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| # This example shows one way to access subsets of CEDEN data via the California open data portal API (it's not | |
| # necessarily the only or best way though) - if you find any problems or have questions, please contact: [email protected] | |
| # This example applies to the following CEDEN datasets on the open data portal: | |
| # Toxicity: https://data.ca.gov/dataset/surface-water-toxicity-results/resource/bd484e9b-426a-4ba6-ba4d-f5f8ce095836 | |
| # Benthic Macroinvertebrates: https://data.ca.gov/dataset/surface-water-benthic-macroinvertebrate-results/resource/3dfee140-47d5-4e29-99ae-16b9b12a404f | |
| # (NOTE: other CEDEN datasets are split by year, and cannont be queried across multiple years using this method -- for other CEDEN datasets, see: https://gist.github.com/daltare/2de1517ad1e315c4b1cad01278de96dd) | |
| # This example assumes that you have your own API key saved in a system environment variable | |
| # named: "data_portal_key" (to obtain an API key, create an account at data.ca.gov, then go to your | |
| # account page and look for the "API Key" header in the lower left side of the page) | |
| # NOTE: There appears to be a limit of 32,000 records that can be returned from the API in a single call -- if your API query | |
| # is likely to return more records than that limit, you'll need to break it up into multiple calls to the API | |
| # The function below returns a warning message when this occurs | |
| # load packages | |
| library(ckanr) | |
| library(dplyr) | |
| library(lubridate) | |
| library(httr) | |
| library(jsonlite) | |
| library(glue) | |
| library(readr) | |
| library(purrr) | |
| # set the option to use standard notation rather than scientific notation | |
| options(scipen = 999) | |
| # create a generic function to run an API query and return the formatted results, given a URL for the query | |
| generic_api_query <- function(query_url) { | |
| # encode URL | |
| url_encoded <- URLencode(query_url) | |
| # get the data | |
| query_response <- httr::GET(url_encoded, add_headers(Authorization = Sys.getenv('data_portal_key'))) | |
| query_char <- rawToChar(query_response$content) | |
| query_content <- jsonlite::fromJSON(query_char) | |
| resource_records <- query_content$result$records | |
| # get information about the fields included in the dataset (allows for reording the fields to match the original dataset) | |
| resource_fields <- query_content$result$fields %>% | |
| filter(!id %in% c('_id', '_full_text')) %>% # drop these two fields, which are added by the portal and not actually part of the dataset | |
| pull(id) | |
| # format the data- convert to tibble, set the data types, and reorder the fields to match the order of the original dataset | |
| resource_records <- tibble(resource_records) %>% | |
| type_convert(na = c("", "NaN")) %>% | |
| select(all_of(resource_fields)) | |
| # print a warning if the API limit was reached by the query | |
| if (nrow(resource_records) == 32000) { | |
| warning('WARNING: the API record limit was reached - it\'s likely that some records matching your query were not returned') | |
| } | |
| # return the results | |
| return(resource_records) | |
| } | |
| # create a function to download data from the API, given an input resource ID and optional filters for date, text, and numeric fields | |
| get_api_data <- function(resource_id, filters_date_start = NA, filters_date_end = NA, filters_text = NA, filters_numeric = NA, filters_numeric_drop_na = NA) { | |
| # NOTES: any of the filters_... variables can be left as NA to ignore them | |
| # for date and text filters, enter inputs as named character vectors (multiple name-value pairs can be enterd) -- e.g: c('field_name' = 'query_value') | |
| # for numeric filters, include the condition (>, <, >=, <=, <>) as part of the value (multiple name-condition pairs can be entered) -- e.g.: c('field_name' = '> query_value') | |
| # for the filters_numeric_drop_na field, just enter the name of the field to drop missing numeric values from (multiple field names can be entered) -- e.g., c('field_name') | |
| # format the filter for minimum/starting dates | |
| if (!is.na(filters_date_start[1])) { | |
| query_date_start <- map2_chr(filters_date_start, names(filters_date_start), ~glue("\"{.y}\" >= '{.x}'")) %>% | |
| unname() %>% | |
| glue_collapse(sep = ' AND ') | |
| } else { | |
| query_date_start <- c() | |
| } | |
| # format the filters for maximum/ending dates | |
| if (!is.na(filters_date_end[1])) { | |
| query_date_end <- map2_chr(filters_date_end, names(filters_date_end), ~glue("\"{.y}\" <= '{.x}'")) %>% | |
| unname() %>% | |
| glue_collapse(sep = ' AND ') | |
| } else { | |
| query_date_end <- c() | |
| } | |
| # format the filters for text values | |
| if (!is.na(filters_text[1])) { | |
| query_text_filter <- map2_chr(filters_text, names(filters_text), ~glue("\"{.y}\" = '{.x}'")) %>% | |
| unname() %>% | |
| glue_collapse(sep = ' AND ') | |
| } else { | |
| query_text_filter <- c() | |
| } | |
| # format the filters for numeric values | |
| if (!is.na(filters_numeric[1])) { | |
| query_numeric_filter <- map2_chr(filters_numeric, names(filters_numeric), ~glue("\"{.y}\" {.x}")) %>% | |
| unname() %>% | |
| glue_collapse(sep = ' AND ') | |
| } else { | |
| query_numeric_filter <- c() | |
| } | |
| # format the filters to drop missing/null numeric values | |
| if (!is.na(filters_numeric_drop_na[1])) { | |
| query_numeric_drop_na <- map_chr(filters_numeric_drop_na, ~glue("\"{.x}\" <> '{NaN}'")) %>% | |
| # unname() %>% | |
| glue_collapse(sep = ' AND ') | |
| } else { | |
| query_numeric_drop_na <- c() | |
| } | |
| # combine all of the different filter types into one statement | |
| filters_combined <- glue_collapse(c(query_date_start, query_date_end, query_text_filter, query_numeric_filter, query_numeric_drop_na), sep = ' AND ') | |
| # create URL for the API call | |
| api_url <- glue("https://data.ca.gov/api/3/action/datastore_search_sql?sql=SELECT * from \"{resource_id}\"") | |
| if (length(filters_combined) > 0) { # if there are additional filters, add them | |
| api_url <- glue("{api_url} WHERE {filters_combined}") | |
| } | |
| # submit the API query using the constructed url, and return the resulting data frame | |
| return(generic_api_query(api_url)) | |
| } | |
| #### EXAMPLE QUERY - GET DATA (using the toxicity dataset) #### | |
| # make an API call to get some data (in this case, get samples between 2016-07-01 and 2018-06-30, | |
| # where the analyte name is "Oxygen, Dissolved, Total", the units are "mg/L", and the result value is | |
| # greater than 10 and is not missing/null) | |
| df_toxicity <- get_api_data(resource_id = 'bd484e9b-426a-4ba6-ba4d-f5f8ce095836', | |
| filters_date_start = c('SampleDate' = '2016-07-01'), | |
| filters_date_end = c('SampleDate' = '2018-06-30'), | |
| filters_text = c('Analyte' = 'Oxygen, Dissolved, Total', | |
| 'Unit' = 'mg/L'), | |
| filters_numeric = c('Result' = '> 10'), | |
| filters_numeric_drop_na = c('Result')) | |
| #### EXAMPLE QUERY - VERIFY DATA #### | |
| # verify that records with the correct analyte names and units were returned, and get the number of records | |
| df_toxicity %>% count(Analyte, Unit) | |
| # # A tibble: 1 x 3 | |
| # Analyte Unit n | |
| # <chr> <chr> <int> | |
| # 1 Oxygen, Dissolved, Total mg/L 1463 | |
| # Verify that the sample date range is correct | |
| range(df_toxicity$SampleDate) | |
| # [1] "2016-07-11 UTC" "2018-06-21 UTC" | |
| # Verify that the result range is correct | |
| range(df_toxicity$Result) | |
| # [1] 10.07 88.00 | |
| # view a summary of the entire dataset | |
| glimpse(df_toxicity) | |
| # Rows: 1,463 | |
| # Columns: 88 | |
| # $ Program <chr> "BASMAA Regional Monitoring Coalition", "BASMAA Regional M... | |
| # $ ParentProject <chr> "BASMAA RMC Monitoring in WY2016", "BASMAA RMC Monitoring ... | |
| # $ Project <chr> "ACCWP Creek Status Monitoring in WY2016", "SCVURPPP Pesti... | |
| # $ StationName <chr> "Sausal at E.22nd", "San Tomas Aquino 250m u/s Mission Col... | |
| # $ StationCode <chr> "204SAU030", "205STQ010", "205STQ010", "205STE021", "205ST... | |
| # $ SampleDate <dttm> 2016-07-11, 2016-07-11, 2016-07-11, 2016-07-11, 2016-07-1... | |
| # $ CollectionTime <dttm> 1899-12-30 12:40:00, 1899-12-30 14:30:00, 1899-12-30 14:3... | |
| # $ LocationCode <chr> "Midchannel", "Bank", "Bank", "Bank", "Bank", "Midchannel"... | |
| # $ CollectionDepth <dbl> 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1... | |
| # $ UnitCollectionDepth <chr> "m", "m", "m", "m", "m", "m", "m", "m", "m", "m", "m", "m"... | |
| # $ SampleTypeCode <chr> "Grab", "Grab", "Grab", "FieldBLDup_Grab", "Grab", "Grab",... | |
| # $ CollectionReplicate <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1... | |
| # $ LabReplicate <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0... | |
| # $ ToxBatch <chr> "AMS_071216PP_C1_W_TOX", "KLI_071216_PP_C2_W_TOX", "KLI_07... | |
| # $ LabSampleID <chr> "204SAU030-W-06", "205STQ010-W-01", "205STQ010-W-01", "250... | |
| # $ MatrixName <chr> "samplewater", "samplewater", "samplewater", "samplewater"... | |
| # $ MethodName <chr> "EPA 821/R-02-013", "EPA 821/R-02-013", "EPA 821/R-02-013"... | |
| # $ ToxTestDurCode <chr> "7 days", "7 days", "4 days", "4 days", "4 days", "4 days"... | |
| # $ OrganismName <chr> "Pimephales promelas", "Pimephales promelas", "Selenastrum... | |
| # $ Analyte <chr> "Oxygen, Dissolved, Total", "Oxygen, Dissolved, Total", "O... | |
| # $ Unit <chr> "mg/L", "mg/L", "mg/L", "mg/L", "mg/L", "mg/L", "mg/L", "m... | |
| # $ WQSource <chr> "overlyingwater", "overlyingwater", "overlyingwater", "ove... | |
| # $ TimePointName <chr> "initial", "initial", "final", "initial", "initial", "init... | |
| # $ Result <dbl> 10.2, 12.0, 11.4, 10.1, 10.1, 11.2, 11.0, 11.5, 16.0, 15.0... | |
| # $ ResultQualCode <chr> "=", "=", "=", "=", "=", "=", "=", "=", "=", "=", "=", "="... | |
| # $ ToxResultQACode <chr> "None", "None", "None", "None", "None", "None", "None", "N... | |
| # $ QACode <chr> "None", "None", "None", "None", "None", "None", "None", "N... | |
| # $ BatchVerificationCode <chr> "NR", "NR", "NR", "NR", "NR", "NR", "NR", "NR", "NR", "NR"... | |
| # $ ComplianceCode <chr> "NR", "Com", "Com", "Com", "Com", "Com", "Com", "Com", "NR... | |
| # $ SampleComments <chr> NA, "Same as 205R01411, sampled 2015", "Same as 205R01411,... | |
| # $ CollectionComments <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ ToxTestComments <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ TimePointComments <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ ToxResultComments <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ ToxBatchComments <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ EventCode <chr> "WQ", "WQ", "WQ", "WQ", "WQ", "WQ", "WQ", "WQ", "WQ", "WQ"... | |
| # $ ProtocolCode <chr> "BASMAA_RMC_SOP2016v3", "BASMAA_RMC_SOP2016v3", "BASMAA_RM... | |
| # $ SampleAgency <chr> "Applied Marine Sciences, Inc. California", "Santa Clara V... | |
| # $ GroupSamples <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ CollectionMethodName <chr> "Water_Grab", "Water_Grab", "Water_Grab", "Water_Grab", "W... | |
| # $ Latitude <dbl> 37.78566, 37.38654, 37.38654, 37.41056, 37.41056, 37.61729... | |
| # $ Longitude <dbl> -122.2242, -121.9688, -121.9688, -122.0689, -122.0689, -12... | |
| # $ CollectionDeviceDescription <chr> "Not Recorded", "Not Recorded", "Not Recorded", "Not Recor... | |
| # $ PositionWaterColumn <chr> "Not Recorded", "Not Recorded", "Not Recorded", "Not Recor... | |
| # $ TIENarrative <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ Dilution <dbl> 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100... | |
| # $ ToxPointMethod <chr> "ToxWQMeasurement", "ToxWQMeasurement", "ToxWQMeasurement"... | |
| # $ Treatment <chr> "None", "None", "None", "None", "None", "None", "None", "N... | |
| # $ UnitTreatment <chr> "none", "none", "none", "none", "none", "none", "none", "n... | |
| # $ TreatmentConcentration <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0... | |
| # $ LabAgency <chr> "PER", "PER", "PER", "PER", "PER", "PER", "PER", "PER", "P... | |
| # $ SubmittingAgency <chr> "AMS-CA", "SCVURPPP", "SCVURPPP", "SCVURPPP", "SCVURPPP", ... | |
| # $ ToxBatchStartDate <chr> "Jul 12 2016 2:30PM", "Jul 12 2016 12:00AM", "Jul 12 2016... | |
| # $ RefToxBatch <chr> "25990PPRTPER", "25990PPRTPER", "26019SCRTPER", "26021CHDR... | |
| # $ OrganismAgeAtTestStart <chr> "<48 hrs", "<48 hrs", "6 days", "7 days", "7 days", "7 day... | |
| # $ LabSubmissionCode <chr> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A"... | |
| # $ OccupationMethod <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Walk ... | |
| # $ StartingBank <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "LB", ... | |
| # $ DistanceFromBank <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, -88, N... | |
| # $ UnitDistanceFromBank <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "m", N... | |
| # $ StreamWidth <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, -88, N... | |
| # $ UnitStreamWidth <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "m", N... | |
| # $ StationWaterDepth <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, -88, N... | |
| # $ UnitStationWaterDepth <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "m", N... | |
| # $ HydroMod <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Pipes... | |
| # $ HydroModLoc <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "US", ... | |
| # $ LocationDetailWQComments <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "upstr... | |
| # $ PctControl <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ RepCount <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ Mean <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ StdDev <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ StatMethod <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ Probability <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ Alphalevel <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ EvalThreshold <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ MSD <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ SigEffectCode <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ ChannelWidth <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ UpstreamLength <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ DownstreamLength <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ TotalReach <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... | |
| # $ CalculatedValue <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ PercentEffect <dbl> NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN... | |
| # $ SampleID <chr> "204SAU030-W-06", "205STQ010-W-01", "205STQ010-W-01", "250... | |
| # $ DW_AnalyteName <chr> "Oxygen, Dissolved", "Oxygen, Dissolved", "Oxygen, Dissolv... | |
| # $ DataQuality <chr> "Unknown data quality", "Unknown data quality", "Unknown d... | |
| # $ DataQualityIndicator <chr> "BatchVerificationCode:NR", "BatchVerificationCode:NR", "B... | |
| # $ Datum <chr> "WGS84", "NAD83", "NAD83", "NAD83", "NAD83", "NAD83", "NAD... |
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