Merge pull request #82 from dominikl/merge_ci

Add possibility to use merge-ci java libs

R/zzz.R

@@ -22,17 +22,40 @@
     zipFile <- 'OMERO.java.zip'
 
     getLibs <- Sys.getenv("OMERO_LIBS_DOWNLOAD", unset = NA)
-    if (!is.na(getLibs) && as.logical(getLibs) == TRUE) {
+    if (!is.na(getLibs) && startsWith(tolower(getLibs), 'http')) {
+      # Allows using Java libs from merge-ci builds, e.g.
+      # https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-build/lastBuild/
+      git_info <- GET(getLibs)
+      status <- status_code(git_info)
+      if (status != 200) {
+        packageStartupMessage("Request failed. ", getLibs, " returned ", status)
+        acc <- 'n'
+      } else {
+        git_info <- content(git_info, "text")
+        ex <- ">(OMERO\\.java-\\S+\\.zip)<"
+        r <- gregexpr(ex, git_info)
+        res <- regmatches(git_info, r)
+        zipFile <- substr(res[[1]], 2, nchar(res[[1]])-1)
+        baseURL <- getLibs
+        if (endsWith(getLibs, '/'))
+          baseURL <- paste(baseURL, "artifact/src/target", sep = '')
+        else
+          baseURL <- paste(baseURL, "artifact/src/target", sep = '/') 
+        acc <- 'y'
+      }
+    }
+    else if (!is.na(getLibs) && as.logical(getLibs) == TRUE) {
       acc <- 'y'
     } else {
-      packageStartupMessage('Have to download OMERO Java libraries ', baseURL, '/', zipFile, '\nProceed? [y/n]')
+      packageStartupMessage('Have to download OMERO Java libraries from downloads.openmicroscopy.org.\nProceed? [y/n]')
       acc <- readLines(con = stdin(), n=1, ok=TRUE)
     }
 
     if (length(acc) > 0 && (acc[[1]] == 'y' || acc[[1]] == 'Y')) {
-      packageStartupMessage('Downloading...')
       dest <- paste(omeroLibs, zipFile, sep = '/')
-      GET(paste(baseURL, zipFile, sep = '/'), write_disk(dest, overwrite=TRUE))
+      dlURL <- paste(baseURL, zipFile, sep = '/')
+      packageStartupMessage(paste('Downloading', dlURL, '...'))
+      GET(dlURL, write_disk(dest, overwrite=TRUE))
       packageStartupMessage('Extracting...')
       unzip(dest, exdir = omeroLibs)
       unzippedLibs <- NA

jupyter/Dockerfile

@@ -6,6 +6,7 @@ ARG ROMERO_VERSION=
 ARG ROMERO_BRANCH_USER=ome
 ARG ROMERO_BRANCH=master
 ARG INSTALL_SCRIPT_URL=https://raw.githubusercontent.com/ome/rOMERO-gateway/master/install.R
+ARG OMERO_LIBS_DOWNLOAD=TRUE
 
 USER root
 RUN apt-get update -y && \
@@ -30,13 +31,14 @@ RUN conda env update -n r-omero -q -f .setup/environment-r-omero.yml && \
 
 # build/install rOMERO
 ENV _JAVA_OPTIONS="-Xss2560k -Xmx2g"
+
 RUN cd /opt/romero && \
     curl -sf $INSTALL_SCRIPT_URL --output install.R
 RUN if [ -z ${ROMERO_VERSION} ]; then \
     bash -c "source activate r-omero && Rscript /opt/romero/install.R --user=$ROMERO_BRANCH_USER --branch=$ROMERO_BRANCH --quiet"; else \
     bash -c "source activate r-omero && Rscript /opt/romero/install.R --version=$ROMERO_VERSION --quiet"; fi
 
-ENV OMERO_LIBS_DOWNLOAD=TRUE
+ENV OMERO_LIBS_DOWNLOAD=${OMERO_LIBS_DOWNLOAD}
 RUN bash -c "source activate r-omero && echo \"library('romero.gateway')\" | R --no-save"
 
 COPY --chown=1000:100 Get_Started.ipynb notebooks/