From 8c9acc5f8985f5ca131cbfe1700e11fa8cfa4b1a Mon Sep 17 00:00:00 2001
From: gv1 <gv1@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 20 Aug 2009 12:51:14 +0000
Subject: [PATCH] fixed a type in the main parameter help listing
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11609 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/io/ReadAndWriteEntry.java | 29 ++++++++++++++-----
1 file changed, 21 insertions(+), 8 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java b/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
index 21ea9592a..63119c8bd 100644
--- a/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
+++ b/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
@@ -266,10 +266,10 @@ public class ReadAndWriteEntry
// note that read_only and noprompt -D parameters redundant now
System.out.println("New parameters:");
- System.out.println("-c\the URL for your Chado database e.g. db.genedb.org:5432/snapshot?genedb_ro (if not using default)");
+ System.out.println("-c\tthe URL for your Chado database e.g. db.genedb.org:5432/snapshot?genedb_ro (if not using default)");
System.out.println("-u\t[swing|console|script] the UI mode : run in swing (with popup dialog boxes) mode, run in console mode (choices entered in the console window), or in script mode (all choices default to continue, all parameters passed on command line) ");
System.out.println("-p\tthe password for connecting to the Chado database");
-
+ System.out.println("-fp\t the file path (the folder you want to save the files in)");
System.exit(0);
}
@@ -280,6 +280,8 @@ public class ReadAndWriteEntry
boolean include_diana_extensions = true;
String suffix = ".embl";
+ String filePath = "";
+
for(int i = 0; i < args.length; i++)
{
String key = args[i].toLowerCase();
@@ -325,6 +327,10 @@ public class ReadAndWriteEntry
{
System.setProperty("chadoPassword", args[i + 1]);
}
+ if (key.equals("-fp"))
+ {
+ filePath = args[i + 1];
+ }
}
// run this after all the system properties have been set
@@ -362,32 +368,39 @@ public class ReadAndWriteEntry
files.toArray(names);
}
+ if (filePath.length() != 0)
+ {
+ filePath += "/";
+ }
for(int i=0;i < names.length; i++)
{
System.out.println("read :: "+names[i]+" write :: "+names[i]+suffix);
+ logger4j.info("read :: "+names[i]+" write :: "+names[i]+suffix);
+
Entry entry = ReadAndWriteEntry.readEntryFromDatabase(names[i], ENTRY_SOURCE);
try
{
ReadAndWriteEntry.writeDatabaseEntryToFile(
- entry, new File(names[i]+suffix), flatten, ignoreObsolete,
+ entry, new File(filePath + names[i]+suffix), flatten, ignoreObsolete,
false, include_diana_extensions,
format, null);
+ System.out.println("done");
+ logger4j.info("done");
}
catch(EntryInformationException eie)
{
- //UI.warn(eie.getMessage(), "UhOh!");
- //eie.printStackTrace();
-
String label = "Destination format can't handle all keys/qualifiers - continue?";
boolean canContinue = UI.booleanUserInput(label, eie.getMessage());
if (canContinue)
{
- ReadAndWriteEntry.writeDatabaseEntryToFile(entry, new File(
- names[i] + suffix), flatten, ignoreObsolete, true,
+ ReadAndWriteEntry.writeDatabaseEntryToFile(entry, new File(filePath + names[i] + suffix),
+ flatten, ignoreObsolete, true,
include_diana_extensions, format, null);
+ System.out.println("done");
+ logger4j.info("done");
}
}
entry.dispose();
--
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