source: trunk/build.xml @ 6050

Revision 6050, 14.4 KB checked in by curtis, 10 years ago (diff)

Clean up some copyright notices, and fix scan-deps.pl handling of lwf-stubs.

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 code generator
15    Package for generating other code, including the Bio-Formats metadata API,
16    related documentation, Ice bindings, and Bio-Formats C++ bindings headers
17    -=-
18    JAR file:      loci-autogen.jar
19    Path:          components/autogen
20    Project deps:  Bio-Formats, LOCI Common
21    Library deps:  Apache Velocity
22    Optional:      (none)
23    License:       GPL
24
25Bio-Formats Ice framework
26    Bindings for Bio-Formats client/server communication enabling
27    cross-language interoperability
28    -=-
29    JAR file:      bf-ice.jar
30    Path:          components/bf-ice
31    Project deps:  Bio-Formats, LOCI Common
32    Library deps:  Ice, Apache log4j
33    Optional:      (none)
34    License:       GPL
35
36Bio-Formats
37    A library for reading and writing popular microscopy file formats
38    -=-
39    JAR file:      bio-formats.jar
40    Path:          components/bio-formats
41    Project deps:  LOCI Common, OME-XML Java library, JAI Image I/O Tools,
42                   MDB Tools (Java port), Apache Jakarta POI,
43                   Luratech LuraWave stubs
44    Library deps:  JGoodies Forms, Apache log4j, NetCDF,
45                   Simple Logging Facade for Java API, TestNG
46    Optional:      OME I/O, OME Notes
47    License:       GPL
48
49WiscScan Flow Cytometry
50    Server application for flow cytometry with WiscScan using JVMLink
51    -=-
52    JAR file:      flow-cytometry.jar
53    Path:          components/flow-cytometry
54    Project deps:  Bio-Formats, LOCI Common
55    Library deps:  ImageJ, VisAD
56    Optional:      (none)
57    License:       BSD
58
59LOCI Checkstyle checks
60    LOCI's Checkstyle extensions, for checking source code style
61    -=-
62    JAR file:      loci-checks.jar
63    Path:          components/checkstyle
64    Project deps:  (none)
65    Library deps:  Checkstyle
66    Optional:      (none)
67    License:       Public domain
68
69LOCI Common
70    A library containing common I/O and reflection classes
71    -=-
72    JAR file:      loci-common.jar
73    Path:          components/common
74    Project deps:  (none)
75    Library deps:  Simple Logging Facade for Java API, TestNG
76    Optional:      (none)
77    License:       GPL
78
79LOCI Plugins for ImageJ
80    A collection of plugins for ImageJ, including the Bio-Formats Importer,
81    Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser, Stack
82    Colorizer and Stack Slicer
83    -=-
84    JAR file:      loci_plugins.jar
85    Path:          components/loci-plugins
86    Project deps:  Bio-Formats, LOCI Common
87    Library deps:  JGoodies Forms, ImageJ, Apache log4j
88    Optional:      OME I/O, VisBio
89    License:       GPL
90
91OME I/O
92    A library for OME database import, upload and download
93    -=-
94    JAR file:      ome-io.jar
95    Path:          components/ome-io
96    Project deps:  Bio-Formats, LOCI Common
97    Library deps:  Apache log4j, Simple Logging Facade for Java API,
98                   OMERO Client, OMERO Common, TestNG
99    Optional:      OME-Java
100    License:       GPL
101
102OME Plugins for ImageJ
103    A collection of plugins for ImageJ, including the Download from OME and
104    Upload to OME plugins
105    -=-
106    JAR file:      ome_plugins.jar
107    Path:          components/ome-plugins
108    Project deps:  Bio-Formats, LOCI Common, LOCI Plugins for ImageJ, OME I/O
109    Library deps:  ImageJ
110    Optional:      (none)
111    License:       GPL
112
113OME-XML Java library
114    A library for working with OME-XML metadata structures
115    -=-
116    JAR file:      ome-xml.jar
117    Path:          components/ome-xml
118    Project deps:  (none)
119    Library deps:  (none)
120    Optional:      (none)
121    License:       GPL
122
123SLIM Plotter
124    An application and curve fitting library for visualization and analysis of
125    combined spectral lifetime data
126    -=-
127    JAR file:      SlimPlotter.jar
128    Path:          components/slim-plotter
129    Project deps:  Bio-Formats, LOCI Common, VisBio
130    Library deps:  L-M Fit, VisAD
131    Optional:      (none)
132    License:       GPL
133
134LOCI testing framework
135    Framework for automated and manual testing of the LOCI software packages
136    -=-
137    JAR file:      loci-testing-framework.jar
138    Path:          components/test-suite
139    Project deps:  Bio-Formats, LOCI Common, OME I/O
140    Library deps:  Apache log4j, Simple Logging Facade for Java API, TestNG
141    Optional:      (none)
142    License:       BSD
143
144VisBio
145    A multi-purpose biological analysis tool
146    -=-
147    JAR file:      visbio.jar
148    Path:          components/visbio
149    Project deps:  Bio-Formats, LOCI Common, OME I/O, OME-XML Java library,
150                   Apache Jakarta POI
151    Library deps:  Apple eAWT stubs, JGoodies Forms, ImageJ, JUnit,
152                   JGoodies Looks, VisAD
153    Optional:      (none)
154    License:       GPL
155
156===============================================================================
157The following components are considered "legacy" but still available:
158
159JVMLink
160    A library for communicating between a Java Virtual Machine and other
161    programs (e.g., C++ applications) via IP over localhost (or remotely)
162    -=-
163    JAR file:      jvmlink.jar
164    Path:          components/legacy/jvmlink
165    Project deps:  LOCI Common
166    Optional:      (none)
167    License:       BSD
168
169Multi-LUT
170    A demo application for visually exploring multi-spectral image data
171    -=-
172    JAR file:      MultiLUT.jar
173    Path:          components/legacy/multi-lut
174    Project deps:  (none)
175    Optional:      (none)
176    License:       Public domain
177
178OME Metadata Editor
179    An application for exploration and editing of OME-XML and OME-TIFF metadata
180    -=-
181    JAR file:      ome-editor.jar
182    Path:          components/legacy/ome-editor
183    Project deps:  Bio-Formats, LOCI Common, OME-XML Java library
184    Optional:      (none)
185    License:       LGPL
186
187OME Notes
188    A library for flexible organization and presentation of OME-XML metadata
189    within a graphical browser and editor interface
190    -=-
191    JAR file:      ome-notes.jar
192    Path:          components/legacy/ome-notes
193    Project deps:  Bio-Formats, LOCI Common
194    Optional:      (none)
195    License:       LGPL
196
197===============================================================================
198The following components are forks of third party projects:
199
200JAI Image I/O Tools
201    Java API to handle JPEG and JPEG2000 files
202    -=-
203    JAR file:      jai_imageio.jar
204    Path:          components/forks/jai
205    Project deps:  (none)
206    Optional:      (none)
207    License:       BSD
208    Project URL:   http://jai-imageio.dev.java.net/
209    Notes:         Used by Bio-Formats to read images compressed with JPEG2000
210                   and lossless JPEG. Modified from the 2008-10-14 source to
211                   include support for the YCbCr color space. Several files in
212                   the com.sun.media.jai packages were removed, as they are not
213                   needed by Bio-Formats, and created an additional dependency.
214                   This component will be removed once our changes have been
215                   added to the official JAI CVS repository.
216
217MDB Tools (Java port)
218    Java API to handle Microsoft MDB format (Access)
219    -=-
220    JAR file:      mdbtools-java.jar
221    Path:          components/forks/mdbtools
222    Project deps:  (none)
223    Optional:      (none)
224    License:       LGPL
225    Project URL:   http://sourceforge.net/forum/message.php?msg_id=2550619
226    Notes:         Used by Bio-Formats for Zeiss LSM metadata in MDB files.
227
228Apache Jakarta POI
229    Java API to handle Microsoft OLE 2 Compound Document format (Word, Excel)
230    -=-
231    JAR file:      poi-loci.jar
232    Path:          components/forks/poi
233    Project deps:  LOCI Common
234    Optional:      (none)
235    License:       Apache
236    Project URL:   http://jakarta.apache.org/poi/
237    Notes:         Based on poi-2.5.1-final-20040804.jar, with bugfixes for OLE
238                   v2 and memory efficiency improvements. Used by Bio-Formats
239                   for OLE support (cxd, ipw, oib, zvi). Used by VisBio
240                   overlays logic for XLS export feature.
241
242===============================================================================
243The following components are stubs of third party projects:
244
245Luratech LuraWave stubs
246    Stub of proprietary Java API to handle Luratech LWF compression
247    -=-
248    JAR file:      lwf-stubs.jar
249    Path:          components/stubs/lwf-stubs
250    Project deps:  (none)
251    Optional:      (none)
252    License:       BSD
253    Project URL:   http://www.luratech.com/
254    Notes:         required to compile Bio-Formats's support for Luratech LWF
255                   compression for the Opera Flex format
256
257===============================================================================
258The following external dependencies (in the jar folder) may be required:
259Apple eAWT stubs
260    JAR file:  AppleJavaExtensions.jar
261    URL:       http://developer.apple.com/samplecode/AppleJavaExtensions/
262    Notes:     required to compile Mac-specific functionality on non-Mac OS X
263               machines
264    License:   BSD
265
266Ant-Contrib
267    JAR file:  ant-contrib-1.0b3.jar
268    URL:       http://ant-contrib.sourceforge.net/
269    Notes:     used by tools target to iterate over JAR files ("for" task)
270    License:   Apache
271
272Checkstyle
273    JAR file:  checkstyle-all-5.0.jar
274    URL:       http://checkstyle.sourceforge.net/
275    Notes:     used by style Ant target to check source code style conventions
276    License:   LGPL
277
278Apache Jakarta Commons HttpClient
279    JAR file:  commons-httpclient-2.0-rc2.jar
280    URL:       http://jakarta.apache.org/commons/httpclient/
281    Notes:     required for OME-Java to communicate with OME servers
282    License:   Apache
283
284Apache Jakarta Commons Logging
285    JAR file:  commons-logging.jar
286    URL:       http://jakarta.apache.org/commons/logging/
287    Notes:     used by OME-Java
288    License:   Apache
289
290FindBugs Ant task
291    JAR file:  findbugs-ant.jar
292    URL:       http://findbugs.sourceforge.net/
293    Notes:     used by findbugs Ant target to check for program bugs
294    License:   LGPL
295
296JGoodies Forms
297    JAR file:  forms-1.3.0.jar
298    URL:       http://www.jgoodies.com/freeware/forms/index.html
299    Notes:     used for layout by VisBio, Data Browser and OME Notes
300    License:   BSD
301
302Ice
303    JAR file:  Ice-3.3.1.jar
304    URL:       http://www.zeroc.com/ice.html
305    Notes:     used by Bio-Formats Ice framework
306    License:   GPL
307
308ImageJ
309    JAR file:  ij.jar
310    URL:       http://rsb.info.nih.gov/ij/
311    Notes:     used by LOCI plugins for ImageJ and OME plugins for ImageJ;
312               bundled with VisBio to achieve ImageJ interconnectivity
313    License:   Public domain
314
315JAI ImageIO wrapper
316    JAR file:  clibwrapper_jiio.jar
317    URL:       https://jai-imageio.dev.java.net/
318    Notes:     used by Bio-Formats via reflection for JPEG2000 support (ND2,
319               JP2) and lossless JPEG decompression (DICOM)
320    License:   BSD
321
322JUnit
323    JAR file:  junit.jar
324    URL:       http://www.junit.org/
325    Notes:     unit testing framework used for a few VisBio unit tests
326    License:   Common Public License
327
328L-M Fit
329    JAR file:  lma.jar
330    URL:       http://users.utu.fi/jaolho/
331    Notes:     Levenberg-Marquardt algorithm for exponential curve fitting,
332               used by SLIM Plotter
333    License:   LGPL
334
335Apache log4j
336    JAR file:  log4j-1.2.15.jar
337    URL:       http://logging.apache.org/log4j/
338    Notes:     required by SLF4J implementation
339    License:   Apache
340
341JGoodies Looks
342    JAR file:  looks-2.3.1.jar
343    URL:       http://www.jgoodies.com/freeware/looks/index.html
344    Notes:     used for a nicer Look & Feel by VisBio and OME Metadata Editor
345    License:   BSD
346
347NetCDF
348    JAR file:  netcdf-4.0.jar
349    URL:       http://www.unidata.ucar.edu/software/netcdf-java/
350    Notes:     used by Bio-Formats via reflection for HDF support (Imaris 5.5)
351    License:   LGPL
352
353Simple Logging Facade for Java API
354    JAR file:  slf4j-api-1.5.10.jar
355    URL:       http://www.slf4j.org/
356    Notes:     used for all logging in loci.*
357    License:   BSD
358
359Simple Logging Facade for Java Binding
360    JAR file:  slf4j-log4j12-1.5.10.jar
361    URL:       http://www.slf4j.org/
362    Notes:     used for all logging in loci.*
363    License:   BSD
364
365OME-Java
366    JAR file:  ome-java.jar
367    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
368    Notes:     used by OME I/O to connect to OME servers
369    License:   LGPL
370
371OME-Java deprecated classes
372    JAR file:  ome-java-deprecated.jar
373    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
374    Notes:     used by OME Notes and OME Metadata Editor to work with OME-XML
375    License:   LGPL
376
377OMERO Client
378    JAR file:  omero-client-4.1.1.jar
379    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
380    Notes:     used by OME I/O to connect to OMERO servers
381    License:   GPL
382
383OMERO Common
384    JAR file:  omero-common-4.1.1.jar
385    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
386    Notes:     used by OME I/O to connect to OMERO servers
387    License:   GPL
388
389Skin Look and Feel
390    JAR file:  skinlf.jar
391    URL:       http://skinlf.l2fprod.com/
392    Notes:     not used (may be used in the future for flexible skinning)
393    License:   Custom (BSD-like)
394
395TestNG
396    JAR file:  testng-5.11-jdk15.jar
397    URL:       http://testng.org/
398    Notes:     testing framework used for LOCI software automated test suite
399    License:   Apache
400
401Apache Velocity
402    JAR file:  velocity-1.6.3-dep.jar
403    URL:       http://velocity.apache.org/
404    Notes:     used to autogenerate the loci.formats.meta and loci.formats.ome
405               Bio-Formats packages
406    License:   Apache
407
408VisAD
409    JAR file:  visad-lite.jar
410    URL:       http://www.ssec.wisc.edu/~billh/visad.html
411    Notes:     stripped down VisAD library used by VisBio and SLIM Plotter for
412               interactive visualization
413    License:   LGPL
414
415Apache XML-RPC
416    JAR file:  xmlrpc-1.2-b1.jar
417    URL:       http://ws.apache.org/xmlrpc/
418    Notes:     used by OME-Java library to communicate with OME servers
419    License:   Apache
420-->
421
422<project name="LOCI Software" default="jars" basedir=".">
423  <description>
424    Master build file for all Java software projects at LOCI
425  </description>
426  <import file="ant/toplevel.xml"/>
427</project>
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