source: trunk/build.xml @ 6045

Revision 6045, 14.1 KB checked in by curtis, 10 years ago (diff)

Fix various dependency problems exposed by scan-deps.pl.

Line 
1<!--
2build.xml
3
4Master ant build file for all Java software projects at LOCI.
5Download Apache Ant from http://ant.apache.org/.
6Type "ant -p" for a list of targets.
7
8===============================================================================
9This build file handles the following components.
10For more information on a component, see the
11build.properties file in that component's subtree.
12Run ./scan-deps.pl to programmatically generate this list.
13
14LOCI Common
15    A library containing common I/O and reflection classes
16    -=-
17    JAR file:      loci-common.jar
18    Path:          components/common
19    Project deps:  (none)
20    Library deps:  Simple Logging Facade for Java API, TestNG
21    Optional:      (none)
22    License:       GPL
23
24OME-XML Java library
25    A library for working with OME-XML metadata structures
26    -=-
27    JAR file:      ome-xml.jar
28    Path:          components/ome-xml
29    Project deps:  (none)
30    Library deps:  (none)
31    Optional:      (none)
32    License:       GPL
33
34Bio-Formats
35    A library for reading and writing popular microscopy file formats
36    -=-
37    JAR file:      bio-formats.jar
38    Path:          components/bio-formats
39    Project deps:  LOCI Common, OME-XML Java library, Apache Jakarta POI,
40                   MDB Tools (Java port), JAI Image I/O Tools
41    Library deps:  JGoodies Forms, Luratech LuraWave stubs, Apache log4j,
42                   NetCDF, Simple Logging Facade for Java API, TestNG
43    Optional:      OME I/O, OME Notes
44    License:       GPL
45
46LOCI code generator
47    Package for generating other code, including the Bio-Formats metadata API,
48    related documentation, Ice bindings, and Bio-Formats C++ bindings headers
49    -=-
50    JAR file:      loci-autogen.jar
51    Path:          components/autogen
52    Project deps:  LOCI Common, Bio-Formats
53    Library deps:  Apache Velocity
54    Optional:      (none)
55    License:       GPL
56
57Bio-Formats Ice framework
58    Bindings for Bio-Formats client/server communication enabling
59    cross-language interoperability
60    -=-
61    JAR file:      bf-ice.jar
62    Path:          components/bf-ice
63    Project deps:  LOCI Common, Bio-Formats
64    Library deps:  Ice, Apache log4j
65    Optional:      (none)
66    License:       GPL
67
68LOCI Plugins for ImageJ
69    A collection of plugins for ImageJ, including the Bio-Formats Importer,
70    Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser, Stack
71    Colorizer and Stack Slicer
72    -=-
73    JAR file:      loci_plugins.jar
74    Path:          components/loci-plugins
75    Project deps:  LOCI Common, Bio-Formats
76    Library deps:  JGoodies Forms, ImageJ, Apache log4j
77    Optional:      OME I/O, VisBio
78    License:       GPL
79
80OME I/O
81    A library for OME database import, upload and download
82    -=-
83    JAR file:      ome-io.jar
84    Path:          components/ome-io
85    Project deps:  LOCI Common, Bio-Formats
86    Library deps:  Apache log4j, Simple Logging Facade for Java API,
87                   OMERO Client, OMERO Common, TestNG
88    Optional:      OME-Java
89    License:       GPL
90
91OME Plugins for ImageJ
92    A collection of plugins for ImageJ, including the Download from OME and
93    Upload to OME plugins
94    -=-
95    JAR file:      ome_plugins.jar
96    Path:          components/ome-plugins
97    Project deps:  LOCI Common, Bio-Formats, LOCI Plugins for ImageJ, OME I/O
98    Library deps:  ImageJ
99    Optional:      (none)
100    License:       GPL
101
102VisBio
103    A multi-purpose biological analysis tool
104    -=-
105    JAR file:      visbio.jar
106    Path:          components/visbio
107    Project deps:  LOCI Common, OME-XML Java library, Bio-Formats, OME I/O,
108                   Apache Jakarta POI
109    Library deps:  Apple eAWT stubs, JGoodies Forms, ImageJ, JUnit,
110                   JGoodies Looks, VisAD
111    Optional:      (none)
112    License:       GPL
113
114SLIM Plotter
115    An application and curve fitting library for visualization and analysis of
116    combined spectral lifetime data
117    -=-
118    JAR file:      SlimPlotter.jar
119    Path:          components/slim-plotter
120    Project deps:  LOCI Common, Bio-Formats, VisBio
121    Library deps:  L-M Fit, VisAD
122    Optional:      (none)
123    License:       GPL
124
125WiscScan Flow Cytometry
126    Server application for flow cytometry with WiscScan using JVMLink
127    -=-
128    JAR file:      flow-cytometry.jar
129    Path:          components/flow-cytometry
130    Project deps:  LOCI Common, Bio-Formats
131    Library deps:  ImageJ, VisAD
132    Optional:      (none)
133    License:       BSD
134
135LOCI Checkstyle checks
136    LOCI's Checkstyle extensions, for checking source code style
137    -=-
138    JAR file:      loci-checks.jar
139    Path:          components/checkstyle
140    Project deps:  (none)
141    Library deps:  Checkstyle
142    Optional:      (none)
143    License:       Public domain
144
145LOCI testing framework
146    Framework for automated and manual testing of the LOCI software packages
147    -=-
148    JAR file:      loci-testing-framework.jar
149    Path:          components/test-suite
150    Project deps:  LOCI Common, Bio-Formats, OME I/O
151    Library deps:  Apache log4j, Simple Logging Facade for Java API, TestNG
152    Optional:      (none)
153    License:       BSD
154
155===============================================================================
156The following components are considered "legacy" but still available:
157
158JVMLink
159    A library for communicating between a Java Virtual Machine and other
160    programs (e.g., C++ applications) via IP over localhost (or remotely)
161    -=-
162    JAR file:      jvmlink.jar
163    Path:          components/legacy/jvmlink
164    Project deps:  LOCI Common
165    Optional:      (none)
166    License:       BSD
167
168Multi-LUT
169    A demo application for visually exploring multi-spectral image data
170    -=-
171    JAR file:      MultiLUT.jar
172    Path:          components/legacy/multi-lut
173    Project deps:  (none)
174    Optional:      (none)
175    License:       Public domain
176
177OME Notes
178    A library for flexible organization and presentation of OME-XML metadata
179    within a graphical browser and editor interface
180    -=-
181    JAR file:      ome-notes.jar
182    Path:          components/legacy/ome-notes
183    Project deps:  LOCI Common, Bio-Formats
184    Optional:      (none)
185    License:       LGPL
186
187OME Metadata Editor
188    An application for exploration and editing of OME-XML and OME-TIFF metadata
189    -=-
190    JAR file:      ome-editor.jar
191    Path:          components/legacy/ome-editor
192    Project deps:  LOCI Common, OME-XML Java library, Bio-Formats
193    Optional:      (none)
194    License:       LGPL
195
196===============================================================================
197The following components are forks of third party projects:
198
199Apache Jakarta POI
200    Java API to handle Microsoft OLE 2 Compound Document format (Word, Excel)
201    -=-
202    JAR file:      poi-loci.jar
203    Path:          components/forks/poi
204    Project deps:  LOCI Common
205    Optional:      (none)
206    License:       Apache
207    Project URL:   http://jakarta.apache.org/poi/
208    Notes:         Based on poi-2.5.1-final-20040804.jar, with bugfixes for OLE
209                   v2 and memory efficiency improvements. Used by Bio-Formats
210                   for OLE support (cxd, ipw, oib, zvi). Used by VisBio
211                   overlays logic for XLS export feature.
212
213MDB Tools (Java port)
214    Java API to handle Microsoft MDB format (Access)
215    -=-
216    JAR file:      mdbtools-java.jar
217    Path:          components/forks/mdbtools
218    Project deps:  (none)
219    Optional:      (none)
220    License:       LGPL
221    Project URL:   http://sourceforge.net/forum/message.php?msg_id=2550619
222    Notes:         Used by Bio-Formats for Zeiss LSM metadata in MDB files.
223
224JAI Image I/O Tools
225    Java API to handle JPEG and JPEG2000 files
226    -=-
227    JAR file:      jai_imageio.jar
228    Path:          components/forks/jai
229    Project deps:  (none)
230    Optional:      (none)
231    License:       BSD
232    Project URL:   http://jai-imageio.dev.java.net/
233    Notes:         Used by Bio-Formats to read images compressed with JPEG2000
234                   and lossless JPEG. Modified from the 2008-10-14 source to
235                   include support for the YCbCr color space. Several files in
236                   the com.sun.media.jai packages were removed, as they are not
237                   needed by Bio-Formats, and created an additional dependency.
238                   This component will be removed once our changes have been
239                   added to the official JAI CVS repository.
240
241===============================================================================
242The following external dependencies (in the jar folder) may be required:
243Apple eAWT stubs
244    JAR file:  AppleJavaExtensions.jar
245    URL:       http://developer.apple.com/samplecode/AppleJavaExtensions/
246    Notes:     required to compile Mac-specific functionality on non-Mac OS X
247               machines
248    License:   BSD
249
250Ant-Contrib
251    JAR file:  ant-contrib-1.0b3.jar
252    URL:       http://ant-contrib.sourceforge.net/
253    Notes:     used by tools target to iterate over JAR files ("for" task)
254    License:   Apache
255
256Checkstyle
257    JAR file:  checkstyle-all-5.0.jar
258    URL:       http://checkstyle.sourceforge.net/
259    Notes:     used by style Ant target to check source code style conventions
260    License:   LGPL
261
262Apache Jakarta Commons HttpClient
263    JAR file:  commons-httpclient-2.0-rc2.jar
264    URL:       http://jakarta.apache.org/commons/httpclient/
265    Notes:     required for OME-Java to communicate with OME servers
266    License:   Apache
267
268Apache Jakarta Commons Logging
269    JAR file:  commons-logging.jar
270    URL:       http://jakarta.apache.org/commons/logging/
271    Notes:     used by OME-Java
272    License:   Apache
273
274FindBugs Ant task
275    JAR file:  findbugs-ant.jar
276    URL:       http://findbugs.sourceforge.net/
277    Notes:     used by findbugs Ant target to check for program bugs
278    License:   LGPL
279
280JGoodies Forms
281    JAR file:  forms-1.3.0.jar
282    URL:       http://www.jgoodies.com/freeware/forms/index.html
283    Notes:     used for layout by VisBio, Data Browser and OME Notes
284    License:   BSD
285
286Ice
287    JAR file:  Ice-3.3.1.jar
288    URL:       http://www.zeroc.com/ice.html
289    Notes:     used by Bio-Formats Ice framework
290    License:   GPL
291
292ImageJ
293    JAR file:  ij.jar
294    URL:       http://rsb.info.nih.gov/ij/
295    Notes:     used by LOCI plugins for ImageJ and OME plugins for ImageJ;
296               bundled with VisBio to achieve ImageJ interconnectivity
297    License:   Public domain
298
299JAI ImageIO wrapper
300    JAR file:  clibwrapper_jiio.jar
301    URL:       https://jai-imageio.dev.java.net/
302    Notes:     used by Bio-Formats via reflection for JPEG2000 support (ND2,
303               JP2) and lossless JPEG decompression (DICOM)
304    License:   BSD
305
306JUnit
307    JAR file:  junit.jar
308    URL:       http://www.junit.org/
309    Notes:     unit testing framework used for a few VisBio unit tests
310    License:   Common Public License
311
312L-M Fit
313    JAR file:  lma.jar
314    URL:       http://users.utu.fi/jaolho/
315    Notes:     Levenberg-Marquardt algorithm for exponential curve fitting,
316               used by SLIM Plotter
317    License:   LGPL
318
319Luratech LuraWave stubs
320    JAR file:  lwf-stubs.jar
321    URL:       http://www.luratech.com/
322    Notes:     required to compile Bio-Formats's support for Luratech LWF
323               compression for the Opera Flex format
324    License:   BSD
325
326Apache log4j
327    JAR file:  log4j-1.2.15.jar
328    URL:       http://logging.apache.org/log4j/
329    Notes:     required by SLF4J implementation
330    License:   Apache
331
332JGoodies Looks
333    JAR file:  looks-2.3.1.jar
334    URL:       http://www.jgoodies.com/freeware/looks/index.html
335    Notes:     used for a nicer Look & Feel by VisBio and OME Metadata Editor
336    License:   BSD
337
338NetCDF
339    JAR file:  netcdf-4.0.jar
340    URL:       http://www.unidata.ucar.edu/software/netcdf-java/
341    Notes:     used by Bio-Formats via reflection for HDF support (Imaris 5.5)
342    License:   LGPL
343
344Simple Logging Facade for Java API
345    JAR file:  slf4j-api-1.5.10.jar
346    URL:       http://www.slf4j.org/
347    Notes:     used for all logging in loci.*
348    License:   BSD
349
350Simple Logging Facade for Java Binding
351    JAR file:  slf4j-log4j12-1.5.10.jar
352    URL:       http://www.slf4j.org/
353    Notes:     used for all logging in loci.*
354    License:   BSD
355
356OME-Java
357    JAR file:  ome-java.jar
358    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
359    Notes:     used by OME I/O to connect to OME servers
360    License:   LGPL
361
362OME-Java deprecated classes
363    JAR file:  ome-java-deprecated.jar
364    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
365    Notes:     used by OME Notes and OME Metadata Editor to work with OME-XML
366    License:   LGPL
367
368OMERO Client
369    JAR file:  omero-client-4.1.1.jar
370    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
371    Notes:     used by OME I/O to connect to OMERO servers
372    License:   GPL
373
374OMERO Common
375    JAR file:  omero-common-4.1.1.jar
376    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
377    Notes:     used by OME I/O to connect to OMERO servers
378    License:   GPL
379
380Skin Look and Feel
381    JAR file:  skinlf.jar
382    URL:       http://skinlf.l2fprod.com/
383    Notes:     not used (may be used in the future for flexible skinning)
384    License:   Custom (BSD-like)
385
386TestNG
387    JAR file:  testng-5.11-jdk15.jar
388    URL:       http://testng.org/
389    Notes:     testing framework used for LOCI software automated test suite
390    License:   Apache
391
392Apache Velocity
393    JAR file:  velocity-1.6.3-dep.jar
394    URL:       http://velocity.apache.org/
395    Notes:     used to autogenerate the loci.formats.meta and loci.formats.ome
396               Bio-Formats packages
397    License:   Apache
398
399VisAD
400    JAR file:  visad-lite.jar
401    URL:       http://www.ssec.wisc.edu/~billh/visad.html
402    Notes:     stripped down VisAD library used by VisBio and SLIM Plotter for
403               interactive visualization
404    License:   LGPL
405
406Apache XML-RPC
407    JAR file:  xmlrpc-1.2-b1.jar
408    URL:       http://ws.apache.org/xmlrpc/
409    Notes:     used by OME-Java library to communicate with OME servers
410    License:   Apache
411-->
412
413<project name="LOCI Software" default="jars" basedir=".">
414  <description>
415    Master build file for all Java software projects at LOCI
416  </description>
417  <import file="ant/toplevel.xml"/>
418</project>
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