Bug: CLI import doesn't use absolute paths

[bpindelski]

When doing CLI import testing on gretzky (which has OMERO server in a symlinked directory), the command line import fails when trying to import images from a directory outside the symlink:

omero@gretzky:~/OMERO-CURRENT$ bin/omero import ../De-annotate/Image1.png 
Previous session expired for user-2 on localhost:4064
Server: [localhost]
Username: [user-2]
Password:
Created session 47226bfc-0452-4413-ad84-fdd29fd6392f (user-2@localhost:4064). Idle timeout: 10.0 min. Current group: read-only-1
2012-12-11 11:10:02,004 0          [      main] INFO          ome.formats.importer.ImportConfig  - OMERO Version: 4.4.4-474-d36b08d-dirty-ice33-b72
2012-12-11 11:10:02,010 6          [      main] INFO          ome.formats.importer.ImportConfig  - Bioformats version: 4.5-DEV revision: 404d9d1 date: 11 December 2012
2012-12-11 11:10:02,021 17         [      main] INFO   formats.importer.cli.CommandLineImporter  - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2012-12-11 11:10:02,364 360        [      main] INFO      ome.formats.importer.ImportCandidates  - Depth: 4 Metadata Level: MINIMUM
2012-12-11 11:10:02,369 365        [      main] ERROR     ome.formats.importer.cli.ErrorHandler  - UNREADABLE_FILE: /home/omero/slave/workspace/OMERO-merge-develop/src/dist/../De-annotate/Image1.png
java.io.FileNotFoundException: /home/omero/slave/workspace/OMERO-merge-develop/src/dist/../De-annotate/Image1.png
   at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:398)
   at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:603)
   at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
   at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
   at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
   at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:82)
   at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:466)
2012-12-11 11:10:02,370 366        [      main] INFO      ome.formats.importer.ImportCandidates  - 1 file(s) parsed into 0 group(s) with 0 call(s) to setId in 0ms. (6ms total) [0 unknowns]
2012-12-11 11:10:02,519 515        [      main] WARN                    ome.system.UpgradeCheck  - UPGRADE AVAILABLE:Please upgrade to 4.4.5 See http://trac.openmicroscopy.org.uk/omero for the latest version
2012-12-11 11:10:02,627 623        [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Attempting initial SSL connection to localhost:4064
2012-12-11 11:10:03,315 1311       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Insecure connection requested, falling back
2012-12-11 11:10:03,572 1568       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Server: 4.4.4
2012-12-11 11:10:03,573 1569       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Client: 4.4.4-474-d36b08d-dirty-ice33-b72
2012-12-11 11:10:03,573 1569       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Java Version: 1.6.0_20
2012-12-11 11:10:03,573 1569       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - OS Name: Linux
2012-12-11 11:10:03,573 1569       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - OS Arch: amd64
2012-12-11 11:10:03,573 1569       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - OS Version: 2.6.32-24-server
No imports found

We should resolve the path to an absolute one before import...

[jmoore]

Even with a simple test like this:

10018 moore$ cat Makefile t.java
test: t.class
	cd workspace/server && java -cp ../../ t
	cd current && java -cp ../../ t

t.class : t.java setup
	javac t.java

setup:
	mkdir -p workspace/server
	test -e current || ln -s workspace/server current
	touch workspace/test.txt

.PHONY: setup test
import java.io.*;
import java.util.*;
public class t {
    public static void main(String[] args) {
        find("../test.txt");
        find("../t.java");
    }
    public static void find(String fname) {
        File f = new File(fname);
        System.out.println("Looking for " + f.getAbsolutePath());
        System.out.println("Exists? " + f.exists());
    }
}

The results are still that "../something" from within the symlink fail:

0018 moore$ make test
mkdir -p workspace/server
test -e current || ln -s workspace/server current
touch workspace/test.txt
javac t.java
cd workspace/server && java -cp ../../ t
Looking for /private/tmp/10018/workspace/server/../test.txt
Exists? true
Looking for /private/tmp/10018/workspace/server/../t.java
Exists? false
cd current && java -cp ../../ t
Looking for /private/tmp/10018/workspace/server/../test.txt
Exists? true
Looking for /private/tmp/10018/workspace/server/../t.java
Exists? false

I'm closing this "wontfix" since symlink handling even if bash is confusing enough, I don't know if we should try attempting to workaround from within Java.