diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index cbf3a20..71eec2a 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -83,9 +83,6 @@
vignettes/BacDive-ing-in.Rmd
BacDive-ing-in.Rmd
vignettes/adr-001-JSON-not-XML.Rmd
adr-001-JSON-not-XML.Rmd
vignettes/adr-002-two-download-functions-returning-datasets.Rmd
adr-002-two-download-functions-returning-datasets.Rmd
vignettes/logic-checking-bacdive-datasets.Rmd
logic-checking-bacdive-datasets.Rmd
vignettes/pre-configuring-advanced-searches-and-retrieving-the-results.Rmd
+ pre-configuring-advanced-searches-and-retrieving-the-results.Rmd
Unfortunately, the BacDive Web Service does not allow SQL-like queries for the content of specific fields within the strain’s datasets. If you find the functionality explained in BacDive-ing in too limited, please try the following, semi-automatic approach to using BacDiveR.
+Overview of the possible fields to query and their parameters (contains, exact, begins/ends with)
+Advanced search results
+Copy the URL of the results page from your browser’s address bar. Alternatively, copy it from the “Download list of BacDive Ids” link to the top right of the “hits” list.
Paste the copied URL into a call to the retrieve_search_results("…")
function.
Enjoy the list of downloaded datasets, just as you would after using retrieve_data(searchTerm = ..., searchType = ...)
.
retrieve_data(searchTerm = …, searchType = "taxon")
can be used to download all datasets for the genus or a specific species given in …
. Broader searches are possible through the advanced search, for example for all Archaea:
Archaea_data <- retrieve_search_results("https://bacdive.dsmz.de/advsearch?advsearch=search&site=advsearch&searchparams%5B70%5D%5Bcontenttype%5D=text&searchparams%5B70%5D%5Btypecontent%5D=contains&searchparams%5B70%5D%5Bsearchterm%5D=archaea")
Please note the messages about estimated download times for such large downloads.
+This is not a BacDiveR feature, butbase
R’s saveRDS()
is particularly useful for offline-storage of lots of search results, because downloading them would take rather long. Continuing the Archaea example, the following code writes the dataset to a file, loads it again, and verifies the data integrity:
saveRDS(Archaea_data, "Archaea.rds", version = 3)
+Archaea_data_stored <- readRDS("Archaea.rds")
+identical(Archaea_data, Archaea_data_stored)
+dataset_717 <- retrieve_data(searchTerm = 717, searchType = "bacdive_id")#>dataset_DSM_319 <- retrieve_data(searchTerm = "DSM 319", searchType = "culturecollectionno")#>dataset_AJ000733 <- retrieve_data(searchTerm = "AJ000733", searchType = "sequence")#>datasets_Bh <- retrieve_data(searchTerm = "Bacillus halotolerans")#>#>#>#>
dataset_717 <- retrieve_data(searchTerm = 717, searchType = "bacdive_id")#>dataset_DSM_319 <- retrieve_data(searchTerm = "DSM 319", searchType = "culturecollectionno")#>#>dataset_AJ000733 <- retrieve_data(searchTerm = "AJ000733", searchType = "sequence")#>#>datasets_Bh <- retrieve_data(searchTerm = "Bacillus halotolerans")#>#>#>#>