Update doc

Author: Ludovic Claude

r-ggparci/main.R

@@ -1,5 +1,5 @@
 #'
-#' This script generates the parallel coordinates vislualization and save it as svg file.
+#' This script generates the parallel coordinates visualization and save it as svg file.
 #' The data are obtained from the local databases using a specific query.
 #' This query will be the same for all nodes.
 #'

r-heatmaply/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.1.0
 commit = True
 tag = True
 tag_name = r-heatmaply-{new_version}
@@ -8,3 +8,7 @@ serialize = {major}.{minor}.{patch}
 
 [bumpversion:file:README.md]
 
+[bumpversion:file:Dockerfile]
+search = hbpmip/r-heatmaply:{current_version}
+replace = hbpmip/r-heatmaply:{new_version}
+

r-heatmaply/Dockerfile

@@ -118,7 +118,7 @@ RUN chown -R compute:compute /src/ \
 LABEL eu.humanbrainproject.function=heatmaply \
       eu.humanbrainproject.function.location=node \
       eu.humanbrainproject.function.version=0.1 \
-      eu.humanbrainproject.function.author="Shay Yaacoby, Tal Galili, Loduvic Claude" \
+      eu.humanbrainproject.function.author="Shay Yaacoby, Tal Galili, Ludovic Claude" \
       eu.humanbrainproject.function.organisation="" \
       eu.humanbrainproject.function.date="" \
       org.label-schema.build-date=$BUILD_DATE \

r-heatmaply/README.md

@@ -6,7 +6,7 @@
 
 ```sh
 
-  docker run --rm --env [list of environment variables] hbpmip/r-heatmaply:latest compute
+  docker run --rm --env [list of environment variables] hbpmip/r-heatmaply:0.1.0 compute
 
 ```
 
@@ -17,29 +17,29 @@ where the environment variables are:
    - PARAM_variables : Ignored.
    - PARAM_covariables : The variables to be ploted in the heatmap (as string, comma seperated, eg : "a,b,c")
    - PARAM_* : any other parameters to pass to the R function. See example in the docker-compose file.
-* Execution context:  
-   - JOB_ID : ID of the job  
-   - NODE : Node used for the execution of the script  
-   - IN_DBI_DRIVER   : Class name of the DBI driver for input data  
-   - IN_DBI_DBNAME     : Database name for the database connection for input data  
-   - IN_DBI_HOST     : Host name for the database connection for input data  
-   - IN_DBI_PORT     : Port number for the database connection for input data  
-   - IN_DBI_PASSWORD : Password for the database connection for input data  
-   - IN_DBI_USER     : User for the database connection for input data  
-   - OUT_DBI_DRIVER   : Class name of the DBI driver for output data  
-   - OUT_DBI_DBNAME     : Database name for the database connection for output data  
-   - OUT_DBI_HOST     : Host name for the database connection for output data  
-   - OUT_DBI_PORT     : Port number for the database connection for output data  
-   - OUT_DBI_USER     : User for the database connection for output data  
-   - OUT_DBI_PASSWORD : Password for the database connection for output data  
+* Execution context:
+   - JOB_ID : ID of the job
+   - NODE : Node used for the execution of the script
+   - IN_DBI_DRIVER   : Class name of the DBI driver for input data
+   - IN_DATABASE     : Database name for the database connection for input data
+   - IN_HOST         : Host name for the database connection for input data
+   - IN_PORT         : Port number for the database connection for input data
+   - IN_PASSWORD     : Password for the database connection for input data
+   - IN_USER         : User for the database connection for input data
+   - OUT_DBI_DRIVER  : Class name of the DBI driver for output data
+   - OUT_DATABASE    : Database name for the database connection for output data
+   - OUT_HOST        : Host name for the database connection for output data
+   - OUT_PORT        : Port number for the database connection for output data
+   - OUT_USER        : User for the database connection for output data
+   - OUT_PASSWORD    : Password for the database connection for output data
 
 ## Development process
 
 The goal of this project is to create a Docker image containing the full R environment capable of:
 
 1. Read parameters from the environment and connect to a database
 2. Query the database and prepare the data
-3. Run the algorithm  
+3. Run the algorithm
 4. Format the results into a format that can be easily shared. Here, svg or html.
 5. Save the results into the result database.
 

r-heatmaply/main.R

@@ -14,17 +14,17 @@
 #'    - JOB_ID : ID of the job
 #'    - NODE : Node used for the execution of the script
 #'    - IN_DBI_DRIVER   : Class name of the DBI driver for input data
-#'    - IN_DBI_DBNAME     : Database name for the database connection for input data
-#'    - IN_DBI_HOST     : Host name for the database connection for input data
-#'    - IN_DBI_PORT     : Port number for the database connection for input data
-#'    - IN_DBI_PASSWORD : Password for the database connection for input data
-#'    - IN_DBI_USER     : User for the database connection for input data
-#'    - OUT_DBI_DRIVER   : Class name of the DBI driver for output data
-#'    - OUT_DBI_DBNAME     : Database name for the database connection for output data
-#'    - OUT_DBI_HOST     : Host name for the database connection for output data
-#'    - OUT_DBI_PORT     : Port number for the database connection for output data
-#'    - OUT_DBI_USER     : User for the database connection for output data
-#'    - OUT_DBI_PASSWORD : Password for the database connection for output data
+#'    - IN_DATABASE     : Database name for the database connection for input data
+#'    - IN_HOST         : Host name for the database connection for input data
+#'    - IN_PORT         : Port number for the database connection for input data
+#'    - IN_PASSWORD     : Password for the database connection for input data
+#'    - IN_USER         : User for the database connection for input data
+#'    - OUT_DBI_DRIVER  : Class name of the DBI driver for output data
+#'    - OUT_DATABASE    : Database name for the database connection for output data
+#'    - OUT_HOST        : Host name for the database connection for output data
+#'    - OUT_PORT        : Port number for the database connection for output data
+#'    - OUT_USER        : User for the database connection for output data
+#'    - OUT_PASSWORD    : Password for the database connection for output data
 
 library(rmipadaptor)
 library(heatmaply)