$lag})"; - // final query using lagged issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_lag}) ORDER BY {$order}"; - } else { - // final query using most recent issues - $subquery = "(SELECT max(`issue`) `max_issue`, `epiweek`, `region` FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) GROUP BY `epiweek`, `region`) x"; - $condition = "x.`max_issue` = fv.`issue` AND x.`epiweek` = fv.`epiweek` AND x.`region` = fv.`region`"; - $query = "SELECT {$fields} FROM {$table} JOIN {$subquery} ON {$condition} ORDER BY {$order}"; - } - // get the data from the database - $fields_string = array('release_date', 'region'); - $fields_int = array('issue', 'epiweek', 'lag', 'num_ili', 'num_patients', 'num_providers', 'num_age_0', 'num_age_1', 'num_age_2', 'num_age_3', 'num_age_4', 'num_age_5'); - $fields_float = array('wili', 'ili'); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); -} - -// queries the `fluview_clinical` table -// $epiweeks (required): array of epiweek values/ranges -// $regions (required): array of region names -// $issues (optional): array of epiweek values/ranges -// overrides $lag -// default: most recent issue -// $lag (optional): number of weeks between each epiweek and its issue -// overridden by $issues -// default: most recent issue -function get_fluview_clinical($epiweeks, $regions, $issues, $lag) { - // store the results in an array - $epidata = array(); - // set up for query - $table = "`fluview_clinical` fvc"; - // $fields = 'fvc.`release_date`, fvc.`issue`, fvc.`epiweek`, fvc.`region`, fvc.`lag`, fvc.`total_specimens`, fvc.`total_a_h1n1`, fvc.`total_a_h3`, fvc.`total_a_h3n2v`, fvc.`total_a_no_sub`, fvc.`total_b`, fvc.`total_b_vic`, fvc.`total_b_yam`'; - $fields = "fvc.`release_date`, fvc.`issue`, fvc.`epiweek`, fvc.`region`, fvc.`lag`, fvc.`total_specimens`, fvc.`total_a`, fvc.`total_b`, fvc.`percent_positive`, fvc.`percent_a`, fvc.`percent_b`"; - $order = "fvc.`epiweek` ASC, fvc.`region` ASC, fvc.`issue` ASC"; - // create conditions - $condition_epiweek = filter_integers("fvc.`epiweek`", $epiweeks); - $condition_region = filter_strings("fvc.`region`", $regions); - if ($issues !== null) { - // using specific issues - $condition_issue = filter_integers("fvc.`issue`", $issues); - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_issue}) ORDER BY {$order}"; - } else if ($lag !== null) { - // using lagged issues - $condition_lag = '(fvc.`lag` = {$lag})'; - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_lag}) ORDER BY {$order}"; - } else { - // using most recent issues - $subquery = "(SELECT max(`issue`) `max_issue`, `epiweek`, `region` FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) GROUP BY `epiweek`, `region`) x"; - $condition = "x.`max_issue` = fvc.`issue` AND x.`epiweek` = fvc.`epiweek` AND x.`region` = fvc.`region`"; - $query = "SELECT {$fields} FROM {$table} JOIN {$subquery} ON {$condition} ORDER BY {$order}"; - } - // get the data from the database - $fields_string = array('release_date', 'region'); - $fields_float = array('percent_positive', 'percent_a', 'percent_b'); - $fields_int = array('issue', 'epiweek', 'lag', 'total_specimens', 'total_a', 'total_b'); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the result, if any - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `flusurv` table -// $epiweeks (required): array of epiweek values/ranges -// $locations (required): array of locations names -// $issues (optional): array of epiweek values/ranges -// overrides $lag -// default: most recent issue -// $lag (optional): number of weeks between each epiweek and its issue -// overridden by $issues -// default: most recent issue -function get_flusurv($epiweeks, $locations, $issues, $lag) { - // basic query info - $table = '`flusurv` fs'; - $fields = "fs.`release_date`, fs.`issue`, fs.`epiweek`, fs.`location`, fs.`lag`, fs.`rate_age_0`, fs.`rate_age_1`, fs.`rate_age_2`, fs.`rate_age_3`, fs.`rate_age_4`, fs.`rate_overall`"; - $order = "fs.`epiweek` ASC, fs.`location` ASC, fs.`issue` ASC"; - // build the epiweek filter - $condition_epiweek = filter_integers('fs.`epiweek`', $epiweeks); - // build the location filter - $condition_location = filter_strings('fs.`location`', $locations); - if($issues !== null) { - // build the issue filter - $condition_issue = filter_integers('fs.`issue`', $issues); - // final query using specific issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_location}) AND ({$condition_issue}) ORDER BY {$order}"; - } else if($lag !== null) { - // build the lag filter - $condition_lag = "(fs.`lag` = {$lag})"; - // final query using lagged issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_location}) AND ({$condition_lag}) ORDER BY {$order}"; - } else { - // final query using most recent issues - $subquery = "(SELECT max(`issue`) `max_issue`, `epiweek`, `location` FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_location}) GROUP BY `epiweek`, `location`) x"; - $condition = "x.`max_issue` = fs.`issue` AND x.`epiweek` = fs.`epiweek` AND x.`location` = fs.`location`"; - $query = "SELECT {$fields} FROM {$table} JOIN {$subquery} ON {$condition} ORDER BY {$order}"; - } - // get the data from the database - $epidata = array(); - $fields_string = array('release_date', 'location'); - $fields_int = array('issue', 'epiweek', 'lag'); - $fields_float = array('rate_age_0', 'rate_age_1', 'rate_age_2', 'rate_age_3', 'rate_age_4', 'rate_overall'); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `paho_dengue` table -// $epiweeks (required): array of epiweek values/ranges -// $regions (required): array of region names -// $issues (optional): array of epiweek values/ranges -// overrides $lag -// default: most recent issue -// $lag (optional): number of weeks between each epiweek and its issue -// overridden by $issues -// default: most recent issue -function get_paho_dengue($epiweeks, $regions, $issues, $lag) { - // store the results in an array - $epidata = array(); - // set up for query - $table = "`paho_dengue` pd"; - $fields = "pd.`release_date`, pd.`issue`, pd.`epiweek`, pd.`region`, pd.`lag`, pd.`total_pop`, pd.`serotype`, pd.`num_dengue`, pd.`incidence_rate`, pd.`num_severe`, pd.`num_deaths`"; - $order = "pd.`epiweek` ASC, pd.`region` ASC, pd.`issue` ASC"; - // create conditions - $condition_epiweek = filter_integers("pd.`epiweek`", $epiweeks); - $condition_region = filter_strings("pd.`region`", $regions); - if ($issues !== null) { - // using specific issues - $condition_issue = filter_integers("pd.`issue`", $issues); - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_issue}) ORDER BY {$order}"; - } else if ($lag !== null) { - // using lagged issues - $condition_lag = '(pd.`lag` = {$lag})'; - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_lag}) ORDER BY {$order}"; - } else { - // using most recent issues - $subquery = "(SELECT max(`issue`) `max_issue`, `epiweek`, `region` FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) GROUP BY `epiweek`, `region`) x"; - $condition = "x.`max_issue` = pd.`issue` AND x.`epiweek` = pd.`epiweek` AND x.`region` = pd.`region`"; - $query = "SELECT {$fields} FROM {$table} JOIN {$subquery} ON {$condition} ORDER BY {$order}"; - } - // get the data from the database - $fields_string = array('release_date', 'region', 'serotype'); - $fields_float = array('incidence_rate'); - $fields_int = array('issue', 'epiweek', 'lag', 'total_pop', 'num_dengue', 'num_severe', 'num_deaths'); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the result, if any - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `ecdc_ili` table -// $epiweeks (required): array of epiweek values/ranges -// $regions (required): array of region names -// $issues (optional): array of epiweek values/ranges -// overrides $lag -// default: most recent issue -// $lag (optional): number of weeks between each epiweek and its issue -// overridden by $issues -// default: most recent issue -function get_ecdc_ili($epiweeks, $regions, $issues, $lag) { - // store the results in an array - $epidata = array(); - // set up for query - $table = "`ecdc_ili` ec"; - $fields = "ec.`release_date`, ec.`issue`, ec.`epiweek`, ec.`region`, ec.`lag`, ec.`incidence_rate`"; - $order = "ec.`epiweek` ASC, ec.`region` ASC, ec.`issue` ASC"; - // create conditions - $condition_epiweek = filter_integers("ec.`epiweek`", $epiweeks); - $condition_region = filter_strings("ec.`region`", $regions); - if ($issues !== null) { - // using specific issues - $condition_issue = filter_integers("ec.`issue`", $issues); - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_issue}) ORDER BY {$order}"; - } else if ($lag !== null) { - // using lagged issues - $condition_lag = '(ec.`lag` = {$lag})'; - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_lag}) ORDER BY {$order}"; - } else { - // using most recent issues - $subquery = "(SELECT max(`issue`) `max_issue`, `epiweek`, `region` FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) GROUP BY `epiweek`, `region`) x"; - $condition = "x.`max_issue` = ec.`issue` AND x.`epiweek` = ec.`epiweek` AND x.`region` = ec.`region`"; - $query = "SELECT {$fields} FROM {$table} JOIN {$subquery} ON {$condition} ORDER BY {$order}"; - } - // get the data from the database - $fields_string = array('release_date', 'region'); - $fields_float = array('incidence_rate'); - $fields_int = array('issue', 'epiweek', 'lag'); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the result, if any - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `kcdc_ili` table -// $epiweeks (required): array of epiweek values/ranges -// $regions (required): array of region names -// $issues (optional): array of epiweek values/ranges -// overrides $lag -// default: most recent issue -// $lag (optional): number of weeks between each epiweek and its issue -// overridden by $issues -// default: most recent issue -function get_kcdc_ili($epiweeks, $regions, $issues, $lag) { - // store the results in an array - $epidata = array(); - // set up for query - $table = "`kcdc_ili` kc"; - $fields = "kc.`release_date`, kc.`issue`, kc.`epiweek`, kc.`region`, kc.`lag`, kc.`ili`"; - $order = "kc.`epiweek` ASC, kc.`region` ASC, kc.`issue` ASC"; - // create conditions - $condition_epiweek = filter_integers("kc.`epiweek`", $epiweeks); - $condition_region = filter_strings("kc.`region`", $regions); - if ($issues !== null) { - // using specific issues - $condition_issue = filter_integers("kc.`issue`", $issues); - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_issue}) ORDER BY {$order}"; - } else if ($lag !== null) { - // using lagged issues - $condition_lag = '(kc.`lag` = {$lag})'; - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_lag}) ORDER BY {$order}"; - } else { - // using most recent issues - $subquery = "(SELECT max(`issue`) `max_issue`, `epiweek`, `region` FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) GROUP BY `epiweek`, `region`) x"; - $condition = "x.`max_issue` = kc.`issue` AND x.`epiweek` = kc.`epiweek` AND x.`region` = kc.`region`"; - $query = "SELECT {$fields} FROM {$table} JOIN {$subquery} ON {$condition} ORDER BY {$order}"; - } - // get the data from the database - $fields_string = array('release_date', 'region'); - $fields_float = array('ili'); - $fields_int = array('issue', 'epiweek', 'lag'); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the result, if any - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `gft` table -// $epiweeks (required): array of epiweek values/ranges -// $locations (required): array of location names -function get_gft($epiweeks, $locations) { - // basic query info - $table = '`gft` g'; - $fields = "g.`epiweek`, g.`location`, g.`num`"; - $order = "g.`epiweek` ASC, g.`location` ASC"; - // build the epiweek filter - $condition_epiweek = filter_integers('g.`epiweek`', $epiweeks); - // build the location filter - $condition_location = filter_strings('g.`location`', $locations); - // final query using specific issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_location}) ORDER BY {$order}"; - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, array('location'), array('epiweek', 'num'), null); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `ght` table -// $epiweeks (required): array of epiweek values/ranges -// $locations (required): array of location names -// $query (required): search query or topic ID -function get_ght($epiweeks, $locations, $query) { - // basic query info - $table = '`ght` g'; - $fields = "g.`epiweek`, g.`location`, g.`value`"; - $order = "g.`epiweek` ASC, g.`location` ASC"; - // build the epiweek filter - $condition_epiweek = filter_integers('g.`epiweek`', $epiweeks); - // build the location filter - $condition_location = filter_strings('g.`location`', $locations); - // build the query filter - $condition_query = filter_strings('g.`query`', array($query)); - // final query using specific issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_location}) AND ({$condition_query}) ORDER BY {$order}"; - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, array('location'), array('epiweek'), array('value')); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `twitter` table -// $locations (required): array of location names -// $dates (required): array of date or epiweek values/ranges -// $resolution (required): either 'daily' or 'weekly' -function get_twitter($locations, $dates, $resolution) { - global $dbh; - // basic query info - $table = '`twitter` t'; - // build the date filter and set field names - $fields_string = array('location'); - $fields_int = array('num', 'total'); - $fields_float = array('percent'); - if($resolution === 'daily') { - $date_field = 't.`date`'; - $date_name = 'date'; - $condition_date = filter_dates($date_field, $dates); - array_push($fields_string, $date_name); - } else { - $date_field = 'yearweek(t.`date`, 6)'; - $date_name = 'epiweek'; - $condition_date = filter_integers($date_field, $dates); - array_push($fields_int, $date_name); - } - $fields = "{$date_field} `{$date_name}`, sum(t.`num`) `num`, sum(t.`total`) `total`, round(100 * sum(t.`num`) / sum(t.`total`), 8) `percent`"; - // for consistency (some rows have low `total`, or `num` > `total`), filter out 2% of rows with highest `percent` - $condition_filter = 't.`num` / t.`total` <= 0.019'; - // split locations into national/regional/state - $regions = array(); - $states = array(); - foreach($locations as $location) { - $location = strtolower($location); - if(in_array($location, array('nat', 'hhs1', 'hhs2', 'hhs3', 'hhs4', 'hhs5', 'hhs6', 'hhs7', 'hhs8', 'hhs9', 'hhs10', 'cen1', 'cen2', 'cen3', 'cen4', 'cen5', 'cen6', 'cen7', 'cen8', 'cen9'))) { - array_push($regions, $location); - } else { - array_push($states, $location); - } - } - // initialize the epidata array - $epidata = array(); - // query each region type individually (the data is stored by state, so getting regional data requires some extra processing) - foreach($regions as $region) { - $region = mysqli_real_escape_string($dbh, $region); - if($region === 'nat') { - // final query for U.S. National - $query = "SELECT {$fields}, '{$region}' `location` FROM {$table} WHERE ({$condition_filter}) AND ({$condition_date}) GROUP BY {$date_field} ORDER BY {$date_field} ASC"; - } else { - // build the location filter - $condition_location = "`state` IN (" . get_region_states($region) . ")"; - // final query for HHS Regions - $query = "SELECT {$fields}, '{$region}' `location` FROM {$table} WHERE ({$condition_filter}) AND ({$condition_date}) AND ({$condition_location}) GROUP BY {$date_field} ORDER BY {$date_field} ASC"; - } - // append query results to the epidata array - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - } - // query all states together - if(count($states) !== 0) { - // build the location filter - $condition_location = filter_strings('t.`state`', $states); - // final query for states - $query = "SELECT {$fields}, t.`state` `location` FROM {$table} WHERE ({$condition_filter}) AND ({$condition_date}) AND ({$condition_location}) GROUP BY {$date_field}, t.`state` ORDER BY {$date_field} ASC, t.`state` ASC"; - // append query results to the epidata array - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - } - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `wiki` table -// $articles (required): array of article titles -// $language (required): specify the language of articles we want to retrieve -// $dates (required): array of date or epiweek values/ranges -// $resolution (required): either 'daily' or 'weekly' -// $hours (optional): array of hour values/ranges -// if present, $hours determines which counts are used within each day; otherwise all counts are used -// for example, if hours=[4], then only the 4 AM (UTC) stream is returned -function get_wiki($articles, $language, $dates, $resolution, $hours) { - // required for `mysqli_real_escape_string` - global $dbh; - $language = mysqli_real_escape_string($dbh, $language); - // basic query info - // in a few rare instances (~6 total), `total` is unreasonably high; something glitched somewhere, just ignore it - // $table = '`wiki` w JOIN (SELECT * FROM `wiki_meta` WHERE `total` < 100000000) m ON m.`datetime` = w.`datetime`'; - // We select rows by language and then the problem is converted to the original one, and the rest of code can be same - $table = "( SELECT * FROM `wiki` WHERE `language` = '$language' ) w JOIN (SELECT * FROM `wiki_meta` WHERE `total` < 100000000 AND `language` = '$language' ) m ON m.`datetime` = w.`datetime`"; - // build the date filter and set field names - $fields_string = array('article'); - $fields_int = array('count', 'total', 'hour'); - $fields_float = array('value'); - if($resolution === 'daily') { - $date_field = 'm.`date`'; - $date_name = 'date'; - $condition_date = filter_dates($date_field, $dates); - array_push($fields_string, $date_name); - } else { - $date_field = 'm.`epiweek`'; - $date_name = 'epiweek'; - $condition_date = filter_integers($date_field, $dates); - array_push($fields_int, $date_name); - } - $fields = "{$date_field} `{$date_name}`, w.`article`, sum(w.`count`) `count`, sum(m.`total`) `total`, round(sum(w.`count`) / (sum(m.`total`) * 1e-6), 8) `value`"; - // build the article filter - $condition_article = filter_strings('w.`article`', $articles); - if($hours !== null) { - // filter by specific hours - $condition_hour = filter_integers('hour(m.`datetime`)', $hours); - // final query, only taking counts from specific hours of the day - $query = "SELECT {$fields}, hour(m.`datetime`) `hour` FROM {$table} WHERE ({$condition_date}) AND ({$condition_article}) AND ({$condition_hour}) GROUP BY {$date_field}, w.`article`, hour(m.`datetime`) ORDER BY {$date_field} ASC, w.`article` ASC, hour(m.`datetime`) ASC"; - } else { - // final query, summing over all hours of the day - $query = "SELECT {$fields}, -1 `hour` FROM {$table} WHERE ({$condition_date}) AND ({$condition_article}) GROUP BY {$date_field}, w.`article` ORDER BY {$date_field} ASC, w.`article` ASC"; - } - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `quidel` table -// $locations (required): array of location names -// $epiweeks (required): array of epiweek values/ranges -function get_quidel($locations, $epiweeks) { - // basic query info - $table = '`quidel` q'; - $fields = "q.`location`, q.`epiweek`, q.`value`"; - $order = "q.`epiweek` ASC, q.`location` ASC"; - // data type of each field - $fields_string = array('location'); - $fields_int = array('epiweek'); - $fields_float = array('value'); - // build the location filter - $condition_location = filter_strings('q.`location`', $locations); - // build the epiweek filter - $condition_epiweek = filter_integers('q.`epiweek`', $epiweeks); - // the query - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_location}) AND ({$condition_epiweek}) ORDER BY {$order}"; - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `norostat_point` table -// $locations (required): single location value (str listing included states) -// $epiweeks (required): array of epiweek values/ranges -function get_norostat($location, $epiweeks) { - // todo add release/issue args - // - // build the filters: - $condition_location = filter_strings('`norostat_raw_datatable_location_pool`.`location`', [$location]); - $condition_epiweek = filter_integers('`latest`.`epiweek`', $epiweeks); - // get the data from the database - $epidata = array(); - // (exclude "location" from output to reduce size & ugliness of result, - // transfer bandwidth required; it would just be a repeated echo of the input - // $location) - $fields_string = array('release_date'); - $fields_int = array('epiweek', 'value'); - $query = " - SELECT `latest`.`release_date`, `latest`.`epiweek`, `latest`.`new_value` AS `value` - FROM `norostat_point_diffs` AS `latest` - LEFT JOIN `norostat_raw_datatable_location_pool` USING (`location_id`) - LEFT JOIN ( - SELECT * FROM `norostat_point_diffs` - ) `later` - ON `latest`.`location_id` = `later`.`location_id` AND - `latest`.`epiweek` = `later`.`epiweek` AND - (`latest`.`release_date`, `latest`.`parse_time`) < - (`later`.`release_date`, `later`.`parse_time`) AND - `later`.`new_value` IS NOT NULL - WHERE ({$condition_location}) AND - ({$condition_epiweek}) AND - `later`.`parse_time` IS NULL AND - `latest`.`new_value` IS NOT NULL - "; - // xxx may reorder epiweeks - execute_query($query, $epidata, $fields_string, $fields_int, null); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `afhsb_00to13` table -// $epiweeks (required): array of epiweek values/ranges -// $locations (required): array of location names -// $flu_types (required): array of flu types -function get_afhsb($locations, $epiweeks, $flu_types) { - global $dbh; - $epidata = array(); - // split locations into national/regional/state - $location_dict = array("hhs" => array(), "cen" => array(), - "state" => array(), "country" => array()); - foreach($locations as $location) { - $location = strtolower($location); - if(substr($location, 0, 3) === "hhs") { - array_push($location_dict["hhs"], $location); - } elseif (substr($location, 0, 3) === "cen") { - array_push($location_dict["cen"], $location); - } elseif (strlen($location) === 3) { - array_push($location_dict["country"], $location); - } elseif (strlen($location) === 2) { - array_push($location_dict["state"], $location); - } - } - // split flu types into disjoint/subset - $disjoint_flus = array(); - $subset_flus = array(); - foreach($flu_types as $flu_type) { - if(in_array($flu_type, array('flu1','flu2-flu1','flu3-flu2','ili-flu3'))) { - array_push($disjoint_flus, $flu_type); - } elseif(in_array($flu_type, array('flu2','flu3','ili'))) { - array_push($subset_flus, $flu_type); - } - } - foreach($location_dict as $location_type=>$locs) { - if(!empty($locs)) { - _get_afhsb_by_table($epidata, $location_type, $epiweeks, $locs, $disjoint_flus, $subset_flus); - } - } - return count($epidata) === 0 ? null : $epidata; -} - -// A helper function to query afhsb tables -function _get_afhsb_by_table(&$epidata, $location_type, $epiweeks, $locations, $disjoint_flus, $subset_flus) { - // basic query info - $table = (in_array($location_type, array("hhs", "cen"))) ? "afhsb_00to13_region" : "afhsb_00to13_state"; - $fields = "`epiweek`, `{$location_type}` `location`, sum(`visit_sum`) `visit_sum`"; - $group = '`epiweek`, `location`'; - $order = "`epiweek` ASC, `location` ASC"; - $fields_string = array('location', 'flu_type'); - $fields_int = array('epiweek', 'visit_sum'); - // build the epiweek filter - $condition_epiweek = filter_integers('`epiweek`', $epiweeks); - // build the location filter - $condition_location = filter_strings($location_type, $locations); - - // subset flu types: flu2, flu3, ili - $flu_mapping = array('flu2' => array('flu1','flu2-flu1'), - 'flu3' => array('flu1','flu2-flu1','flu3-flu2'), - 'ili' => array('flu1','flu2-flu1','flu3-flu2','ili-flu3')); - foreach($subset_flus as $subset_flu) { - $condition_flu = filter_strings('`flu_type`', $flu_mapping[$subset_flu]); - $query = "SELECT {$fields}, '{$subset_flu}' `flu_type` FROM {$table} - WHERE ({$condition_epiweek}) AND ({$condition_location}) AND ({$condition_flu}) - GROUP BY {$group} ORDER BY {$order}"; - execute_query($query, $epidata, $fields_string, $fields_int, null); - } - // disjoint flu types: flu1, flu2-flu1, flu3-flu2, ili-flu3 - if(!empty($disjoint_flus)){ - $condition_flu = filter_strings('`flu_type`', $disjoint_flus); - $query = "SELECT {$fields}, `flu_type` FROM {$table} - WHERE ({$condition_epiweek}) AND ({$condition_location}) AND ({$condition_flu}) - GROUP BY {$group},`flu_type` ORDER BY {$order},`flu_type`"; - execute_query($query, $epidata, $fields_string, $fields_int, null); - } -} - -// queries the `nidss_flu` table -// $epiweeks (required): array of epiweek values/ranges -// $regions (required): array of region names -// $issues (optional): array of epiweek values/ranges -// overrides $lag -// default: most recent issue -// $lag (optional): number of weeks between each epiweek and its issue -// overridden by $issues -// default: most recent issue -function get_nidss_flu($epiweeks, $regions, $issues, $lag) { - // basic query info - $table = '`nidss_flu` nf'; - $fields = "nf.`release_date`, nf.`issue`, nf.`epiweek`, nf.`region`, nf.`lag`, nf.`visits`, nf.`ili`"; - $order = "nf.`epiweek` ASC, nf.`region` ASC, nf.`issue` ASC"; - // build the epiweek filter - $condition_epiweek = filter_integers('nf.`epiweek`', $epiweeks); - // build the region filter - $condition_region = filter_strings('nf.`region`', $regions); - if($issues !== null) { - // build the issue filter - $condition_issue = filter_integers('nf.`issue`', $issues); - // final query using specific issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_issue}) ORDER BY {$order}"; - } else if($lag !== null) { - // build the lag filter - $condition_lag = "(nf.`lag` = {$lag})"; - // final query using lagged issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) AND ({$condition_lag}) ORDER BY {$order}"; - } else { - // final query using most recent issues - $subquery = "(SELECT max(`issue`) `max_issue`, `epiweek`, `region` FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_region}) GROUP BY `epiweek`, `region`) x"; - $condition = "x.`max_issue` = nf.`issue` AND x.`epiweek` = nf.`epiweek` AND x.`region` = nf.`region`"; - $query = "SELECT {$fields} FROM {$table} JOIN {$subquery} ON {$condition} ORDER BY {$order}"; - } - // get the data from the database - $epidata = array(); - $fields_string = array('release_date', 'region'); - $fields_int = array('issue', 'epiweek', 'lag', 'visits'); - $fields_float = array('ili'); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `nidss_dengue` table -// $epiweeks (required): array of epiweek values/ranges -// $locations (required): array of region and/or location names -function get_nidss_dengue($epiweeks, $locations) { - global $dbh; - // build the epiweek filter - $condition_epiweek = filter_integers('nd.`epiweek`', $epiweeks); - // get the data from the database - $epidata = array(); - $fields_string = array('location'); - $fields_int = array('epiweek', 'count'); - foreach($locations as $location) { - $location = mysqli_real_escape_string($dbh, $location); - $query = " - SELECT - nd2.`epiweek`, nd2.`location`, count(1) `num_locations`, sum(nd2.`count`) `count` - FROM ( - SELECT - nd1.`epiweek`, CASE WHEN q.`query` = nd1.`location` THEN nd1.`location` WHEN q.`query` = nd1.`region` THEN nd1.`region` ELSE nd1.`nat` END `location`, nd1.`count` - FROM ( - SELECT - `epiweek`, `location`, `region`, 'nationwide' `nat`, `count` - FROM - `nidss_dengue` nd - WHERE {$condition_epiweek} - ) nd1 - JOIN ( - SELECT - '{$location}' `query` - ) q - ON - q.`query` IN (nd1.`location`, nd1.`region`, nd1.`nat`) - ) nd2 - GROUP BY - nd2.`epiweek`, nd2.`location` - "; - execute_query($query, $epidata, $fields_string, $fields_int, null); - } - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `forecasts` table -// $system (required): system name -// $epiweek (required): epiweek on which the forecast was made -function get_forecast($system, $epiweek) { - global $dbh; - // get the data from the database - $system = mysqli_real_escape_string($dbh, $system); - $query = "SELECT `system`, `epiweek`, `json` FROM `forecasts` WHERE `system` = '{$system}' AND `epiweek` = {$epiweek}"; - $epidata = array(); - $fields_string = array('system', 'json'); - $fields_int = array('epiweek'); - execute_query($query, $epidata, $fields_string, $fields_int, null); - // parse forecast data - if(count($epidata) === 1 && array_key_exists('json', $epidata[0])) { - $epidata[0]['forecast'] = json_decode($epidata[0]['json']); - unset($epidata[0]['json']); - } - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `cdc_extract` table -// $epiweeks (required): array of epiweek values/ranges -// $locations (required): array of location names -function get_cdc($epiweeks, $locations) { - global $dbh; - // basic query info - $table = '`cdc_extract` c'; - $group = "c.`epiweek`"; - $order = "c.`epiweek` ASC"; - $fields_string = array('location'); - $fields_int = array('epiweek', 'num1', 'num2', 'num3', 'num4', 'num5', 'num6', 'num7', 'num8', 'total'); - // build the epiweek filter - $condition_epiweek = filter_integers('c.`epiweek`', $epiweeks); - // split locations into national/regional/state - $regions = array(); - $states = array(); - foreach($locations as $location) { - $location = strtolower($location); - if(in_array($location, array('nat', 'hhs1', 'hhs2', 'hhs3', 'hhs4', 'hhs5', 'hhs6', 'hhs7', 'hhs8', 'hhs9', 'hhs10', 'cen1', 'cen2', 'cen3', 'cen4', 'cen5', 'cen6', 'cen7', 'cen8', 'cen9'))) { - array_push($regions, $location); - } else { - array_push($states, $location); - } - } - // initialize the epidata array - $epidata = array(); - // query each region type individually (the data is stored by state, so getting regional data requires some extra processing) - foreach($regions as $region) { - $region = mysqli_real_escape_string($dbh, $region); - $fields = "'{$region}' `location`, c.`epiweek`, sum(c.`num1`) `num1`, sum(c.`num2`) `num2`, sum(c.`num3`) `num3`, sum(c.`num4`) `num4`, sum(c.`num5`) `num5`, sum(c.`num6`) `num6`, sum(c.`num7`) `num7`, sum(c.`num8`) `num8`, sum(c.`total`) `total`"; - if($region === 'nat') { - // final query for U.S. National - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) GROUP BY {$group} ORDER BY {$order}"; - } else { - // build the location filter - $condition_location = "`state` IN (" . get_region_states($region) . ")"; - // final query for HHS Regions - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_location}) GROUP BY {$group} ORDER BY {$order}"; - } - // append query results to the epidata array - execute_query($query, $epidata, $fields_string, $fields_int, null); - } - // query all states together - if(count($states) !== 0) { - $fields = "c.`state` `location`, c.`epiweek`, c.`num1`, c.`num2`, c.`num3`, c.`num4`, c.`num5`, c.`num6`, c.`num7`, c.`num8`, c.`total`"; - // build the location filter - $condition_location = filter_strings('c.`state`', $states); - // final query for states - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_epiweek}) AND ({$condition_location}) ORDER BY {$order}, c.`state` ASC"; - // append query results to the epidata array - execute_query($query, $epidata, $fields_string, $fields_int, null); - } - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `sensors` table -// $names (required): array of sensor names -// $locations (required): array of location names -// $epiweeks (required): array of epiweek values/ranges -function get_sensors($names, $locations, $epiweeks) { - // basic query info - $table = '`sensors` s'; - $fields = "s.`name`, s.`location`, s.`epiweek`, s.`value`"; - $order = "s.`epiweek` ASC, s.`name` ASC, s.`location` ASC"; - // data type of each field - $fields_string = array('name', 'location'); - $fields_int = array('epiweek'); - $fields_float = array('value'); - // build the name filter - $condition_name = filter_strings('s.`name`', $names); - // build the location filter - $condition_location = filter_strings('s.`location`', $locations); - // build the epiweek filter - $condition_epiweek = filter_integers('s.`epiweek`', $epiweeks); - // the query - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_name}) AND ({$condition_location}) AND ({$condition_epiweek}) ORDER BY {$order}"; - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `dengue_sensors` table -// $names (required): array of sensor names -// $locations (required): array of location names -// $epiweeks (required): array of epiweek values/ranges -function get_dengue_sensors($names, $locations, $epiweeks) { - // basic query info - $table = '`dengue_sensors` s'; - $fields = "s.`name`, s.`location`, s.`epiweek`, s.`value`"; - $order = "s.`epiweek` ASC, s.`name` ASC, s.`location` ASC"; - // data type of each field - $fields_string = array('name', 'location'); - $fields_int = array('epiweek'); - $fields_float = array('value'); - // build the name filter - $condition_name = filter_strings('s.`name`', $names); - // build the location filter - $condition_location = filter_strings('s.`location`', $locations); - // build the epiweek filter - $condition_epiweek = filter_integers('s.`epiweek`', $epiweeks); - // the query - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_name}) AND ({$condition_location}) AND ({$condition_epiweek}) ORDER BY {$order}"; - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `nowcasts` table -// $locations (required): array of location names -// $epiweeks (required): array of epiweek values/ranges -function get_nowcast($locations, $epiweeks) { - // basic query info - $table = '`nowcasts` n'; - $fields = "n.`location`, n.`epiweek`, n.`value`, n.`std`"; - $order = "n.`epiweek` ASC, n.`location` ASC"; - // data type of each field - $fields_string = array('location'); - $fields_int = array('epiweek'); - $fields_float = array('value', 'std'); - // build the location filter - $condition_location = filter_strings('n.`location`', $locations); - // build the epiweek filter - $condition_epiweek = filter_integers('n.`epiweek`', $epiweeks); - // the query - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_location}) AND ({$condition_epiweek}) ORDER BY {$order}"; - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `dengue_nowcasts` table -// $locations (required): array of location names -// $epiweeks (required): array of epiweek values/ranges -function get_dengue_nowcast($locations, $epiweeks) { - // basic query info - $table = '`dengue_nowcasts` n'; - $fields = "n.`location`, n.`epiweek`, n.`value`, n.`std`"; - $order = "n.`epiweek` ASC, n.`location` ASC"; - // data type of each field - $fields_string = array('location'); - $fields_int = array('epiweek'); - $fields_float = array('value', 'std'); - // build the location filter - $condition_location = filter_strings('n.`location`', $locations); - // build the epiweek filter - $condition_epiweek = filter_integers('n.`epiweek`', $epiweeks); - // the query - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_location}) AND ({$condition_epiweek}) ORDER BY {$order}"; - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `covidcast` table. -// $source (required): name of upstream data source -// $signals (required): array of names for signals derived from upstream data -// $time_type (required): temporal resolution (e.g. day, week) -// $geo_type (required): spatial resolution (e.g. county, msa, state) -// $time_values (required): array of time values/ranges -// $geo_values (required): string, array of string, or `*` as a wildcard for all -// locations (specific to `$geo_type`) -// $issues (optional): array of time values/ranges -// overrides $lag -// default: most recent issue -// $lag (optional): number of time units between each time value and its issue -// overridden by $issues -// default: most recent issue -function get_covidcast($source, $signals, $time_type, $geo_type, $time_values, $geo_values, $as_of, $issues, $lag) { - // required for `mysqli_real_escape_string` - global $dbh; - $source = mysqli_real_escape_string($dbh, $source); - $time_type = mysqli_real_escape_string($dbh, $time_type); - $geo_type = mysqli_real_escape_string($dbh, $geo_type); - // basic query info - $table = '`covidcast` t'; - $fields = "t.`signal`, t.`time_value`, t.`geo_value`, t.`value`, t.`stderr`, t.`sample_size`, t.`direction`, t.`issue`, t.`lag`, t. `missing_value`, t. `missing_stderr`, t. `missing_sample_size`"; - $order = "t.`signal` ASC, t.`time_value` ASC, t.`geo_value` ASC, t.`issue` ASC"; - // data type of each field - $fields_string = array('geo_value', 'signal'); - $fields_int = array('time_value', 'direction', 'issue', 'lag', 'missing_value', 'missing_stderr', 'missing_sample_size'); - $fields_float = array('value', 'stderr', 'sample_size'); - // build the source, signal, time, and location (type and id) filters - $condition_source = "t.`source` = '{$source}'"; - $condition_signal = filter_strings('t.`signal`', $signals); - $condition_time_type = "t.`time_type` = '{$time_type}'"; - $condition_geo_type = "t.`geo_type` = '{$geo_type}'"; - $condition_time_value = filter_integers('t.`time_value`', $time_values); - - if ($geo_values === '*') { - // the wildcard query should return data for all locations in `geo_type` - $condition_geo_value = 'TRUE'; - } else if (is_array($geo_values)) { - // return data for multiple location - $condition_geo_value = filter_strings('t.`geo_value`', $geo_values); - } else { - // return data for a particular location - $geo_escaped_value = mysqli_real_escape_string($dbh, $geo_values); - $condition_geo_value = "t.`geo_value` = '{$geo_escaped_value}'"; - } - $conditions = "({$condition_source}) AND ({$condition_signal}) AND ({$condition_time_type}) AND ({$condition_geo_type}) AND ({$condition_time_value}) AND ({$condition_geo_value})"; - - $subquery = ""; - if ($issues !== null) { - //build the issue filter - $condition_issue = filter_integers('t.`issue`', $issues); - $condition_version = $condition_issue; - } else if ($lag !== null) { - //build the lag filter - $condition_lag = "(t.`lag` = {$lag})"; - $condition_version = $condition_lag; - } else if ($as_of !== null) { - // fetch most recent issues with as of - $sub_condition_asof = "(`issue` <= {$as_of})"; - $sub_fields = "max(`issue`) `max_issue`, `time_type`, `time_value`, `source`, `signal`, `geo_type`, `geo_value`"; - $sub_group = "`time_type`, `time_value`, `source`, `signal`, `geo_type`, `geo_value`"; - $sub_condition = "x.`max_issue` = t.`issue` AND x.`time_type` = t.`time_type` AND x.`time_value` = t.`time_value` AND x.`source` = t.`source` AND x.`signal` = t.`signal` AND x.`geo_type` = t.`geo_type` AND x.`geo_value` = t.`geo_value`"; - $subquery = "JOIN (SELECT {$sub_fields} FROM {$table} WHERE ({$conditions} AND {$sub_condition_asof}) GROUP BY {$sub_group}) x ON {$sub_condition}"; - $condition_version = 'TRUE'; - } else { - // fetch most recent issue fast - $condition_version = '(t.`is_latest_issue` IS TRUE)'; - } - // the query - $query = "SELECT {$fields} FROM {$table} {$subquery} WHERE {$conditions} AND ({$condition_version}) ORDER BY {$order}"; - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -function get_signal_dash_status_data() { - $query = 'SELECT enabled_signal.`name`, - enabled_signal.`source`, - enabled_signal.`covidcast_signal`, - status.`latest_issue`, - status.`latest_time_value` - FROM (SELECT `id`, `name`, `source`, `covidcast_signal`, `latest_status_update` - FROM `dashboard_signal` - WHERE `enabled`) AS enabled_signal - LEFT JOIN `dashboard_signal_status` AS status - ON enabled_signal.`latest_status_update` = status.`date` - AND enabled_signal.`id` = status.`signal_id`'; - - $epidata = array(); - $fields_string = array('name', 'source', 'covidcast_signal', 'latest_issue', 'latest_time_value'); - execute_query($query, $epidata, $fields_string, null /* fields_int */, null /* fields_float */); - - $coverage = get_signal_dash_coverage_data(); - - $out = array(); - foreach ($epidata as $signal) { - if (isset($coverage[$signal['name']])) { - $signal_with_coverage = $signal; - $signal_with_coverage['coverage'] = $coverage[$signal['name']]; - $out[] = $signal_with_coverage; - } - } - - // return the data - return count($out) === 0 ? null : $out; -} - -function get_signal_dash_coverage_data() { - $query = 'SELECT enabled_signal.`name`, - coverage.`date`, - coverage.`geo_type`, - coverage.`count` - FROM (SELECT `id`, `name`, `latest_coverage_update` - FROM `dashboard_signal` - WHERE `enabled`) AS enabled_signal - LEFT JOIN `dashboard_signal_coverage` AS coverage - ON enabled_signal.`id` = coverage.`signal_id` - ORDER BY `id` ASC, `date` DESC'; - - $epidata = array(); - $fields_string = array('name', 'date', 'geo_type'); - $fields_int = array('count'); - execute_query($query, $epidata, $fields_string, $fields_int, null /* fields_float */); - - $out = array(); - foreach ($epidata as $row) { - $name = $row['name']; - $geo_type = $row['geo_type']; - $timedata = array(); - $timedata['date'] = $row['date']; - $timedata['count'] =$row['count']; - - if (!isset($out[$name])) { - $out[$name] = array(); - } - - if(!isset($out[$name][$geo_type])) { - $out[$name][$geo_type] = array(); - } - - $out[$name][$geo_type][] = $timedata; - } - - // return the data - return count($out) === 0 ? null : $out; -} - -// queries the `covidcast_meta_cache` table for metadata -function get_covidcast_meta() { - // complain if the cache is more than 75 minutes old - $max_age = 75 * 60; - - // basic query info - $query = 'SELECT UNIX_TIMESTAMP(NOW()) - `timestamp` AS `age`, `epidata` FROM `covidcast_meta_cache` LIMIT 1'; - - // get the data from the database - global $dbh; - $epidata = null; - $result = mysqli_query($dbh, $query); - if($row = mysqli_fetch_array($result)) { - // parse and use the cached response - $epidata = json_decode($row['epidata'], true); - - if (intval($row['age']) > $max_age && strlen($row['epidata']) > 0) { - error_log('covidcast_meta cache is stale: '.$row['age']); - } - } - - if ($epidata !== null) { - // filter rows - $time_types = extract_values($_REQUEST['time_types'], 'str'); - $signals = isset($_REQUEST['signals']) ? array_map(function($signal) { - return explode(':', $signal, 2); - }, extract_values($_REQUEST['signals'], 'str')) : null; - $geo_types = extract_values($_REQUEST['geo_types'], 'str'); - - if ($time_types !== null || $signals !== null || $geo_types !== null) { - $epidata = array_values(array_filter($epidata, function($row) use(&$time_types, &$signals, &$geo_types) { - if ($time_types !== null && !in_array($row['time_type'], $time_types)) { - return false; - } - if ($geo_types !== null && !in_array($row['geo_type'], $geo_types)) { - return false; - } - if ($signals === null || count($signals) === 0) { - return true; - } - // filter by signal - foreach($signals as $signal) { - // match source and (signal or no signal or signal = *) - if ($row['data_source'] === $signal[0] && (count($signal) === 1 || $row['signal'] === $signal[1] || $signal[1] === '*')) { - return true; - } - } - return false; - })); - } - // filter fields - if (isset($_REQUEST['fields'])) { - $fields = extract_values($_REQUEST['fields'], 'str'); - - $epidata = array_map(function($row) use(&$fields) { - $filtered_row = []; - foreach($fields as $field) { - if (isset($row[$field])) { - $filtered_row[$field] = $row[$field]; - } - } - return $filtered_row; - }, $epidata); - } - } - - // return the data - $has_values = $epidata !== null && count($epidata) > 0; - return $has_values ? $epidata : null; -} - -// queries the `covid_hosp_state_timeseries` table -// $states (required): array of state abbreviations -// $dates (required): array of date values/ranges -// $issues (optional): array of date values/ranges -// default: most recent issue -function get_covid_hosp_state_timeseries($states, $dates, $issues) { - $epidata = array(); - $table = '`covid_hosp_state_timeseries` c'; - $fields = implode(', ', array( - 'c.`issue`', - 'c.`state`', - 'c.`date`', - 'c.`critical_staffing_shortage_today_yes`', - 'c.`critical_staffing_shortage_today_no`', - 'c.`critical_staffing_shortage_today_not_reported`', - 'c.`critical_staffing_shortage_anticipated_within_week_yes`', - 'c.`critical_staffing_shortage_anticipated_within_week_no`', - 'c.`critical_staffing_shortage_anticipated_within_week_not_reported`', - 'c.`hospital_onset_covid`', - 'c.`hospital_onset_covid_coverage`', - 'c.`inpatient_beds`', - 'c.`inpatient_beds_coverage`', - 'c.`inpatient_beds_used`', - 'c.`inpatient_beds_used_coverage`', - 'c.`inpatient_beds_used_covid`', - 'c.`inpatient_beds_used_covid_coverage`', - 'c.`previous_day_admission_adult_covid_confirmed`', - 'c.`previous_day_admission_adult_covid_confirmed_coverage`', - 'c.`previous_day_admission_adult_covid_suspected`', - 'c.`previous_day_admission_adult_covid_suspected_coverage`', - 'c.`previous_day_admission_pediatric_covid_confirmed`', - 'c.`previous_day_admission_pediatric_covid_confirmed_coverage`', - 'c.`previous_day_admission_pediatric_covid_suspected`', - 'c.`previous_day_admission_pediatric_covid_suspected_coverage`', - 'c.`staffed_adult_icu_bed_occupancy`', - 'c.`staffed_adult_icu_bed_occupancy_coverage`', - 'c.`staffed_icu_adult_patients_confirmed_suspected_covid`', - 'c.`staffed_icu_adult_patients_confirmed_suspected_covid_coverage`', - 'c.`staffed_icu_adult_patients_confirmed_covid`', - 'c.`staffed_icu_adult_patients_confirmed_covid_coverage`', - 'c.`total_adult_patients_hosp_confirmed_suspected_covid`', - 'c.`total_adult_patients_hosp_confirmed_suspected_covid_coverage`', - 'c.`total_adult_patients_hosp_confirmed_covid`', - 'c.`total_adult_patients_hosp_confirmed_covid_coverage`', - 'c.`total_pediatric_patients_hosp_confirmed_suspected_covid`', - 'c.`total_pediatric_patients_hosp_confirmed_suspected_covid_coverage`', - 'c.`total_pediatric_patients_hosp_confirmed_covid`', - 'c.`total_pediatric_patients_hosp_confirmed_covid_coverage`', - 'c.`total_staffed_adult_icu_beds`', - 'c.`total_staffed_adult_icu_beds_coverage`', - 'c.`inpatient_beds_utilization`', - 'c.`inpatient_beds_utilization_coverage`', - 'c.`inpatient_beds_utilization_numerator`', - 'c.`inpatient_beds_utilization_denominator`', - 'c.`percent_of_inpatients_with_covid`', - 'c.`percent_of_inpatients_with_covid_coverage`', - 'c.`percent_of_inpatients_with_covid_numerator`', - 'c.`percent_of_inpatients_with_covid_denominator`', - 'c.`inpatient_bed_covid_utilization`', - 'c.`inpatient_bed_covid_utilization_coverage`', - 'c.`inpatient_bed_covid_utilization_numerator`', - 'c.`inpatient_bed_covid_utilization_denominator`', - 'c.`adult_icu_bed_covid_utilization`', - 'c.`adult_icu_bed_covid_utilization_coverage`', - 'c.`adult_icu_bed_covid_utilization_numerator`', - 'c.`adult_icu_bed_covid_utilization_denominator`', - 'c.`adult_icu_bed_utilization`', - 'c.`adult_icu_bed_utilization_coverage`', - 'c.`adult_icu_bed_utilization_numerator`', - 'c.`adult_icu_bed_utilization_denominator`', - )); - // basic query info - $order = "c.`date` ASC, c.`state` ASC, c.`issue` ASC"; - // build the date filter - $condition_date = filter_integers('c.`date`', $dates); - // build the state filter - $condition_state = filter_strings('c.`state`', $states); - if($issues !== null) { - // build the issue filter - $condition_issue = filter_integers('c.`issue`', $issues); - // final query using specific issues - $query = "WITH c as (SELECT {$fields}, ROW_NUMBER() OVER (PARTITION BY date, state, issue ORDER BY record_type) row FROM {$table} WHERE ({$condition_date}) AND ({$condition_state}) AND ({$condition_issue})) SELECT {$fields} FROM c where row = 1 ORDER BY {$order}"; - } else { - // final query using most recent issues - $subquery = "(SELECT max(`issue`) `max_issue`, `date`, `state` FROM {$table} WHERE ({$condition_date}) AND ({$condition_state}) GROUP BY `date`, `state`) x"; - $condition = "x.`max_issue` = c.`issue` AND x.`date` = c.`date` AND x.`state` = c.`state`"; - $query = "WITH c as (SELECT {$fields}, ROW_NUMBER() OVER (PARTITION BY date, state, issue ORDER BY record_type) row FROM {$table} JOIN {$subquery} ON {$condition}) select {$fields} FROM c WHERE row = 1 ORDER BY {$order}"; - } - // get the data from the database - $fields_string = array('state'); - $fields_int = array( - 'issue', - 'date', - 'critical_staffing_shortage_today_yes', - 'critical_staffing_shortage_today_no', - 'critical_staffing_shortage_today_not_reported', - 'critical_staffing_shortage_anticipated_within_week_yes', - 'critical_staffing_shortage_anticipated_within_week_no', - 'critical_staffing_shortage_anticipated_within_week_not_reported', - 'hospital_onset_covid', - 'hospital_onset_covid_coverage', - 'inpatient_beds', - 'inpatient_beds_coverage', - 'inpatient_beds_used', - 'inpatient_beds_used_coverage', - 'inpatient_beds_used_covid', - 'inpatient_beds_used_covid_coverage', - 'previous_day_admission_adult_covid_confirmed', - 'previous_day_admission_adult_covid_confirmed_coverage', - 'previous_day_admission_adult_covid_suspected', - 'previous_day_admission_adult_covid_suspected_coverage', - 'previous_day_admission_pediatric_covid_confirmed', - 'previous_day_admission_pediatric_covid_confirmed_coverage', - 'previous_day_admission_pediatric_covid_suspected', - 'previous_day_admission_pediatric_covid_suspected_coverage', - 'staffed_adult_icu_bed_occupancy', - 'staffed_adult_icu_bed_occupancy_coverage', - 'staffed_icu_adult_patients_confirmed_suspected_covid', - 'staffed_icu_adult_patients_confirmed_suspected_covid_coverage', - 'staffed_icu_adult_patients_confirmed_covid', - 'staffed_icu_adult_patients_confirmed_covid_coverage', - 'total_adult_patients_hosp_confirmed_suspected_covid', - 'total_adult_patients_hosp_confirmed_suspected_covid_coverage', - 'total_adult_patients_hosp_confirmed_covid', - 'total_adult_patients_hosp_confirmed_covid_coverage', - 'total_pediatric_patients_hosp_confirmed_suspected_covid', - 'total_pediatric_patients_hosp_confirmed_suspected_covid_coverage', - 'total_pediatric_patients_hosp_confirmed_covid', - 'total_pediatric_patients_hosp_confirmed_covid_coverage', - 'total_staffed_adult_icu_beds', - 'total_staffed_adult_icu_beds_coverage', - 'inpatient_beds_utilization_coverage', - 'inpatient_beds_utilization_numerator', - 'inpatient_beds_utilization_denominator', - 'percent_of_inpatients_with_covid_coverage', - 'percent_of_inpatients_with_covid_numerator', - 'percent_of_inpatients_with_covid_denominator', - 'inpatient_bed_covid_utilization_coverage', - 'inpatient_bed_covid_utilization_numerator', - 'inpatient_bed_covid_utilization_denominator', - 'adult_icu_bed_covid_utilization_coverage', - 'adult_icu_bed_covid_utilization_numerator', - 'adult_icu_bed_covid_utilization_denominator', - 'adult_icu_bed_utilization_coverage', - 'adult_icu_bed_utilization_numerator', - 'adult_icu_bed_utilization_denominator', - ); - $fields_float = array( - 'inpatient_beds_utilization', - 'percent_of_inpatients_with_covid', - 'inpatient_bed_covid_utilization', - 'adult_icu_bed_covid_utilization', - 'adult_icu_bed_utilization', - ); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `covid_hosp_facility` table -// $hospital_pks (required): array of facility identifiers (`hospital_pk`) -// $collection_weeks (required): array of date values/ranges -// $publication_dates (optional): array of date values/ranges -// default: most recent issue -function get_covid_hosp_facility($hospital_pks, $collection_weeks, $publication_dates) { - $epidata = array(); - $table = '`covid_hosp_facility` c'; - $fields = implode(', ', array( - 'c.`publication_date`', - 'c.`hospital_pk`', - 'c.`collection_week`', - 'c.`state`', - 'c.`ccn`', - 'c.`hospital_name`', - 'c.`address`', - 'c.`city`', - 'c.`zip`', - 'c.`hospital_subtype`', - 'c.`fips_code`', - 'c.`is_metro_micro`', - 'c.`total_beds_7_day_avg`', - 'c.`all_adult_hospital_beds_7_day_avg`', - 'c.`all_adult_hospital_inpatient_beds_7_day_avg`', - 'c.`inpatient_beds_used_7_day_avg`', - 'c.`all_adult_hospital_inpatient_bed_occupied_7_day_avg`', - 'c.`total_adult_patients_hosp_confirmed_suspected_covid_7d_avg`', - 'c.`total_adult_patients_hospitalized_confirmed_covid_7_day_avg`', - 'c.`total_pediatric_patients_hosp_confirmed_suspected_covid_7d_avg`', - 'c.`total_pediatric_patients_hospitalized_confirmed_covid_7_day_avg`', - 'c.`inpatient_beds_7_day_avg`', - 'c.`total_icu_beds_7_day_avg`', - 'c.`total_staffed_adult_icu_beds_7_day_avg`', - 'c.`icu_beds_used_7_day_avg`', - 'c.`staffed_adult_icu_bed_occupancy_7_day_avg`', - 'c.`staffed_icu_adult_patients_confirmed_suspected_covid_7d_avg`', - 'c.`staffed_icu_adult_patients_confirmed_covid_7_day_avg`', - 'c.`total_patients_hospitalized_confirmed_influenza_7_day_avg`', - 'c.`icu_patients_confirmed_influenza_7_day_avg`', - 'c.`total_patients_hosp_confirmed_influenza_and_covid_7d_avg`', - 'c.`total_beds_7_day_sum`', - 'c.`all_adult_hospital_beds_7_day_sum`', - 'c.`all_adult_hospital_inpatient_beds_7_day_sum`', - 'c.`inpatient_beds_used_7_day_sum`', - 'c.`all_adult_hospital_inpatient_bed_occupied_7_day_sum`', - 'c.`total_adult_patients_hosp_confirmed_suspected_covid_7d_sum`', - 'c.`total_adult_patients_hospitalized_confirmed_covid_7_day_sum`', - 'c.`total_pediatric_patients_hosp_confirmed_suspected_covid_7d_sum`', - 'c.`total_pediatric_patients_hospitalized_confirmed_covid_7_day_sum`', - 'c.`inpatient_beds_7_day_sum`', - 'c.`total_icu_beds_7_day_sum`', - 'c.`total_staffed_adult_icu_beds_7_day_sum`', - 'c.`icu_beds_used_7_day_sum`', - 'c.`staffed_adult_icu_bed_occupancy_7_day_sum`', - 'c.`staffed_icu_adult_patients_confirmed_suspected_covid_7d_sum`', - 'c.`staffed_icu_adult_patients_confirmed_covid_7_day_sum`', - 'c.`total_patients_hospitalized_confirmed_influenza_7_day_sum`', - 'c.`icu_patients_confirmed_influenza_7_day_sum`', - 'c.`total_patients_hosp_confirmed_influenza_and_covid_7d_sum`', - 'c.`total_beds_7_day_coverage`', - 'c.`all_adult_hospital_beds_7_day_coverage`', - 'c.`all_adult_hospital_inpatient_beds_7_day_coverage`', - 'c.`inpatient_beds_used_7_day_coverage`', - 'c.`all_adult_hospital_inpatient_bed_occupied_7_day_coverage`', - 'c.`total_adult_patients_hosp_confirmed_suspected_covid_7d_cov`', - 'c.`total_adult_patients_hospitalized_confirmed_covid_7_day_coverage`', - 'c.`total_pediatric_patients_hosp_confirmed_suspected_covid_7d_cov`', - 'c.`total_pediatric_patients_hosp_confirmed_covid_7d_cov`', - 'c.`inpatient_beds_7_day_coverage`', - 'c.`total_icu_beds_7_day_coverage`', - 'c.`total_staffed_adult_icu_beds_7_day_coverage`', - 'c.`icu_beds_used_7_day_coverage`', - 'c.`staffed_adult_icu_bed_occupancy_7_day_coverage`', - 'c.`staffed_icu_adult_patients_confirmed_suspected_covid_7d_cov`', - 'c.`staffed_icu_adult_patients_confirmed_covid_7_day_coverage`', - 'c.`total_patients_hospitalized_confirmed_influenza_7_day_coverage`', - 'c.`icu_patients_confirmed_influenza_7_day_coverage`', - 'c.`total_patients_hosp_confirmed_influenza_and_covid_7d_cov`', - 'c.`previous_day_admission_adult_covid_confirmed_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_18_19_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_20_29_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_30_39_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_40_49_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_50_59_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_60_69_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_70_79_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_80plus_7_day_sum`', - 'c.`previous_day_admission_adult_covid_confirmed_unknown_7_day_sum`', - 'c.`previous_day_admission_pediatric_covid_confirmed_7_day_sum`', - 'c.`previous_day_covid_ed_visits_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_18_19_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_20_29_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_30_39_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_40_49_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_50_59_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_60_69_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_70_79_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_80plus_7_day_sum`', - 'c.`previous_day_admission_adult_covid_suspected_unknown_7_day_sum`', - 'c.`previous_day_admission_pediatric_covid_suspected_7_day_sum`', - 'c.`previous_day_total_ed_visits_7_day_sum`', - 'c.`previous_day_admission_influenza_confirmed_7_day_sum`', - )); - // basic query info - $order = "c.`collection_week` ASC, c.`hospital_pk` ASC, c.`publication_date` ASC"; - // build the date filter - $condition_collection_week = filter_integers('c.`collection_week`', $collection_weeks); - // build the state filter - $condition_hospital_pk = filter_strings('c.`hospital_pk`', $hospital_pks); - if($publication_dates !== null) { - // build the issue filter - $condition_publication_date = filter_integers('c.`publication_date`', $publication_dates); - // final query using specific issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition_collection_week}) AND ({$condition_hospital_pk}) AND ({$condition_publication_date}) ORDER BY {$order}"; - } else { - // final query using most recent issues - $subquery = "(SELECT max(`publication_date`) `max_publication_date`, `collection_week`, `hospital_pk` FROM {$table} WHERE ({$condition_collection_week}) AND ({$condition_hospital_pk}) GROUP BY `collection_week`, `hospital_pk`) x"; - $condition = "x.`max_publication_date` = c.`publication_date` AND x.`collection_week` = c.`collection_week` AND x.`hospital_pk` = c.`hospital_pk`"; - $query = "SELECT {$fields} FROM {$table} JOIN {$subquery} ON {$condition} ORDER BY {$order}"; - } - // get the data from the database - $fields_string = array( - 'hospital_pk', - 'state', - 'ccn', - 'hospital_name', - 'address', - 'city', - 'zip', - 'hospital_subtype', - 'fips_code', - ); - $fields_int = array( - 'publication_date', - 'collection_week', - 'is_metro_micro', - 'total_beds_7_day_sum', - 'all_adult_hospital_beds_7_day_sum', - 'all_adult_hospital_inpatient_beds_7_day_sum', - 'inpatient_beds_used_7_day_sum', - 'all_adult_hospital_inpatient_bed_occupied_7_day_sum', - 'total_adult_patients_hosp_confirmed_suspected_covid_7d_sum', - 'total_adult_patients_hospitalized_confirmed_covid_7_day_sum', - 'total_pediatric_patients_hosp_confirmed_suspected_covid_7d_sum', - 'total_pediatric_patients_hospitalized_confirmed_covid_7_day_sum', - 'inpatient_beds_7_day_sum', - 'total_icu_beds_7_day_sum', - 'total_staffed_adult_icu_beds_7_day_sum', - 'icu_beds_used_7_day_sum', - 'staffed_adult_icu_bed_occupancy_7_day_sum', - 'staffed_icu_adult_patients_confirmed_suspected_covid_7d_sum', - 'staffed_icu_adult_patients_confirmed_covid_7_day_sum', - 'total_patients_hospitalized_confirmed_influenza_7_day_sum', - 'icu_patients_confirmed_influenza_7_day_sum', - 'total_patients_hosp_confirmed_influenza_and_covid_7d_sum', - 'total_beds_7_day_coverage', - 'all_adult_hospital_beds_7_day_coverage', - 'all_adult_hospital_inpatient_beds_7_day_coverage', - 'inpatient_beds_used_7_day_coverage', - 'all_adult_hospital_inpatient_bed_occupied_7_day_coverage', - 'total_adult_patients_hosp_confirmed_suspected_covid_7d_cov', - 'total_adult_patients_hospitalized_confirmed_covid_7_day_coverage', - 'total_pediatric_patients_hosp_confirmed_suspected_covid_7d_cov', - 'total_pediatric_patients_hosp_confirmed_covid_7d_cov', - 'inpatient_beds_7_day_coverage', - 'total_icu_beds_7_day_coverage', - 'total_staffed_adult_icu_beds_7_day_coverage', - 'icu_beds_used_7_day_coverage', - 'staffed_adult_icu_bed_occupancy_7_day_coverage', - 'staffed_icu_adult_patients_confirmed_suspected_covid_7d_cov', - 'staffed_icu_adult_patients_confirmed_covid_7_day_coverage', - 'total_patients_hospitalized_confirmed_influenza_7_day_coverage', - 'icu_patients_confirmed_influenza_7_day_coverage', - 'total_patients_hosp_confirmed_influenza_and_covid_7d_cov', - 'previous_day_admission_adult_covid_confirmed_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_18_19_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_20_29_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_30_39_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_40_49_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_50_59_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_60_69_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_70_79_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_80plus_7_day_sum', - 'previous_day_admission_adult_covid_confirmed_unknown_7_day_sum', - 'previous_day_admission_pediatric_covid_confirmed_7_day_sum', - 'previous_day_covid_ed_visits_7_day_sum', - 'previous_day_admission_adult_covid_suspected_7_day_sum', - 'previous_day_admission_adult_covid_suspected_18_19_7_day_sum', - 'previous_day_admission_adult_covid_suspected_20_29_7_day_sum', - 'previous_day_admission_adult_covid_suspected_30_39_7_day_sum', - 'previous_day_admission_adult_covid_suspected_40_49_7_day_sum', - 'previous_day_admission_adult_covid_suspected_50_59_7_day_sum', - 'previous_day_admission_adult_covid_suspected_60_69_7_day_sum', - 'previous_day_admission_adult_covid_suspected_70_79_7_day_sum', - 'previous_day_admission_adult_covid_suspected_80plus_7_day_sum', - 'previous_day_admission_adult_covid_suspected_unknown_7_day_sum', - 'previous_day_admission_pediatric_covid_suspected_7_day_sum', - 'previous_day_total_ed_visits_7_day_sum', - 'previous_day_admission_influenza_confirmed_7_day_sum', - ); - $fields_float = array( - 'total_beds_7_day_avg', - 'all_adult_hospital_beds_7_day_avg', - 'all_adult_hospital_inpatient_beds_7_day_avg', - 'inpatient_beds_used_7_day_avg', - 'all_adult_hospital_inpatient_bed_occupied_7_day_avg', - 'total_adult_patients_hosp_confirmed_suspected_covid_7d_avg', - 'total_adult_patients_hospitalized_confirmed_covid_7_day_avg', - 'total_pediatric_patients_hosp_confirmed_suspected_covid_7d_avg', - 'total_pediatric_patients_hospitalized_confirmed_covid_7_day_avg', - 'inpatient_beds_7_day_avg', - 'total_icu_beds_7_day_avg', - 'total_staffed_adult_icu_beds_7_day_avg', - 'icu_beds_used_7_day_avg', - 'staffed_adult_icu_bed_occupancy_7_day_avg', - 'staffed_icu_adult_patients_confirmed_suspected_covid_7d_avg', - 'staffed_icu_adult_patients_confirmed_covid_7_day_avg', - 'total_patients_hospitalized_confirmed_influenza_7_day_avg', - 'icu_patients_confirmed_influenza_7_day_avg', - 'total_patients_hosp_confirmed_influenza_and_covid_7d_avg', - ); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries the `covid_hosp_facility` table for hospital discovery -// $state (optional): 2-letter state abbreviation -// $ccn (optional): cms certification number (ccn) of the given facility -// $city (optional): name of -// $zip (optional): 2-letter state abbreviation -// $fips_code (optional): 2-letter state abbreviation -// note: exactly one of the above parameters should be non-null. if more than -// one is non-null, then only the first filter will be used. -function get_covid_hosp_facility_lookup($state, $ccn, $city, $zip, $fips_code) { - $epidata = array(); - $table = '`covid_hosp_facility` c'; - $fields = implode(', ', array( - 'c.`hospital_pk`', - 'MAX(c.`state`) `state`', - 'MAX(c.`ccn`) `ccn`', - 'MAX(c.`hospital_name`) `hospital_name`', - 'MAX(c.`address`) `address`', - 'MAX(c.`city`) `city`', - 'MAX(c.`zip`) `zip`', - 'MAX(c.`hospital_subtype`) `hospital_subtype`', - 'MAX(c.`fips_code`) `fips_code`', - 'MAX(c.`is_metro_micro`) `is_metro_micro`', - )); - // basic query info - $group = 'c.`hospital_pk`'; - $order = "c.`hospital_pk` ASC"; - // build the filter - // these are all fast because the table has indexes on each of these fields - $condition = 'FALSE'; - if ($state !== null) { - $condition = filter_strings('c.`state`', $state); - } else if ($ccn !== null) { - $condition = filter_strings('c.`ccn`', $ccn); - } else if ($city !== null) { - $condition = filter_strings('c.`city`', $city); - } else if ($zip !== null) { - $condition = filter_strings('c.`zip`', $zip); - } else if ($fips_code !== null) { - $condition = filter_strings('c.`fips_code`', $fips_code); - } - // final query using specific issues - $query = "SELECT {$fields} FROM {$table} WHERE ({$condition}) GROUP BY {$group} ORDER BY {$order}"; - // get the data from the database - $fields_string = array( - 'hospital_pk', - 'state', - 'ccn', - 'hospital_name', - 'address', - 'city', - 'zip', - 'hospital_subtype', - 'fips_code', - ); - $fields_int = array('is_metro_micro'); - $fields_float = null; - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - -// queries a bunch of epidata tables -function get_meta() { - // query and return metadata - return array(array( - '_api' => array( - 'minute' => meta_api(60), - 'hour' => meta_api(60 * 60), - 'day' => meta_api(60 * 60 * 24), - 'week' => meta_api(60 * 60 * 24 * 7), - 'month' => meta_api(60 * 60 * 24 * 30), - ), - 'fluview' => meta_fluview(), - 'twitter' => meta_twitter(), - 'wiki' => meta_wiki(), - 'delphi' => meta_delphi(), - )); -} -function meta_api($seconds) { - $epidata = array(); - $seconds = intval($seconds); - $query = "SELECT count(1) `num_hits`, count(distinct `ip`) `unique_ips`, sum(`num_rows`) `rows_returned` FROM `api_analytics` WHERE `datetime` >= date_sub(now(), interval {$seconds} second)"; - $fields_int = array('num_hits', 'unique_ips', 'rows_returned'); - execute_query($query, $epidata, null, $fields_int, null); - return count($epidata) === 0 ? null : $epidata; -} -function meta_fluview() { - $epidata = array(); - $query = 'SELECT max(`release_date`) `latest_update`, max(`issue`) `latest_issue`, count(1) `table_rows` FROM `fluview`'; - $fields_string = array('latest_update'); - $fields_int = array('latest_issue', 'table_rows'); - execute_query($query, $epidata, $fields_string, $fields_int, null); - return count($epidata) === 0 ? null : $epidata; -} -function meta_twitter() { - $epidata = array(); - $query = 'SELECT x.`date` `latest_update`, x.`table_rows`, count(distinct t.`state`) `num_states` FROM (SELECT max(`date`) `date`, count(1) `table_rows` FROM `twitter`) x JOIN `twitter` t ON t.`date` = x.`date`'; - $fields_string = array('latest_update'); - $fields_int = array('num_states', 'table_rows'); - execute_query($query, $epidata, $fields_string, $fields_int, null); - return count($epidata) === 0 ? null : $epidata; -} -function meta_wiki() { - $epidata = array(); - //$query = 'SELECT date_sub(max(`datetime`), interval 5 hour) `latest_update`, count(1) `table_rows` FROM `wiki_meta`'; // GMT to EST - $query = 'SELECT max(`datetime`) `latest_update`, count(1) `table_rows` FROM `wiki_meta`'; - $fields_string = array('latest_update'); - $fields_int = array('table_rows'); - execute_query($query, $epidata, $fields_string, $fields_int, null); - return count($epidata) === 0 ? null : $epidata; -} -function get_meta_norostat() { - // put behind appropriate auth check - $epidata_releases = array(); - $query = 'SELECT DISTINCT `release_date` FROM `norostat_raw_datatable_version_list`'; - execute_query($query, $epidata_releases, array('release_date'), null, null); - $epidata_locations = array(); - $query = 'SELECT DISTINCT `location` FROM `norostat_raw_datatable_location_pool`'; - execute_query($query, $epidata_locations, array('location'), null, null); - $epidata = array( - "releases" => $epidata_releases, - "locations" => $epidata_locations - ); - return $epidata; -} -function get_meta_afhsb() { - // put behind appropriate auth check - $table1 = 'afhsb_00to13_state'; - $table2 = 'afhsb_13to17_state'; - $epidata = array(); - $string_keys = array('state', 'country'); - $int_keys = array('flu_severity'); - foreach($string_keys as $key) { - $epidata_key = array(); - $query = "SELECT DISTINCT `{$key}` FROM (select `{$key}` from `{$table1}` union select `{$key}` from `{$table2}`) t"; - execute_query($query, $epidata_key, array($key), null, null); - $epidata[$key] = $epidata_key; - } - foreach($int_keys as $key) { - $epidata_key = array(); - $query = "SELECT DISTINCT `{$key}` FROM (select `{$key}` from `{$table1}` union select `{$key}` from `{$table2}`) t"; - - execute_query($query, $epidata_key, null, array($key), null); - $epidata[$key] = $epidata_key; - } - return $epidata; -} -function meta_delphi() { - $epidata = array(); - $query = 'SELECT `system`, min(`epiweek`) `first_week`, max(`epiweek`) `last_week`, count(1) `num_weeks` FROM `forecasts` GROUP BY `system` ORDER BY `system` ASC'; - $fields_string = array('system'); - $fields_int = array('first_week', 'last_week', 'num_weeks'); - execute_query($query, $epidata, $fields_string, $fields_int, null); - return count($epidata) === 0 ? null : $epidata; -} - -function get_covidcast_nowcast($source, $signals, $sensor_names, $time_type, $geo_type, $time_values, $geo_values, $as_of, $issues, $lag) { - // required for `mysqli_real_escape_string` - global $dbh; - $source = mysqli_real_escape_string($dbh, $source); - $time_type = mysqli_real_escape_string($dbh, $time_type); - $geo_type = mysqli_real_escape_string($dbh, $geo_type); - // basic query info - $table = '`covidcast_nowcast` t'; - $fields = "t.`signal`, t.`time_value`, t.`geo_value`, t.`value`, t.`issue`, t.`lag`"; - $order = "t.`signal` ASC, t.`time_value` ASC, t.`geo_value` ASC, t.`issue` ASC"; - // data type of each field - $fields_string = array('geo_value', 'signal'); - $fields_int = array('time_value', 'issue', 'lag'); - $fields_float = array('value'); - // build the source, signal, time, and location (type and id) filters - $condition_source = "t.`source` = '{$source}'"; - $condition_signal = filter_strings('t.`signal`', $signals); - $condition_sensor_name = filter_strings('t.`sensor_name`', $sensor_names); - $condition_time_type = "t.`time_type` = '{$time_type}'"; - $condition_geo_type = "t.`geo_type` = '{$geo_type}'"; - $condition_time_value = filter_integers('t.`time_value`', $time_values); - - if ($geo_values === '*') { - // the wildcard query should return data for all locations in `geo_type` - $condition_geo_value = 'TRUE'; - } else if (is_array($geo_values)) { - // return data for multiple location - $condition_geo_value = filter_strings('t.`geo_value`', $geo_values); - } else { - // return data for a particular location - $geo_escaped_value = mysqli_real_escape_string($dbh, $geo_values); - $condition_geo_value = "t.`geo_value` = '{$geo_escaped_value}'"; - } - $conditions = "({$condition_source}) AND ({$condition_signal}) AND ({$condition_sensor_name}) AND ({$condition_time_type}) AND ({$condition_geo_type}) AND ({$condition_time_value}) AND ({$condition_geo_value})"; - - $subquery = ""; - if ($issues !== null) { - //build the issue filter - $condition_issue = filter_integers('t.`issue`', $issues); - $query = "SELECT {$fields} FROM {$table} {$subquery} WHERE {$conditions} AND ({$condition_issue}) ORDER BY {$order}"; - } else if ($lag !== null) { - //build the lag filter - $condition_lag = "(t.`lag` = {$lag})"; - $query = "SELECT {$fields} FROM {$table} {$subquery} WHERE {$conditions} AND ({$condition_lag}) ORDER BY {$order}"; - } else if ($as_of !== null) { - // fetch most recent issues with as of - $sub_condition_asof = "(`issue` <= {$as_of})"; - $sub_fields = "max(`issue`) `max_issue`, `time_type`, `time_value`, `source`, `signal`, `geo_type`, `geo_value`"; - $sub_group = "`time_type`, `time_value`, `source`, `signal`, `geo_type`, `geo_value`"; - $sub_condition = "x.`max_issue` = t.`issue` AND x.`time_type` = t.`time_type` AND x.`time_value` = t.`time_value` AND x.`source` = t.`source` AND x.`signal` = t.`signal` AND x.`geo_type` = t.`geo_type` AND x.`geo_value` = t.`geo_value`"; - $subquery = "JOIN (SELECT {$sub_fields} FROM {$table} WHERE ({$conditions} AND {$sub_condition_asof}) GROUP BY {$sub_group}) x ON {$sub_condition}"; - $condition_version = 'TRUE'; - $query = "SELECT {$fields} FROM {$table} {$subquery} WHERE {$conditions} AND ({$condition_version}) ORDER BY {$order}"; - } else { - // fetch most recent issue fast - $query = "WITH t as (SELECT {$fields}, ROW_NUMBER() OVER (PARTITION BY t.`time_type`, t.`time_value`, t.`source`, t.`signal`, t.`geo_type`, t.`geo_value` ORDER BY t.`issue` DESC) row FROM {$table} {$subquery} WHERE {$conditions}) SELECT {$fields} FROM t where row = 1 ORDER BY {$order}"; - } - // get the data from the database - $epidata = array(); - execute_query($query, $epidata, $fields_string, $fields_int, $fields_float); - // return the data - return count($epidata) === 0 ? null : $epidata; -} - - -// all responses will have a result field -$data = array('result' => -1); -// connect to the database -if(database_connect()) { - - // select the data source - // endpoint parameter with a fallback to source parameter for compatibility reasons - $endpoint = isset($_REQUEST['endpoint']) ? strtolower($_REQUEST['endpoint']) : (isset($_REQUEST['source']) ? strtolower($_REQUEST['source']) : null); - - if($endpoint === 'fluview') { - if(require_all($data, array('epiweeks', 'regions'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $regions = extract_values($_REQUEST['regions'], 'str'); - $issues = isset($_REQUEST['issues']) ? extract_values($_REQUEST['issues'], 'int') : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - $authorized = isset($_REQUEST['auth']) && $_REQUEST['auth'] === $AUTH['fluview']; - // get the data - $epidata = get_fluview($epiweeks, $regions, $issues, $lag, $authorized); - store_result($data, $epidata); - } - } else if($endpoint === 'fluview_meta') { - // get the data - $epidata = meta_fluview(); - store_result($data, $epidata); - } else if ($endpoint === 'fluview_clinical') { - if(require_all($data, array('epiweeks', 'regions'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $regions = extract_values($_REQUEST['regions'], 'str'); - $issues = isset($_REQUEST['issues']) ? extract_values($_REQUEST['issues'], 'int') : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - // get the data - $epidata = get_fluview_clinical($epiweeks, $regions, $issues, $lag); - store_result($data, $epidata); - } - } else if($endpoint === 'flusurv') { - if(require_all($data, array('epiweeks', 'locations'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $locations = extract_values($_REQUEST['locations'], 'str'); - $issues = isset($_REQUEST['issues']) ? extract_values($_REQUEST['issues'], 'int') : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - // get the data - $epidata = get_flusurv($epiweeks, $locations, $issues, $lag); - store_result($data, $epidata); - } - } else if ($endpoint === 'paho_dengue') { - if(require_all($data, array('epiweeks', 'regions'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $regions = extract_values($_REQUEST['regions'], 'str'); - $issues = isset($_REQUEST['issues']) ? extract_values($_REQUEST['issues'], 'int') : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - // get the data - $epidata = get_paho_dengue($epiweeks, $regions, $issues, $lag); - store_result($data, $epidata); - } - } else if ($endpoint === 'ecdc_ili') { - if(require_all($data, array('epiweeks', 'regions'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $regions = extract_values($_REQUEST['regions'], 'str'); - $issues = isset($_REQUEST['issues']) ? extract_values($_REQUEST['issues'], 'int') : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - // get the data - $epidata = get_ecdc_ili($epiweeks, $regions, $issues, $lag); - store_result($data, $epidata); - } - } else if ($endpoint === 'kcdc_ili') { - if(require_all($data, array('epiweeks', 'regions'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $regions = extract_values($_REQUEST['regions'], 'str'); - $issues = isset($_REQUEST['issues']) ? extract_values($_REQUEST['issues'], 'int') : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - // get the data - $epidata = get_kcdc_ili($epiweeks, $regions, $issues, $lag); - store_result($data, $epidata); - } - } else if($endpoint === 'ilinet' || $endpoint === 'stateili') { - // these two sources are now combined into fluview - $data['message'] = 'use fluview instead'; - } else if($endpoint === 'gft') { - if(require_all($data, array('epiweeks', 'locations'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $locations = extract_values($_REQUEST['locations'], 'str'); - // get the data - $epidata = get_gft($epiweeks, $locations); - store_result($data, $epidata); - } - } else if($endpoint === 'ght') { - if(require_all($data, array('auth', 'epiweeks', 'locations', 'query'))) { - if($_REQUEST['auth'] === $AUTH['ght']) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $locations = extract_values($_REQUEST['locations'], 'str'); - $query = $_REQUEST['query']; - // get the data - $epidata = get_ght($epiweeks, $locations, $query); - store_result($data, $epidata); - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'twitter') { - if(require_all($data, array('auth', 'locations'))) { - if($_REQUEST['auth'] === $AUTH['twitter']) { - // parse the request - $locations = extract_values($_REQUEST['locations'], 'str'); - if(require_any($data, array('dates', 'epiweeks'))) { - if(isset($_REQUEST['dates'])) { - $resolution = 'daily'; - $dates = extract_values($_REQUEST['dates'], 'int'); - } else { - $resolution = 'weekly'; - $dates = extract_values($_REQUEST['epiweeks'], 'int'); - } - // get the data - $epidata = get_twitter($locations, $dates, $resolution); - store_result($data, $epidata); - } - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'wiki') { - if(require_all($data, array('articles', 'language'))) { - // parse the request - $articles = extract_values($_REQUEST['articles'], 'str'); - $language = $_REQUEST['language']; - if(require_any($data, array('dates', 'epiweeks'))) { - if(isset($_REQUEST['dates'])) { - $resolution = 'daily'; - $dates = extract_values($_REQUEST['dates'], 'int'); - } else { - $resolution = 'weekly'; - $dates = extract_values($_REQUEST['epiweeks'], 'int'); - } - $hours = isset($_REQUEST['hours']) ? extract_values($_REQUEST['hours'], 'int') : null; - // get the data - $epidata = get_wiki($articles, $language, $dates, $resolution, $hours); - store_result($data, $epidata); - } - } - } else if($endpoint === 'quidel') { - if(require_all($data, array('auth', 'locations', 'epiweeks'))) { - if($_REQUEST['auth'] === $AUTH['quidel']) { - // parse the request - $locations = extract_values($_REQUEST['locations'], 'str'); - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - // get the data - $epidata = get_quidel($locations, $epiweeks); - store_result($data, $epidata); - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'norostat') { - if(require_all($data, array('auth', 'location', 'epiweeks'))) { - if($_REQUEST['auth'] === $AUTH['norostat']) { - // parse the request - $location = $_REQUEST['location']; - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - // get the data - $epidata = get_norostat($location, $epiweeks); - store_result($data, $epidata); - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'afhsb') { - if(require_all($data, array('auth', 'locations', 'epiweeks', 'flu_types'))) { - if($_REQUEST['auth'] === $AUTH['afhsb']) { - // parse the request - $locations = extract_values($_REQUEST['locations'], 'str'); - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $flu_types = extract_values($_REQUEST['flu_types'], 'str'); - // get the data - $epidata = get_afhsb($locations, $epiweeks, $flu_types); - store_result($data, $epidata); - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'nidss_flu') { - if(require_all($data, array('epiweeks', 'regions'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $regions = extract_values($_REQUEST['regions'], 'str'); - $issues = isset($_REQUEST['issues']) ? extract_values($_REQUEST['issues'], 'int') : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - // get the data - $epidata = get_nidss_flu($epiweeks, $regions, $issues, $lag); - store_result($data, $epidata); - } - } else if($endpoint === 'nidss_dengue') { - if(require_all($data, array('epiweeks', 'locations'))) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $locations = extract_values($_REQUEST['locations'], 'str'); - // get the data - $epidata = get_nidss_dengue($epiweeks, $locations); - store_result($data, $epidata); - } - } else if($endpoint === 'delphi') { - if(require_all($data, array('system', 'epiweek'))) { - // parse the request - $system = $_REQUEST['system']; - $epiweek = intval($_REQUEST['epiweek']); - // get the data - $epidata = get_forecast($system, $epiweek); - store_result($data, $epidata); - } - } else if($endpoint === 'signals') { - // this sources is now replaced by sensors - $data['message'] = 'use sensors instead'; - } else if($endpoint === 'cdc') { - if(require_all($data, array('auth', 'epiweeks', 'locations'))) { - if($_REQUEST['auth'] === $AUTH['cdc']) { - // parse the request - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - $locations = extract_values($_REQUEST['locations'], 'str'); - // get the data - $epidata = get_cdc($epiweeks, $locations); - store_result($data, $epidata); - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'sensors') { - if(require_all($data, array('names', 'locations', 'epiweeks'))) { - if(!array_key_exists('auth', $_REQUEST)) { - $auth_tokens_presented = array(); - } else { - $auth_tokens_presented = extract_values($_REQUEST['auth'], 'str'); - } - $names = extract_values($_REQUEST['names'], 'str'); - $n_names = count($names); - $n_auth_tokens_presented = count($auth_tokens_presented); - $max_valid_granular_tokens_per_name = max(array_map('count', $GRANULAR_SENSOR_AUTH_TOKENS)); - // The number of valid granular tokens is related to the number of auth token checks that a single query could perform. Use the max number of valid granular auth tokens per name in the check below as a way to prevent leakage of sensor names (but revealing the number of sensor names) via this interface. Treat all sensors as non-open for convenience of calculation. - if($n_names === 0) { - // Check whether no names were provided to prevent edge-case issues in error message below, and in case surrounding behavior changes in the future: - $data['message'] = 'no sensor names provided'; - } else if($n_auth_tokens_presented > 1) { - $data['message'] = 'currently, only a single auth token is allowed to be presented at a time; please issue a separate query for each sensor name using only the corresponding token'; - } else if( - // Check whether max number of presented-vs.-acceptable token comparisons that would be performed is over the set limits, avoiding calculation of numbers > PHP_INT_MAX/100: - // Global auth token comparison limit check: - $n_auth_tokens_presented > $MAX_GLOBAL_AUTH_CHECKS_PER_SENSOR_QUERY || - // Granular auth token comparison limit check: - $n_names > (int)((PHP_INT_MAX/100-1)/max(1,$max_valid_granular_tokens_per_name)) || - $n_auth_tokens_presented > (int)(PHP_INT_MAX/100/max(1,$n_names*$max_valid_granular_tokens_per_name)) || - $n_auth_tokens_presented * $n_names * $max_valid_granular_tokens_per_name > $MAX_GRANULAR_AUTH_CHECKS_PER_SENSOR_QUERY - ) { - $data['message'] = 'too many sensors requested and/or auth tokens presented; please divide sensors into batches and/or use only the tokens needed for the sensors requested'; - } else if(count($auth_tokens_presented) > $MAX_AUTH_KEYS_PROVIDED_PER_SENSOR_QUERY) { - // this check should be redundant with >1 check as well as global check above - $data['message'] = 'too many auth tokens presented'; - } else { - $unauthenticated_or_nonexistent_sensors = array(); - foreach($names as $name) { - $sensor_is_open = in_array($name, $OPEN_SENSORS); - // test whether they provided the "global" auth token that works for all sensors: - $sensor_authenticated_globally = in_array($AUTH['sensors'], $auth_tokens_presented); - // test whether they provided a "granular" auth token for one of the - // sensor_subsets containing this sensor (if any): - $sensor_authenticated_granularly = false; - if(array_key_exists($name, $GRANULAR_SENSOR_AUTH_TOKENS)) { - $acceptable_granular_tokens_for_sensor = $GRANULAR_SENSOR_AUTH_TOKENS[$name]; - // check for nonempty intersection between provided and acceptable - // granular auth tokens: - foreach($acceptable_granular_tokens_for_sensor as $acceptable_granular_token) { - if(in_array($acceptable_granular_token, $auth_tokens_presented)) { - $sensor_authenticated_granularly = true; - break; - } - } - } // (else: there are no granular tokens for this sensor; can't authenticate granularly) - if(! $sensor_is_open && - ! $sensor_authenticated_globally && - ! $sensor_authenticated_granularly) { - // authentication failed for this sensor; append to list: - array_push($unauthenticated_or_nonexistent_sensors, $name); - } - } - if (!empty($unauthenticated_or_nonexistent_sensors)) { - $data['message'] = 'unauthenticated/nonexistent sensor(s): ' . implode(',', $unauthenticated_or_nonexistent_sensors); - // // Alternative message that may enable shorter tokens: - // $data['message'] = 'some/all sensors requested were unauthenticated/nonexistent'; - } else { - // parse the request - $locations = extract_values($_REQUEST['locations'], 'str'); - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - // get the data - $epidata = get_sensors($names, $locations, $epiweeks); - store_result($data, $epidata); - } - } - } - } else if($endpoint === 'dengue_sensors') { - if(require_all($data, array('auth', 'names', 'locations', 'epiweeks'))) { - if($_REQUEST['auth'] === $AUTH['sensors']) { - // parse the request - $names = extract_values($_REQUEST['names'], 'str'); - $locations = extract_values($_REQUEST['locations'], 'str'); - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - // get the data - $epidata = get_dengue_sensors($names, $locations, $epiweeks); - store_result($data, $epidata); - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'nowcast') { - if(require_all($data, array('locations', 'epiweeks'))) { - // parse the request - $locations = extract_values($_REQUEST['locations'], 'str'); - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - // get the data - $epidata = get_nowcast($locations, $epiweeks); - store_result($data, $epidata); - } - } else if($endpoint === 'dengue_nowcast') { - if(require_all($data, array('locations', 'epiweeks'))) { - // parse the request - $locations = extract_values($_REQUEST['locations'], 'str'); - $epiweeks = extract_values($_REQUEST['epiweeks'], 'int'); - // get the data - $epidata = get_dengue_nowcast($locations, $epiweeks); - store_result($data, $epidata); - } - } else if($endpoint === 'meta') { - // get the data - $epidata = get_meta(); - store_result($data, $epidata); - } else if($endpoint === 'meta_norostat') { - if(require_all($data, array('auth'))) { - if($_REQUEST['auth'] === $AUTH['norostat']) { - $epidata = get_meta_norostat(); - store_result($data, $epidata); - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'meta_afhsb') { - if(require_all($data, array('auth'))) { - if($_REQUEST['auth'] === $AUTH['afhsb']) { - $epidata = get_meta_afhsb(); - store_result($data, $epidata); - } else { - $data['message'] = 'unauthenticated'; - } - } - } else if($endpoint === 'covidcast') { - if(require_all($data, array('data_source', 'time_type', 'geo_type', 'time_values')) - && require_any($data, array('signal', 'signals')) - && require_any($data, array('geo_value', 'geo_values'))) { - // parse the request - $time_values = extract_dates($_REQUEST['time_values']); - $as_of = isset($_REQUEST['as_of']) ? parse_date($_REQUEST['as_of']) : null; - $issues = isset($_REQUEST['issues']) ? extract_dates($_REQUEST['issues']) : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - $signals = extract_values(isset($_REQUEST['signals']) ? $_REQUEST['signals'] : $_REQUEST['signal'], 'string'); - $geo_values = isset($_REQUEST['geo_value']) ? $_REQUEST['geo_value'] : extract_values($_REQUEST['geo_values'], 'string'); - // get the data - $epidata = get_covidcast( - $_REQUEST['data_source'], - $signals, - $_REQUEST['time_type'], - $_REQUEST['geo_type'], - $time_values, - $geo_values, - $as_of, - $issues, - $lag); - if(isset($_REQUEST['format']) && $_REQUEST['format']=="tree") { - //organize results by signal - $epi_tree = array(); - $key = -1; - foreach ($epidata as $row) { - if ($key != $row['signal']) { - $key = $row['signal']; - $epi_tree[$key] = array(); - } - unset($row['signal']); - array_push($epi_tree[$key],$row); - } - $epidata = array($epi_tree); - } - store_result($data, $epidata); - } - } else if($endpoint === 'covidcast_meta') { - // get the metadata - $epidata = get_covidcast_meta(); - store_result($data, $epidata); - } else if($endpoint === 'signal_dashboard_status') { - $signal_dash_data = get_signal_dash_status_data(); - store_result($data, $signal_dash_data); - } else if($endpoint === 'signal_dashboard_coverage') { - $signal_dash_data = get_signal_dash_coverage_data(); - store_result($data, $signal_dash_data); - } else if($endpoint === 'covid_hosp' || $source === 'covid_hosp_state_timeseries') { - if(require_all($data, array('states', 'dates'))) { - // parse the request - $states = extract_values($_REQUEST['states'], 'str'); - $dates = extract_values($_REQUEST['dates'], 'int'); - $issues = isset($_REQUEST['issues']) ? extract_values($_REQUEST['issues'], 'int') : null; - // get the data - $epidata = get_covid_hosp_state_timeseries($states, $dates, $issues); - store_result($data, $epidata); - } - } else if($endpoint === 'covid_hosp_facility') { - if(require_all($data, array('hospital_pks', 'collection_weeks'))) { - // parse the request - $hospital_pks = extract_values($_REQUEST['hospital_pks'], 'str'); - $collection_weeks = extract_values($_REQUEST['collection_weeks'], 'int'); - $publication_dates = isset($_REQUEST['publication_dates']) ? extract_values($_REQUEST['publication_dates'], 'int') : null; - // get the data - $epidata = get_covid_hosp_facility($hospital_pks, $collection_weeks, $publication_dates); - store_result($data, $epidata); - } - } else if($endpoint === 'covid_hosp_facility_lookup') { - if(require_any($data, array('state', 'ccn', 'city', 'zip', 'fips_code'))) { - $state = isset($_REQUEST['state']) ? extract_values($_REQUEST['state'], 'str') : null; - $ccn = isset($_REQUEST['ccn']) ? extract_values($_REQUEST['ccn'], 'str') : null; - $city = isset($_REQUEST['city']) ? extract_values($_REQUEST['city'], 'str') : null; - $zip = isset($_REQUEST['zip']) ? extract_values($_REQUEST['zip'], 'str') : null; - $fips_code = isset($_REQUEST['fips_code']) ? extract_values($_REQUEST['fips_code'], 'str') : null; - // get the data - $epidata = get_covid_hosp_facility_lookup($state, $ccn, $city, $zip, $fips_code); - store_result($data, $epidata); - } - } else if($endpoint === 'covidcast_nowcast') { - if(require_all($data, array('data_source', 'time_type', 'geo_type', 'time_values', 'signals', 'sensor_names')) - && require_any($data, array('geo_value', 'geo_values'))) { - // parse the request - $time_values = extract_dates($_REQUEST['time_values']); - $as_of = isset($_REQUEST['as_of']) ? parse_date($_REQUEST['as_of']) : null; - $issues = isset($_REQUEST['issues']) ? extract_dates($_REQUEST['issues']) : null; - $lag = isset($_REQUEST['lag']) ? intval($_REQUEST['lag']) : null; - $signals = extract_values(isset($_REQUEST['signals']) ? $_REQUEST['signals'] : $_REQUEST['signal'], 'string'); - $sensor_names = extract_values(isset($_REQUEST['sensor_names']) ? $_REQUEST['sensor_names'] : $_REQUEST['sensor_names'], 'sensor_names'); - $geo_values = isset($_REQUEST['geo_value']) ? $_REQUEST['geo_value'] : extract_values($_REQUEST['geo_values'], 'string'); - // get the data - $epidata = get_covidcast_nowcast( - $_REQUEST['data_source'], - $signals, - $sensor_names, - $_REQUEST['time_type'], - $_REQUEST['geo_type'], - $time_values, - $geo_values, - $as_of, - $issues, - $lag); - store_result($data, $epidata); - } - } else { - $data['message'] = 'no data source specified'; - } - // API analytics - record_analytics($endpoint, $data); -} else { - $data['message'] = 'database error'; -} - -if(isset($_REQUEST['format']) && $_REQUEST['format'] == "csv") { - send_csv($data); -} else if(isset($_REQUEST['format']) && $_REQUEST['format'] == "json") { - send_json($data); -} else { - // send the response as a json object - header('Content-Type: application/json'); - echo json_encode($data); -} -?> diff --git a/src/server/api_helpers.php b/src/server/api_helpers.php deleted file mode 100644 index 076033801..000000000 --- a/src/server/api_helpers.php +++ /dev/null @@ -1,420 +0,0 @@ - $first) { - // add the range as an array - array_push($values, array($first, $last)); - } else { - // the range is inverted, this is an error - return null; - } - } else { - // this is a single value - if($type === 'int') { - // cast to integer - $value = intval($part); - } else { - // interpret the string literally - $value = $part; - } - // add the extracted value to the list - array_push($values, $value); - } - } - // success, return the list - return $values; -} - -/** - * parses a given string in format YYYYMMDD or YYYY-MM-DD to a number in the form YYYYMMDD - */ -function parse_date($s) { - return intval(str_replace('-', '', $s)); -} - -// extracts an array of values and/or ranges from a string -// $str: the string to parse -function extract_dates($str) { - if($str === null || strlen($str) === 0) { - // nothing to do - return null; - } - $values = array(); - // split on commas and loop over each entry, which could be either a single value or a range of values - $parts = explode(',', $str); - - $push_range = function($first, $last) { - $first = parse_date($first); - $last = parse_date($last); - if($last === $first) { - // the first and last numbers are the same, just treat it as a singe value - return $first; - } - if($last > $first) { - // add the range as an array - return array($first, $last); - } - // the range is inverted, this is an error - return false; - }; - - foreach($parts as $part) { - if(strpos($part, '-') === false && strpos($part, ':') === false) { - // YYYYMMDD - array_push($values, parse_date($part)); - continue; - } - if (strpos($part, ':') !== false) { - // YYYY-MM-DD:YYYY-MM-DD - $range = explode(':', $part); - $r = $push_range($range[0], $range[1]); - if ($r === false) { - return null; - } - array_push($values, $r); - } - // YYYY-MM-DD or YYYYMMDD-YYYYMMDD - // split on the dash - $range = explode('-', $part); - if (count($range) === 2) { - // YYYYMMDD-YYYYMMDD - $r = $push_range($range[0], $range[1]); - if ($r === false) { - return null; - } - array_push($values, $r); - continue; - } - // YYYY-MM-DD - array_push($values, parse_date($part)); - } - // success, return the list - return $values; -} - -// give a comma-separated, quoted list of states in an HHS or Census region -function get_region_states($region) { - switch($region) { - case 'hhs1': return "'VT', 'CT', 'ME', 'MA', 'NH', 'RI'"; - case 'hhs2': return "'NJ', 'NY'"; - case 'hhs3': return "'DE', 'DC', 'MD', 'PA', 'VA', 'WV'"; - case 'hhs4': return "'AL', 'FL', 'GA', 'KY', 'MS', 'NC', 'TN', 'SC'"; - case 'hhs5': return "'IL', 'IN', 'MI', 'MN', 'OH', 'WI'"; - case 'hhs6': return "'AR', 'LA', 'NM', 'OK', 'TX'"; - case 'hhs7': return "'IA', 'KS', 'MO', 'NE'"; - case 'hhs8': return "'CO', 'MT', 'ND', 'SD', 'UT', 'WY'"; - case 'hhs9': return "'AZ', 'CA', 'HI', 'NV'"; - case 'hhs10': return "'AK', 'ID', 'OR', 'WA'"; - case 'cen1': return "'CT', 'ME', 'MA', 'NH', 'RI', 'VT'"; - case 'cen2': return "'NJ', 'NY', 'PA'"; - case 'cen3': return "'IL', 'IN', 'MI', 'OH', 'WI'"; - case 'cen4': return "'IA', 'KS', 'MN', 'MO', 'NE', 'ND', 'SD'"; - case 'cen5': return "'DE', 'DC', 'FL', 'GA', 'MD', 'NC', 'SC', 'VA', 'WV'"; - case 'cen6': return "'AL', 'KY', 'MS', 'TN'"; - case 'cen7': return "'AR', 'LA', 'OK', 'TX'"; - case 'cen8': return "'AZ', 'CO', 'ID', 'MT', 'NV', 'NM', 'UT', 'WY'"; - case 'cen9': return "'AK', 'CA', 'HI', 'OR', 'WA'"; - } - return null; -} - -function record_analytics($source, $data) { - global $dbh; - $ip = mysqli_real_escape_string($dbh, isset($_SERVER['REMOTE_ADDR']) ? $_SERVER['REMOTE_ADDR'] : ''); - $ua = mysqli_real_escape_string($dbh, isset($_SERVER['HTTP_USER_AGENT']) ? $_SERVER['HTTP_USER_AGENT'] : ''); - $source = mysqli_real_escape_string($dbh, isset($source) ? $source : ''); - $result = intval($data['result']); - $num_rows = intval(isset($data['epidata']) ? count($data['epidata']) : 0); - mysqli_query($dbh, "INSERT INTO `api_analytics` (`datetime`, `ip`, `ua`, `source`, `result`, `num_rows`) VALUES (now(), '{$ip}', '{$ua}', '{$source}', {$result}, {$num_rows})"); -} - -function send_status(&$data) { - if (intval($data["result"]) > 0 || intval($data["result"]) == -2) { - return FALSE; - } - if ($data["message"] == 'database error') { - http_response_code(500); - } else if ($data["message"] == 'unauthenticated') { - http_response_code(401); - } else { - http_response_code(400); // bad request - } - header('Content-Type: application/json'); - echo json_encode($data); - return TRUE; -} - -function send_csv(&$data) { - if (send_status($data)) { - return; - } - header('Content-Type: text/csv'); - header('Content-Disposition: attachment; filename=epidata.csv'); - - if (intval($data["result"]) == -2) { - // empty - return; - } - - $rows = $data["epidata"]; - $headers = array_keys($rows[0]); - $out = fopen('php://output', 'w'); - fputcsv($out, $headers); - foreach ($rows as $row) { - fputcsv($out, $row); - } - fclose($out); -} - -function send_json(&$data) { - if (send_status($data)) { - return; - } - header('Content-Type: application/json'); - - if (intval($data["result"]) == -2) { - echo json_encode(array()); - } else { - echo json_encode($data["epidata"]); - } -} - -?> diff --git a/src/server/database_config.php b/src/server/database_config.php deleted file mode 100644 index 1667f134d..000000000 --- a/src/server/database_config.php +++ /dev/null @@ -1,7 +0,0 @@ - 'delphi_database_epidata', - 'port' => 3306, -); -?>