[MOBY-guts] biomoby commit
Martin Senger
senger at dev.open-bio.org
Fri Feb 22 09:37:39 UTC 2008
senger
Fri Feb 22 04:37:39 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory dev.open-bio.org:/tmp/cvs-serv29790/src/Clients/help
Modified Files:
BaseCmdLineClient_usage.txt CacheRegistryClient_usage.txt
CreateMobyInput_usage.txt MobyCmdLineClient_usage.txt
MobyDigest_usage.txt MobyGraphs_usage.txt
MosesGenerators_usage.txt TestingMobyParser_usage.txt
Log Message:
* Change, Fixed: On various places (starting with
org.biomoby.shared.Utils), starting to use Apache commons-io
library (it was necessary in Utils.java because the method
inputStreamToString() was broken anyway).
* Added: a common parent to the command-line clients
(org.biomoby.client.CmdLineHelper) - brinking more and unified
features to these clients.
moby-live/Java/src/Clients/help BaseCmdLineClient_usage.txt,1.3,1.4 CacheRegistryClient_usage.txt,1.7,1.8 CreateMobyInput_usage.txt,1.3,1.4 MobyCmdLineClient_usage.txt,1.12,1.13 MobyDigest_usage.txt,1.6,1.7 MobyGraphs_usage.txt,1.7,1.8 MosesGenerators_usage.txt,1.2,1.3 TestingMobyParser_usage.txt,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt 2006/05/09 13:32:09 1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt 2008/02/22 09:37:39 1.4
@@ -54,4 +54,4 @@
-o <output-file>
[Note: You can also use -argsfile <filename> to read arguments from a
-file. See details in src/Client/help/argsfile.example.]
+file. See details in src/Clients/help/argsfile.example.]
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2005/12/13 15:01:29 1.7
+++ /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2008/02/22 09:37:39 1.8
@@ -13,10 +13,8 @@
where <find-arguments> specify what Moby registry to connect to
-e <URL>
<URL> is an endpoint of a Moby registry
- (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl)
-uri <namespace>
<namespace> is a URI defining Moby registry's namespace
- (default: http://mobycentral.icapture.ubc.ca/MOBY/Central)
where <other-arguments> are:
-fill ... remove the current cache and reread all
@@ -59,4 +57,4 @@
-v ... verbose mode (prints also decorations)
[Note: You can also use -argsfile <filename> to read arguments from a
-file. See details in src/Client/help/argsfile.example.]
+file. See details in src/Clients/help/argsfile.example.]
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt 2006/02/08 05:57:41 1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt 2008/02/22 09:37:39 1.4
@@ -21,10 +21,8 @@
<dir> is a directory with cached entities of a Moby registry
-e <URL>
<URL> is an endpoint of a Moby registry
- (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl)
-uri <namespace>
<namespace> is a URI defining Moby registry's namespace
- (default: http://mobycentral.icapture.ubc.ca/MOBY/Central)
where <other-arguments> are:
@@ -33,4 +31,4 @@
-v ... verbose mode (prints also decorations)
[Note: You can also use -argsfile <filename> to read arguments from a
-file. See details in src/Client/help/argsfile.example.]
+file. See details in src/Clients/help/argsfile.example.]
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2007/05/31 13:42:51 1.12
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2008/02/22 09:37:39 1.13
@@ -14,10 +14,8 @@
-e <URL>
<URL> ia an endpoint of a Moby registry
- (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl)
-uri <namespace>
<namespace> is a URI defining Moby registry's namespace
- (default: http://mobycentral.icapture.ubc.ca/MOBY/Central)
or
-registry <registry-synonym>
<registry-synonym> is a convenient way to specify a known registry;
@@ -223,4 +221,4 @@
[Undocumented and 'in-the-progress' options: -async, -url <service-url>.]
[Note: You can also use -argsfile <filename> to read arguments from a
-file. See details in src/Client/help/argsfile.example.]
+file. See details in src/Clients/help/argsfile.example.]
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt 2006/02/08 05:57:41 1.6
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt 2008/02/22 09:37:39 1.7
@@ -9,10 +9,8 @@
what cache to use instead):
-e <URL>
<URL> ia an endpoint of a Moby registry
- (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl)
-uri <namespace>
<namespace> is a URI defining Moby registry's namespace
- (default: http://mobycentral.icapture.ubc.ca/MOBY/Central)
-cachedir <dir>
a directory where to cache information from a Moby registry;
@@ -42,4 +40,4 @@
-v[erbose] ... verbose
[Note: You can also use -argsfile <filename> to read arguments from a
-file. See details in src/Client/help/argsfile.example.]
+file. See details in src/Clients/help/argsfile.example.]
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2005/09/04 13:45:37 1.7
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2008/02/22 09:37:39 1.8
@@ -7,13 +7,6 @@
where <find-arguments> specify what Moby registry to connect to (or
what cache to use instead):
- -e <URL>
- <URL> ia an endpoint of a Moby registry
- (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl)
- -uri <namespace>
- <namespace> is a URI defining Moby registry's namespace
- (default: http://mobycentral.icapture.ubc.ca/MOBY/Central)
-
-cachedir <dir>
a directory where to cache information from a Moby registry;
depending on -e and -uri there will be a subdirectory in <dir>
@@ -22,6 +15,16 @@
exist it is created and filled with date fetched from the Moby
registry
+ -e <URL>
+ <URL> is an endpoint of a Moby registry
+ -uri <namespace>
+ <namespace> is a URI defining Moby registry's namespace
+ or
+ -registry <registry-synonym>
+ <registry-synonym> is a convenient way to specify a known registry;
+ the list of known registries can be obtained by the -lr option
+ from the MobyCmdLineClient (run-cmdline-client -lr)
+
where <other-arguments> are:
General arguments:
@@ -121,4 +124,4 @@
By default it does not.
[Note: You can also use -argsfile <filename> to read arguments from a
-file. See details in src/Client/help/argsfile.example.]
+file. See details in src/Clients/help/argsfile.example.]
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt 2005/09/04 13:45:37 1.2
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt 2008/02/22 09:37:39 1.3
@@ -8,9 +8,9 @@
set CLASSPATH and
java MosesGenerator -h[elp]
java MosesGenerator [<options>] <filename>
-or (using Ant)
- ./build.sh [properties] moses-datatypes
- ./build.sh [properties] moses-services
+or
+ ant [properties] moses-datatypes
+ ant [properties] moses-services
where <options> for generating code for Biomoby data types are:
-dt ... generate data types
@@ -35,6 +35,12 @@
-auth icapture -service '(?i)test'
where the main <options> for both generators are:
+ -cachedir <local-dir>
+ A local directory where are cached Biomoby object. Use
+ this option even if you do not have a cache - and it will
+ be created so the next time generators will run faster
+ (but still they need to go to registry for list of names).
+
-e <endpoint>
A URL of a Biomoby registry where this generator will go to
fetch information about generated entities.
@@ -42,11 +48,11 @@
-uri <namespace>
A namespace/URI of a Biomoby registry. Again its default
value is usually fine.
- -cachedir <local-dir>
- A local directory where are cached Biomoby object. Use
- this option even if you do not have a cache - and it will
- be created so the next time generators will run faster
- (but still they need to go to registry for list of names).
+ or
+ -registry <registry-synonym>
+ <registry-synonym> is a convenient way to specify a known registry;
+ the list of known registries can be obtained by the -lr option
+ from the MobyCmdLineClient (run-cmdline-client -lr)
where the remaining <options> for both generators are:
-q ... less verbose mode (quiet)
@@ -63,4 +69,4 @@
this program is not on your PATH, specify here where it is.
[Note: You can also use -argsfile <filename> to read arguments from a
-file. See details in src/Client/help/argsfile.example.]
+file. See details in src/Clients/help/argsfile.example.]
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2005/09/04 13:45:37 1.2
+++ /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2008/02/22 09:37:39 1.3
@@ -27,4 +27,4 @@
types, are not up-to-date)
[Note: You can also use -argsfile <filename> to read arguments from a
-file. See details in src/Client/help/argsfile.example.]
+file. See details in src/Clients/help/argsfile.example.]
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