From 84bce8d5d9ecfa696b98860bc971834f1b370aee Mon Sep 17 00:00:00 2001 From: pietervsd Date: Tue, 29 Oct 2024 14:58:52 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20inbo/inb?= =?UTF-8?q?olims@e1c9f2b281d55278f56cd7c351ffdf7f173b33ba=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- CODE_OF_CONDUCT.html | 2 +- CONTRIBUTING.html | 2 +- LICENSE.html | 2 +- articles/index.html | 2 +- articles/reading_lims_results.html | 2 +- authors.html | 6 +- index.html | 15 ++- news/index.html | 2 +- pkgdown.yml | 4 +- reference/create_archief_labels_bat.html | 2 +- reference/date_as_text.html | 2 +- reference/get_all_report_fields.html | 2 +- reference/get_report_config_info.html | 2 +- reference/inbolims-package.html | 2 +- reference/index.html | 14 ++- reference/interpret_texture_content.html | 2 +- reference/lims_connect.html | 2 +- reference/lims_report_export.html | 2 +- reference/lims_report_samples.html | 2 +- reference/lims_report_xtab.html | 2 +- reference/lims_result_statistics.html | 2 +- reference/lims_sample_information.html | 130 +++++++++++++++++++++ reference/lims_table_fields.html | 124 ++++++++++++++++++++ reference/link_labo_id.html | 2 +- reference/parse_sql_report_query.html | 2 +- reference/parse_texture_content.html | 2 +- reference/read_lims_data.html | 2 +- reference/sample_fields_from_template.html | 113 ++++++++++++++++++ reference/show_available_templates.html | 2 +- reference/tex_csv_2_json.html | 2 +- reference/write_texture_files.html | 2 +- sitemap.xml | 3 + 33 files changed, 423 insertions(+), 36 deletions(-) create mode 100644 reference/lims_sample_information.html create mode 100644 reference/lims_table_fields.html create mode 100644 reference/sample_fields_from_template.html diff --git a/404.html b/404.html index 6f9ae0a..830efef 100644 --- a/404.html +++ b/404.html @@ -101,7 +101,7 @@

Page not found (404)

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 48d0b23..efc73ca 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -81,7 +81,7 @@

Contributor Code of Conduct

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 4ec65ff..ffd5f6f 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -105,7 +105,7 @@

Thanks for contributing!
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/LICENSE.html b/LICENSE.html index aed5d49..9b03cdb 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -271,7 +271,7 @@

How to Apply These Terms
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/articles/index.html b/articles/index.html index b8a74f7..bad2458 100644 --- a/articles/index.html +++ b/articles/index.html @@ -72,7 +72,7 @@

All vignettes

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/articles/reading_lims_results.html b/articles/reading_lims_results.html index ed81142..e3ef39c 100644 --- a/articles/reading_lims_results.html +++ b/articles/reading_lims_results.html @@ -283,7 +283,7 @@

Basisstatistieken

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/authors.html b/authors.html index 82b91d0..665fa2b 100644 --- a/authors.html +++ b/authors.html @@ -71,9 +71,9 @@

Citation

-

Verschelde, Pieter (2024) inbolims: Utilities to query the INBO lab analysis datawarehouse. Version 0.2.10. https://inbo.github.io/inbolims/

+

Verschelde, Pieter (2024) inbolims: Utilities to query the INBO lab analysis datawarehouse. Version 0.2.11. https://inbo.github.io/inbolims/

@Manual{,
-  title = {inbolims: Utilities to query the INBO lab analysis datawarehouse. Version 0.2.10},
+  title = {inbolims: Utilities to query the INBO lab analysis datawarehouse. Version 0.2.11},
   author = {Pieter Verschelde},
   year = {2024},
   url = {https://inbo.github.io/inbolims/},
@@ -92,7 +92,7 @@ 
Citation

 
 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.1.

 

 
       
diff --git a/index.html b/index.html
index 0dd290d..e2395ff 100644
--- a/index.html
+++ b/index.html
@@ -112,14 +112,19 @@ 
Eerste gebruiklibrary(inbolims)
 
 #maak connectie met databank
-connection <- lims_connect()
-
-#haal de rapportgegevens binnen uit de databank
+connection <- lims_connect()
+

Je kan op voorhand al de staalinformatie ophalen via lims_sample_information. Je kan je project selecteren. Dit mogen er ook meerdere zijn en eventueel joker karakters mogen ook gebruikt worden.

+

Standaard worden defaultvelden getoond, maar je kan zelf ook kiezen welke velden je wil zien eventueel gecombineerd met een template, met de variabele fields.

+

Via de functie sample_fields_from_template kan je te weten komen welke templates beschikbaar zijn en welke velden onderdeem uitmaken in elk van de templates. Met de functie lims_table_fields kan je voor elke tabel zien welke velden het datawarehouse in aanbieding heeft.

+
#illustratieve stap: krijg de staalinformatie (optioneel)
+staal_info <- lims_sample_information(connection, project = c("I-19W001-02"))
+

De belangrijkste functie is het inlezen van alle rapportdata. In de toekomst zal die functie ook verbeterd worden zodat ook gemakkelijk kan achterhaald worden wat er historisch allemaal bestond van analyse- en componentnamen.

+
#haal de rapportgegevens binnen uit de databank
 rapport_data <- read_lims_data(connection = connection,
                                project = c("I-19W001-02"),
                                sql_template = "default",
                                show_query = FALSE)
-
+

Bovenstaande code haalt de data op voor het project I-19W001-02 (project = “I-19W001-02”) volgens de standaardtemplate (template = “default”) en de query die gebruikt is om het datawarehouse te bevragen wordt getoond (show_query = TRUE). Als eerste variabele moet de databank connectie opgegeven worden, zodat de routine weet waar de gegevens uit gehaald moeten worden.

@@ -251,7 +256,7 @@

Dev status

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/news/index.html b/news/index.html index 9f92afb..4b31aef 100644 --- a/news/index.html +++ b/news/index.html @@ -99,7 +99,7 @@

inbolims 0.2.6
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/pkgdown.yml b/pkgdown.yml index d02d27d..6cef6fb 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,9 +1,9 @@ pandoc: 3.1.11 -pkgdown: 2.1.0 +pkgdown: 2.1.1 pkgdown_sha: ~ articles: reading_lims_results: reading_lims_results.html -last_built: 2024-08-28T14:16Z +last_built: 2024-10-29T14:58Z urls: reference: https://inbo.github.io/inbolims/reference article: https://inbo.github.io/inbolims/articles diff --git a/reference/create_archief_labels_bat.html b/reference/create_archief_labels_bat.html index dd90572..ca46abb 100644 --- a/reference/create_archief_labels_bat.html +++ b/reference/create_archief_labels_bat.html @@ -123,7 +123,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/date_as_text.html b/reference/date_as_text.html index db9b8ad..37be989 100644 --- a/reference/date_as_text.html +++ b/reference/date_as_text.html @@ -95,7 +95,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/get_all_report_fields.html b/reference/get_all_report_fields.html index 4134d1f..1962e23 100644 --- a/reference/get_all_report_fields.html +++ b/reference/get_all_report_fields.html @@ -113,7 +113,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/get_report_config_info.html b/reference/get_report_config_info.html index d893702..dc396ff 100644 --- a/reference/get_report_config_info.html +++ b/reference/get_report_config_info.html @@ -121,7 +121,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/inbolims-package.html b/reference/inbolims-package.html index 6cc4ade..e764e3b 100644 --- a/reference/inbolims-package.html +++ b/reference/inbolims-package.html @@ -87,7 +87,7 @@

Author

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/index.html b/reference/index.html index 84746ba..4e937a6 100644 --- a/reference/index.html +++ b/reference/index.html @@ -100,6 +100,14 @@

All functions lims_result_statistics()

Title

+ +

lims_sample_information()

+ +

Verkrijg de sample informatie

+ +

lims_table_fields()

+ +

Get all availaible column names from a table in the data warehouse

link_labo_id()

@@ -116,6 +124,10 @@

All functions read_lims_data()

Haal rapportdata uit LIMS DWH

+ +

sample_fields_from_template()

+ +

Velden uit sample_field_template

show_available_templates()

@@ -141,7 +153,7 @@

All functions
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/interpret_texture_content.html b/reference/interpret_texture_content.html index 1a834f1..26408ca 100644 --- a/reference/interpret_texture_content.html +++ b/reference/interpret_texture_content.html @@ -99,7 +99,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/lims_connect.html b/reference/lims_connect.html index 3463804..4c33c63 100644 --- a/reference/lims_connect.html +++ b/reference/lims_connect.html @@ -114,7 +114,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/lims_report_export.html b/reference/lims_report_export.html index 2c1b3ee..674b56b 100644 --- a/reference/lims_report_export.html +++ b/reference/lims_report_export.html @@ -95,7 +95,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/lims_report_samples.html b/reference/lims_report_samples.html index 050ab1e..0496122 100644 --- a/reference/lims_report_samples.html +++ b/reference/lims_report_samples.html @@ -101,7 +101,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/lims_report_xtab.html b/reference/lims_report_xtab.html index f934949..20189d9 100644 --- a/reference/lims_report_xtab.html +++ b/reference/lims_report_xtab.html @@ -114,7 +114,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/lims_result_statistics.html b/reference/lims_result_statistics.html index 6f1eec5..7f175c4 100644 --- a/reference/lims_result_statistics.html +++ b/reference/lims_result_statistics.html @@ -107,7 +107,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/lims_sample_information.html b/reference/lims_sample_information.html new file mode 100644 index 0000000..3f2b281 --- /dev/null +++ b/reference/lims_sample_information.html @@ -0,0 +1,130 @@ + +Verkrijg de sample informatie — lims_sample_information • inbolims + + +
+
+ + + +
+
+
+

Verkrijg de sample informatie

+ Source: R/lims_sample_information.R + +
+ +
+

Verkrijg de informatie van stalen voor gekozen projecten

+
+ +
+ 
lims_sample_information(con, project, fields = "template:default")
+
+ +
+

Arguments

+ + +
con
+

connectie naar lims dwh

+ + +
project
+

een character string met projecten, eventueel met SQL jokertekens "%" en "_"

+ + +
fields
+

welke velden wil je terugkrijgen, indien het begint met "template:" wordt een staaltemplate gekozen , anders is dat gewoon een vector van velden. Je kan "template:" en eigen veldnamen combineren bv. c("template:default", "FieldObserver", "FieldSamplingDate")

+ +
+
+

Value

+

tibble met sample informatie

+
+ +
+

Examples

+ 
library(inbolims)
+con <- lims_connect()
+#> Error in pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE): ! ODBC failed with error 00000 from [unixODBC][Driver Manager].
+#> ✖ Can't open lib 'SQL Server' : file not found
+#> ℹ From nanodbc/nanodbc.cpp:1150.
+sample_info <- lims_sample_information(con, project = "I-20G%")
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': object 'con' not found
+sample_info <- 
+lims_sample_information(
+ con,
+ project = c("I-19G024-01", "I-20G%"),
+ fields = c("template:default", "FieldSamplingDate"))
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': object 'con' not found
+
+
+
+ +
+ + +
+

Developed by Pieter Verschelde.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + + diff --git a/reference/lims_table_fields.html b/reference/lims_table_fields.html new file mode 100644 index 0000000..be9dd91 --- /dev/null +++ b/reference/lims_table_fields.html @@ -0,0 +1,124 @@ + +Get all availaible column names from a table in the data warehouse — lims_table_fields • inbolims + + +
+
+ + + +
+
+
+

Get all availaible column names from a table in the data warehouse

+ Source: R/lims_table_fields.R + +
+ +
+

Get all availaible column names from a table in the data warehouse

+
+ +
+ 
lims_table_fields(con, table_name, export_type = "character")
+
+ +
+

Arguments

+ + +
con
+

connection to the lims Dwh. Typically by lims_connect()

+ + +
table_name
+

name of the table from which the fields are wanted. Important tables are dimSample and factResult.

+ + +
export_type
+

how to return: "character", "tibble" or "data.frame"

+ +
+
+

Value

+

character vector with column names of the table

+
+ +
+

Examples

+ 
library(inbolims)
+con <- lims_connect()
+#> Error in pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE): ! ODBC failed with error 00000 from [unixODBC][Driver Manager].
+#> ✖ Can't open lib 'SQL Server' : file not found
+#> ℹ From nanodbc/nanodbc.cpp:1150.
+lims_table_fields(con, "dimSample")
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': object 'con' not found
+
+
+
+ +
+ + +
+

Developed by Pieter Verschelde.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + + diff --git a/reference/link_labo_id.html b/reference/link_labo_id.html index 96baf93..b8ab6f2 100644 --- a/reference/link_labo_id.html +++ b/reference/link_labo_id.html @@ -121,7 +121,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/parse_sql_report_query.html b/reference/parse_sql_report_query.html index 9d09089..387067b 100644 --- a/reference/parse_sql_report_query.html +++ b/reference/parse_sql_report_query.html @@ -115,7 +115,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/parse_texture_content.html b/reference/parse_texture_content.html index e05b9a4..a722632 100644 --- a/reference/parse_texture_content.html +++ b/reference/parse_texture_content.html @@ -99,7 +99,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/read_lims_data.html b/reference/read_lims_data.html index 3fafb87..ed52071 100644 --- a/reference/read_lims_data.html +++ b/reference/read_lims_data.html @@ -159,7 +159,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/sample_fields_from_template.html b/reference/sample_fields_from_template.html new file mode 100644 index 0000000..58d4c95 --- /dev/null +++ b/reference/sample_fields_from_template.html @@ -0,0 +1,113 @@ + +Velden uit sample_field_template — sample_fields_from_template • inbolims + + +
+
+ + + +
+
+
+

Velden uit sample_field_template

+ Source: R/sample_fields_from_template.R + +
+ +
+

Velden uit sample_field_template

+
+ +
+ 
sample_fields_from_template(template)
+
+ +
+

Arguments

+ + +
template
+

sample_fields keuze

+ +
+
+

Value

+

character vector met kolomnamen

+
+ +
+

Examples

+ 
sample_fields_from_template("default")
+#> [1] "Project"                  "LabSampleID"             
+#> [3] "FieldSampleID"            "LIMSOriginalSampleNumber"
+#> [5] "SampleStatus"            
+
+
+
+ +
+ + +
+

Developed by Pieter Verschelde.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + + diff --git a/reference/show_available_templates.html b/reference/show_available_templates.html index cc3c0d2..bce1d81 100644 --- a/reference/show_available_templates.html +++ b/reference/show_available_templates.html @@ -84,7 +84,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/tex_csv_2_json.html b/reference/tex_csv_2_json.html index 2900a49..0cfce30 100644 --- a/reference/tex_csv_2_json.html +++ b/reference/tex_csv_2_json.html @@ -91,7 +91,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/write_texture_files.html b/reference/write_texture_files.html index d2a6048..c2702a3 100644 --- a/reference/write_texture_files.html +++ b/reference/write_texture_files.html @@ -99,7 +99,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/sitemap.xml b/sitemap.xml index bf39f04..9a654eb 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -20,10 +20,13 @@ https://inbo.github.io/inbolims/reference/lims_report_samples.html https://inbo.github.io/inbolims/reference/lims_report_xtab.html https://inbo.github.io/inbolims/reference/lims_result_statistics.html +https://inbo.github.io/inbolims/reference/lims_sample_information.html +https://inbo.github.io/inbolims/reference/lims_table_fields.html https://inbo.github.io/inbolims/reference/link_labo_id.html https://inbo.github.io/inbolims/reference/parse_sql_report_query.html https://inbo.github.io/inbolims/reference/parse_texture_content.html https://inbo.github.io/inbolims/reference/read_lims_data.html +https://inbo.github.io/inbolims/reference/sample_fields_from_template.html https://inbo.github.io/inbolims/reference/show_available_templates.html https://inbo.github.io/inbolims/reference/tex_csv_2_json.html https://inbo.github.io/inbolims/reference/write_texture_files.html