Merge pull request #1 from snakemake/throw-java-opt-errors

implement changes in snakemake-wrappers PR 204

Author: johanneskoester

snakemake_wrapper_utils/java.py

@@ -1,21 +1,33 @@
+import sys
+
 def get_java_opts(snakemake):
     """Obtain java_opts from params, and handle resource definitions in resources."""
 
     java_opts = snakemake.params.get("java_opts", "")
     # Getting memory in megabytes, if java opts is not filled with -Xmx parameter
     # By doing so, backward compatibility is preserved
-    if "mem_mb" in snakemake.resources.keys() and not "-Xmx" in java_opts:
+    if "mem_mb" in snakemake.resources.keys():
+        if "-Xmx" in java_opts:
+            sys.exit("You have specified resources.mem_mb and provided `-Xmx` in params.java_opts. For Java memory specifications, please only use resources.mem_mb.")
+        if "-Xmx" in extra:
+            sys.exit("You have specified resources.mem_mb and provided `-Xmx` in params.extra. For Java memory specifications, please only use resources.mem_mb.")
         java_opts += " -Xmx{}M".format(snakemake.resources["mem_mb"])
 
     # Getting memory in gigabytes, for user convenience. Please prefer the use
     # of mem_mb over mem_gb as advised in documentation.
-    elif "mem_gb" in snakemake.resources.keys() and not "-Xmx" in java_opts:
+    elif "mem_gb" in snakemake.resources.keys():
+        if "-Xmx" in java_opts:
+            sys.exit("You have specified resources.mem_gb and provided `-Xmx` in params.java_opts. For Java memory specifications, please only use resources.mem_mb.")
+        if "-Xmx" in extra:
+            sys.exit("You have specified resources.mem_gb and provided `-Xmx` in params.extra. For Java memory specifications, please only use resources.mem_mb.")
         java_opts += " -Xmx{}G".format(snakemake.resources["mem_gb"])
 
     # Getting java temp directory from output files list, if -Djava.io.tmpdir
     # is not provided in java parameters. By doing so, backward compatibility is
     # not broken.
-    if "java_temp" in snakemake.output.keys() and not "-Djava.io.tmpdir" in java_opts:
+    if "java_temp" in snakemake.output.keys():
+        if "-Djava.io.tmpdir" in java_opts:
+            sys.exit("You have specified output.java_temp and provided `-Djava.io.tmpdir` in params.java_opts. Please choose the one you intended and remove the other specification.")
         java_opts += " -Djava.io.tmpdir={}".format(snakemake.output["java_temp"])
 
     return java_opts