Merge branch 'bfabric12' of github.com:fgcz/bfabricShiny into bfabric12

DESCRIPTION

@@ -7,14 +7,14 @@ Authors@R: c(person("Christian", "Trachsel",
         role = c("aut", "cre"), 
         comment = c(ORCID = "0000-0003-1975-3064")))
 Maintainer: Christian Panse <[email protected]>
-Version: 0.12.21
+Version: 0.12.23
 Description: provides a shiny module and read, save, and delete functions to
     interact with the FGCZ's B-Fabric <https://fgcz-bfabric.uzh.ch> system
     using WSDL and REST. Also, the package contains shiny
     applications, e.g., to allow the FGCZ user to automatically generate a
     configuration of queues for Thermo Fisher Scientific and Bruker instruments. 
 Depends:
-    R (>= 4.1)
+    R (>= 4.2)
 Imports:
     PKI,
     base64enc,

README.md

@@ -2,6 +2,7 @@
 
 [![JIB](https://img.shields.io/badge/JIB-10.1515%2Fjib.2022.0031-brightgreen)](https://doi.org/10.1515/jib-2022-0031)
 [![codecov](https://codecov.io/gh/fgcz/bfabricShiny/branch/bfabric11/graph/badge.svg?token=Q9G0WFEH6K)](https://codecov.io/gh/fgcz/bfabricShiny)
+![Downloads](https://img.shields.io/github/downloads/fgcz/bfabricShiny/total)
 
 
 # bfabricShiny R package
@@ -111,12 +112,27 @@ system.file("shiny", "queue_generator10", package = "bfabricShiny") |>
 ```{bash}
 python3 bfabric_flask.py 
 ```
+If a certified key is available, Flask will use SSL certificate and run on port 5001. Otherwise it will run using http and port 5000.
+Note that the port configuration can be changed in the bfabric\_flask.py script.
+```{python}
+# code snippet from bfabric_flask.py:
+if exists('/etc/ssl/fgcz-host.pem') and exists('/etc/ssl/private/fgcz-host_key.pem'):    
+    app.run(debug=False, host="0.0.0.0", port=5001, ssl_context=('/etc/ssl/fgcz-host.pem', '/etc/ssl/private/fgcz-host_key.pem'))
+else:
+   app.run(debug=False, host="127.0.0.1", port=5000)
+```
+See [bfabric\_flask.py on GitHub](https://github.com/fgcz/bfabricPy/blob/bfabric12/bfabric/scripts/bfabric_flask.py) for more details.
 
-- simple json test 
+- simple tests 
 
 ```{bash}
 curl http://127.0.0.1:5000/sample/1
 ```
+```{r}
+# R
+rv <- httr::POST("https://host:5001/read", body = jsonlite::toJSON(list(login = "login", webservicepassword = "webservicepassword", endpoint = "user", query = list("login" = "cpanse"))), encode = "json")
+httr::content(rv)
+```
 
 ## Sample Query
 

inst/shiny/bfabric_rawDiag/server.R

@@ -925,8 +925,10 @@ output$qc <- renderPlot({
     msg <- paste0("bfabricShiny::uploadResource ...")
     message(msg)
     progress$set(message = msg)
-
+
+
     resources <- bf$resources()
+
     rvupload <- bfabricShiny::uploadResource(
       login = bf$login(),
       webservicepassword = bf$webservicepassword(),
@@ -940,7 +942,7 @@ output$qc <- renderPlot({
       resourcename = sprintf("%s.pdf", "rawDiag"),
       file = pdfFilename
     )
-    print(rvupload)
+    message(rvupload)
     values$wuid <- rvupload$workunit[[1]]$`_id`
     msg <- paste0("The current plot is available as workunit ", values$wuid)
     message(msg)