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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, which have been split into separate | |
| # resources by year (due to file size limitations) | |
| # Water Chemistry: https://data.ca.gov/dataset/surface-water-chemistry-results | |
| # Habitat: https://data.ca.gov/dataset/surface-water-habitat-results | |
| # Tissue: https://data.ca.gov/dataset/surface-water-aquatic-organism-tissue-sample-results | |
| # It 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 | |
| # NOTE: to query across all years in this dataset, you'll need to enter the package/dataset ID for the chemistry data, | |
| # rather than the ID for an individual resource (since the data is split into multiple years, need to query across | |
| # multiple resources) - the package IDs for the datasets this example applies to are: | |
| # Water Chemistry: 28d7a81d-6458-47bd-9b79-4fcbfbb88671 | |
| # Habitat: f5edfd1b-a9b3-48eb-a33e-9c246ab85adf | |
| # Tissue: 38cb5cca-1500-42e7-b359-e8e3c5d1e087 | |
| # load packages | |
| library(ckanr) | |
| library(dplyr) | |
| library(lubridate) | |
| library(httr) | |
| library(jsonlite) | |
| library(glue) | |
| library(readr) | |
| library(stringr) | |
| 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")) %>% # move this part to the function below, so that it's not done separately each time | |
| mutate_all(as.character) %>% # to make sure the data frames from each year can be combined | |
| 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 that takes a single year, a dataframe of resource_ids (by year), and the API filters, then returns the correct id | |
| format_url_year <- function(query_year, resource_id_table, filters_date_start, filters_date_end, filters_text, filters_numeric, filters_numeric_drop_na) { | |
| # get the resource ID corresponding to the given year | |
| resource_id <- resource_id_table %>% | |
| filter(year == query_year) %>% | |
| pull(resource_id) | |
| # get the range of start and end dates (in case there are different dates entered for different fields) | |
| dates_start <- range(as.Date(unname(filters_date_start))) | |
| dates_end <- range(as.Date(unname(filters_date_end))) | |
| # get the years to use the starting date filters for | |
| if (!is.na(filters_date_start)[1]) { | |
| use_date_query_years_start <- c(year(min(dates_start)):year(max(dates_start))) | |
| } else ( | |
| use_date_query_years_start <- c() | |
| ) | |
| # get the years to use the ending date filters for | |
| if (!is.na(filters_date_end)[1]) { | |
| use_date_query_years_end <- year(min(dates_end)):year(max(dates_end)) # just in case there are multiple start or end dates, make sure the date filters are applied to years needed | |
| } else { | |
| use_date_query_years_end <- c() | |
| } | |
| # format the filter for minimum/starting dates | |
| if (!is.na(filters_date_start[1]) & (query_year %in% use_date_query_years_start)) { | |
| 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_year %in% use_date_query_years_end)) { | |
| 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}") | |
| } | |
| return(api_url) | |
| } | |
| # 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(package_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 blank | |
| # 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') | |
| # get a table of the resource IDs in the dataset | |
| package_info <- package_show(package_id, as = 'table', | |
| url = 'https://data.ca.gov/', | |
| key = Sys.getenv('data_portal_key')) | |
| package_resources <- package_info$resources | |
| package_resources <- package_resources %>% | |
| filter(format %in% c('CSV')) %>% # filter for just the resources containing csv files | |
| select(name, id) %>% # drop un-needed fields | |
| mutate(name = str_replace(name, pattern = 'CEDEN Water Chemistry Data Prior to 2000', '1999')) %>% # use 1999 to represent any year prior to 2000, since all pre-2000 data is in one resource | |
| mutate(name = parse_number(name)) %>% # extract the year from the resource name | |
| rename(year = name, resource_id = id) | |
| # determine the range of resources to query, based on the start and end dates (check for multiple/different start or end dates for different fields) | |
| dates_start <- range(as.Date(unname(filters_date_start))) | |
| dates_end <- range(as.Date(unname(filters_date_end))) | |
| # get the first year to query | |
| if (is.na(filters_date_start[1]) | year(min(dates_start)) < 2000) { | |
| year_start <- 1999 # treat 1999 as the first year, since all data prior to 2000 is in one resource/file | |
| } else { | |
| year_start <- year(min(dates_start)) | |
| } | |
| # get the last year to query | |
| if (is.na(filters_date_end[1]) | year(max(dates_end)) > max(package_resources$year)) { | |
| year_end <- max(package_resources$year) # only query up to the latest year for which data is available | |
| } else { | |
| year_end <- year(max(dates_end)) | |
| } | |
| # get the range of years to query | |
| query_years_range <- year_start:year_end # get the minimum of the start dates, and the max of the end dates, to know which resources to query | |
| # pass the query filter data to a separate function to build a url for each year, then run the query for each year | |
| # and combine into a single data frame | |
| return(map_df(query_years_range, ~ format_url_year(., package_resources, filters_date_start, | |
| filters_date_end, filters_text, filters_numeric, | |
| filters_numeric_drop_na) %>% | |
| generic_api_query()) %>% | |
| type_convert(na = c("", "NaN")) # detect field types and convert | |
| ) | |
| } | |
| #### EXAMPLE QUERY - GET DATA (using the water chemistry 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_chemistry <- get_api_data(package_id = '28d7a81d-6458-47bd-9b79-4fcbfbb88671', | |
| 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_chemistry %>% count(Analyte, Unit) | |
| # # A tibble: 1 x 3 | |
| # Analyte Unit n | |
| # <chr> <chr> <int> | |
| # 1 Oxygen, Dissolved, Total mg/L 13589 | |
| # Verify that the sample date range is correct | |
| range(df_chemistry$SampleDate) | |
| # [1] "2016-07-01 UTC" "2018-06-28 UTC" | |
| # Verify that the result range is correct | |
| range(df_chemistry$Result) | |
| # [1] 10.00012 591.00000 | |
| # view a summary of the entire dataset | |
| glimpse(df_chemistry) | |
| # Rows: 13,589 | |
| # Columns: 72 | |
| # $ Program <chr> "Central Coast Cooperative Monitoring Program for Agriculture", "Central... | |
| # $ ParentProject <chr> "RWB3 Cooperative Monitoring Program", "RWB3 Cooperative Monitoring Prog... | |
| # $ Project <chr> "RWB 3 Cooperative Monitoring Program", "RWB 3 Cooperative Monitoring Pr... | |
| # $ StationName <chr> "Alisal Slough @ White Barn", "Bradley Channel @ Jones St", "Bradley Cha... | |
| # $ StationCode <chr> "309ASB", "312BCJ", "312BCJ", "312BCJ", "312BCJ", "309BLA", "309BLA", "3... | |
| # $ SampleDate <dttm> 2016-12-13, 2016-08-24, 2016-09-27, 2016-10-24, 2016-11-22, 2016-09-27,... | |
| # $ CollectionTime <dttm> 1899-12-30 13:55:00, 1899-12-30 09:01:00, 1899-12-30 15:25:00, 1899-12-... | |
| # $ LocationCode <chr> "Midchannel", "Midchannel", "Midchannel", "Midchannel", "Midchannel", "M... | |
| # $ CollectionDepth <dbl> 0.12, 0.12, 0.12, 0.12, 0.09, 0.12, 0.12, 0.12, 0.03, 0.12, 0.12, 0.12, ... | |
| # $ UnitCollectionDepth <chr> "m", "m", "m", "m", "m", "m", "m", "m", "m", "m", "m", "m", "m", "m", "m... | |
| # $ SampleTypeCode <chr> "Not Recorded", "Not Recorded", "Not Recorded", "Not Recorded", "Not Rec... | |
| # $ CollectionReplicate <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, ... | |
| # $ ResultsReplicate <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, ... | |
| # $ LabBatch <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ LabSampleID <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ MatrixName <chr> "samplewater", "samplewater", "samplewater", "samplewater", "samplewater... | |
| # $ MethodName <chr> "FieldMeasure", "FieldMeasure", "FieldMeasure", "FieldMeasure", "FieldMe... | |
| # $ Analyte <chr> "Oxygen, Dissolved, Total", "Oxygen, Dissolved, Total", "Oxygen, Dissolv... | |
| # $ Unit <chr> "mg/L", "mg/L", "mg/L", "mg/L", "mg/L", "mg/L", "mg/L", "mg/L", "mg/L", ... | |
| # $ Result <dbl> 10.40, 10.86, 17.25, 11.56, 10.79, 12.60, 13.90, 10.13, 13.37, 11.50, 11... | |
| # $ Observation <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ MDL <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ RL <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ ResultQualCode <chr> "=", "=", "=", "=", "=", "=", "=", "=", "=", "=", "=", "=", "=", "=", "=... | |
| # $ QACode <chr> "None", "None", "None", "None", "None", "None", "None", "None", "None", ... | |
| # $ BatchVerification <chr> "NR", "NR", "NR", "NR", "NR", "NR", "NR", "NR", "NR", "NR", "NR", "NR", ... | |
| # $ ComplianceCode <chr> "Com", "Com", "Com", "Com", "Com", "Com", "Com", "Com", "Com", "Com", "C... | |
| # $ SampleComments <chr> NA, "Samples were returned to SMX without ever being sent to FGL. Resam... | |
| # $ CollectionComments <chr> NA, NA, NA, "Chlorophyll a sample sent to Sierra", NA, NA, NA, NA, NA, N... | |
| # $ ResultsComments <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ BatchComments <lgl> NA, NA, NA, 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", "WQ", "WQ", ... | |
| # $ ProtocolCode <chr> "CMP_QAPP_2012", "CMP_QAPP_2012", "CMP_QAPP_2012", "CMP_QAPP_2012", "CMP... | |
| # $ SampleAgency <chr> "PER", "TetraTech", "TetraTech", "TetraTech", "TetraTech", "PER", "PER",... | |
| # $ GroupSamples <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ CollectionMethodName <chr> "Field Method", "Field Method", "Field Method", "Field Method", "Field M... | |
| # $ Latitude <dbl> 36.72545, 34.94544, 34.94544, 34.94544, 34.94544, 36.70852, 36.70852, 34... | |
| # $ Longitude <dbl> -121.7302, -120.4168, -120.4168, -120.4168, -120.4168, -121.7489, -121.7... | |
| # $ CollectionDeviceDescription <chr> "PER_Hydrolab DS4a", "YSI 6820 v2", "YSI 6820 v2", "YSI 6820 v2", "YSI 6... | |
| # $ CalibrationDate <dttm> 2016-12-13, 2016-08-23, 2016-09-27, 2016-10-24, 2016-11-22, 2016-09-27,... | |
| # $ PositionWaterColumn <chr> "Subsurface", "Subsurface", "Subsurface", "Subsurface", "Subsurface", "S... | |
| # $ PrepPreservationName <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ PrepPreservationDate <dttm> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,... | |
| # $ DigestExtractMethod <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ DigestExtractDate <dttm> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,... | |
| # $ AnalysisDate <dttm> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,... | |
| # $ DilutionFactor <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ ExpectedValue <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ LabAgency <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ SubmittingAgency <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ SubmissionCode <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ OccupationMethod <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ StartingBank <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ DistanceFromBank <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ UnitDistanceFromBank <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ StreamWidth <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ UnitStreamWidth <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ StationWaterDepth <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ UnitStationWaterDepth <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ HydroMod <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ HydroModLoc <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ LocationDetailWQComments <chr> NA, NA, NA, 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, NA, NA, NA, ... | |
| # $ UpstreamLength <lgl> NA, NA, NA, 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, NA, NA, NA, ... | |
| # $ TotalReach <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ LocationDetailBAComments <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ SampleID <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... | |
| # $ DW_AnalyteName <chr> "Oxygen, Dissolved", "Oxygen, Dissolved", "Oxygen, Dissolved", "Oxygen, ... | |
| # $ DataQuality <chr> "Unknown data quality", "Unknown data quality", "Unknown data quality", ... | |
| # $ DataQualityIndicator <chr> "BatchVerification:NR", "BatchVerification:NR", "BatchVerification:NR", ... | |
| # $ Datum <chr> "NAD83", "NAD83", "NAD83", "NAD83", "NAD83", "NAD83", "NAD83", "NAD83", ... |
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