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 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -95,6 +92,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html index d173954..0349625 100644 --- a/docs/ISSUE_TEMPLATE.html +++ b/docs/ISSUE_TEMPLATE.html @@ -83,9 +83,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -95,6 +92,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index da54593..1a5f1ac 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -83,9 +83,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -95,6 +92,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/PULL_REQUEST_TEMPLATE.html b/docs/PULL_REQUEST_TEMPLATE.html index 79737fc..5947a47 100644 --- a/docs/PULL_REQUEST_TEMPLATE.html +++ b/docs/PULL_REQUEST_TEMPLATE.html @@ -83,9 +83,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -95,6 +92,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/articles/BacDive-ing-in.html b/docs/articles/BacDive-ing-in.html index 099705c..b2a6f3b 100644 --- a/docs/articles/BacDive-ing-in.html +++ b/docs/articles/BacDive-ing-in.html @@ -54,9 +54,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -66,6 +63,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • @@ -95,7 +95,7 @@

    BacDive-ing in

    Retrieving data(sets) from BacDive

    Katrin Leinweber

    -

    2018-09-08

    +

    2018-09-09

    Source: vignettes/BacDive-ing-in.Rmd diff --git a/docs/articles/BacDive-ing-in_files/figure-html/ggplot-1.png b/docs/articles/BacDive-ing-in_files/figure-html/ggplot-1.png index f4f8174..b2fcd1f 100644 Binary files a/docs/articles/BacDive-ing-in_files/figure-html/ggplot-1.png and b/docs/articles/BacDive-ing-in_files/figure-html/ggplot-1.png differ diff --git a/docs/articles/adr-001-JSON-not-XML.html b/docs/articles/adr-001-JSON-not-XML.html index 2d01202..fee434d 100644 --- a/docs/articles/adr-001-JSON-not-XML.html +++ b/docs/articles/adr-001-JSON-not-XML.html @@ -54,9 +54,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -66,6 +63,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • @@ -94,7 +94,7 @@

    ADR 1: Using JSON internally, instead of XML

    Katrin Leinweber

    -

    2018-09-08

    +

    2018-09-09

    Source: vignettes/adr-001-JSON-not-XML.Rmd diff --git a/docs/articles/adr-002-two-download-functions-returning-datasets.html b/docs/articles/adr-002-two-download-functions-returning-datasets.html index 2bc0652..4efc672 100644 --- a/docs/articles/adr-002-two-download-functions-returning-datasets.html +++ b/docs/articles/adr-002-two-download-functions-returning-datasets.html @@ -54,9 +54,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -66,6 +63,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • @@ -94,7 +94,7 @@

    ADR 2: Two download functions that return full datasets by default

    Katrin Leinweber

    -

    2018-09-08

    +

    2018-09-09

    Source: vignettes/adr-002-two-download-functions-returning-datasets.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 0084c41..2cb8881 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -83,9 +83,6 @@
  • BacDive-ing in
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  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -95,6 +92,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • @@ -130,10 +130,10 @@

    All vignettes

    diff --git a/docs/articles/logic-checking-bacdive-datasets.html b/docs/articles/logic-checking-bacdive-datasets.html index 47dae81..dd656a4 100644 --- a/docs/articles/logic-checking-bacdive-datasets.html +++ b/docs/articles/logic-checking-bacdive-datasets.html @@ -54,9 +54,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -66,6 +63,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • @@ -94,7 +94,7 @@

    Logic-Checking BacDive Datasets

    Katrin Leinweber

    -

    2018-09-08

    +

    2018-09-09

    Source: vignettes/logic-checking-bacdive-datasets.Rmd diff --git a/docs/articles/pre-configuring-advanced-searches-and-retrieving-the-results.html b/docs/articles/pre-configuring-advanced-searches-and-retrieving-the-results.html new file mode 100644 index 0000000..e1ea449 --- /dev/null +++ b/docs/articles/pre-configuring-advanced-searches-and-retrieving-the-results.html @@ -0,0 +1,169 @@ + + + + + + + +Pre-Configuring Advanced Searches and Retrieving the Results • BacDiveR + + + + + + + + + +
    +
    + + + +
    +
    +
    +

    Pre-Configuring Advanced Searches and Retrieving the Results

    +

    Katrin Leinweber

    + +

    2018-09-09

    + + Source: vignettes/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.

    +
      +
    1. Visit BacDive.DSMZ.de/AdvSearch and prepare the query you are interested in.
      2. +
    +
    +Overview of the possible fields to query and their parameters (contains, exact, begins/ends with)

    Overview of the possible fields to query and their parameters (contains, exact, begins/ends with)

    +
    +
      +
    1. Run your advanced search (query). The below example searches for all strains whose literature reference includes someone named “Miller”. Note the two “hits” on the right, and the now much longer URL. It contains/encodes all the terms and parameters of your advanced search.
      2. +
    +
    +Advanced search results

    Advanced search results

    +
    +
      +

    1. 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.

      2. +

    2. Paste the copied URL into a call to the retrieve_search_results("…") function.

      3. +

    3. Enjoy the list of downloaded datasets, just as you would after using retrieve_data(searchTerm = ..., searchType = ...).

      4. +
    +
    +

    +Mass-downloading datasets

    +

    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.

    +
    +
    +

    +Storing datasets offline

    +

    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)
    +
    +
    + + + +
    + + + +
    + + + + + diff --git a/docs/authors.html b/docs/authors.html index 7e537e1..44ac67c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -83,9 +83,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -95,6 +92,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/index.html b/docs/index.html index eb901ef..941aaa9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -54,9 +54,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -66,6 +63,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/news/index.html b/docs/news/index.html index 842cd01..c1c03b2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -83,9 +83,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -95,6 +92,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 792a1e3..3c3b4f5 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,8 +3,8 @@ pkgdown: 1.1.0.9000 pkgdown_sha: 982bd327f97b623554b4cca90b86b4fb084aa634 articles: BacDive-ing-in: BacDive-ing-in.html - Semi-automatic-approach: Semi-automatic-approach.html adr-001-JSON-not-XML: adr-001-JSON-not-XML.html adr-002-two-download-functions-returning-datasets: adr-002-two-download-functions-returning-datasets.html logic-checking-bacdive-datasets: logic-checking-bacdive-datasets.html + pre-configuring-advanced-searches-and-retrieving-the-results: pre-configuring-advanced-searches-and-retrieving-the-results.html diff --git a/docs/reference/aggregate_result_URLs.html b/docs/reference/aggregate_result_URLs.html index 8013739..30cc74c 100644 --- a/docs/reference/aggregate_result_URLs.html +++ b/docs/reference/aggregate_result_URLs.html @@ -86,9 +86,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -98,6 +95,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/reference/construct_Renviron_path.html b/docs/reference/construct_Renviron_path.html index 2435020..48ec133 100644 --- a/docs/reference/construct_Renviron_path.html +++ b/docs/reference/construct_Renviron_path.html @@ -86,9 +86,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -98,6 +95,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/reference/construct_url.html b/docs/reference/construct_url.html index 32153d6..f51ce1a 100644 --- a/docs/reference/construct_url.html +++ b/docs/reference/construct_url.html @@ -86,9 +86,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -98,6 +95,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/reference/download.html b/docs/reference/download.html index e79cb65..8339d41 100644 --- a/docs/reference/download.html +++ b/docs/reference/download.html @@ -86,9 +86,6 @@
  • BacDive-ing in
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  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -98,6 +95,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/reference/get_credentials.html b/docs/reference/get_credentials.html index 62e9dad..b8d2209 100644 --- a/docs/reference/get_credentials.html +++ b/docs/reference/get_credentials.html @@ -86,9 +86,6 @@
  • BacDive-ing in
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  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -98,6 +95,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/reference/index.html b/docs/reference/index.html index 9400d3c..540ebdd 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -83,9 +83,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -95,6 +92,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/reference/prepare_Renviron.html b/docs/reference/prepare_Renviron.html index 7d25bcb..c7c45de 100644 --- a/docs/reference/prepare_Renviron.html +++ b/docs/reference/prepare_Renviron.html @@ -86,9 +86,6 @@
  • BacDive-ing in
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  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -98,6 +95,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/reference/repair_escaping.html b/docs/reference/repair_escaping.html index b80975d..c25e593 100644 --- a/docs/reference/repair_escaping.html +++ b/docs/reference/repair_escaping.html @@ -88,9 +88,6 @@
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  • ADR 1: Using JSON internally, instead of XML
    • @@ -100,6 +97,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • diff --git a/docs/reference/retrieve_data.html b/docs/reference/retrieve_data.html index dff4c73..7907968 100644 --- a/docs/reference/retrieve_data.html +++ b/docs/reference/retrieve_data.html @@ -86,9 +86,6 @@
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -98,6 +95,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +
  • @@ -163,7 +163,7 @@

    Value

    Examples

    - 
      
    dataset_717 <- retrieve_data(searchTerm = 717, searchType = "bacdive_id")
    #> 717 
      
    dataset_DSM_319 <- retrieve_data(searchTerm = "DSM 319", searchType = "culturecollectionno")
    #> 20319 
      
    dataset_AJ000733 <- retrieve_data(searchTerm = "AJ000733", searchType = "sequence")
    #> 000733 
      
    datasets_Bh <- retrieve_data(searchTerm = "Bacillus halotolerans")
    #>  
    #> Downloading BacDive IDs: 
    #> 1095 
    #> 1847
    + 
      
    dataset_717 <- retrieve_data(searchTerm = 717, searchType = "bacdive_id")
    #> 717 
      
    dataset_DSM_319 <- retrieve_data(searchTerm = "DSM 319", searchType = "culturecollectionno")
    #> 20319 
    #> 717 
      
    dataset_AJ000733 <- retrieve_data(searchTerm = "AJ000733", searchType = "sequence")
    #> 000733 
    #> 717 
      
    datasets_Bh <- retrieve_data(searchTerm = "Bacillus halotolerans")
    #>  
    #> Downloading BacDive IDs: 
    #> 1095 
    #> 1847
  • BacDive-ing in
    • -
  • - The Semi-Automatic Approach -
  • ADR 1: Using JSON internally, instead of XML
    • @@ -98,6 +95,9 @@
  • Logic-Checking BacDive Datasets
    • +
  • + Pre-Configuring Advanced Searches and Retrieving the Results +