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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--org.emboss.jemboss.server.JembossAuthServer
Jemboss Authenticated Server for SOAP
Field Summary | |
(package private) java.lang.String |
acdDirToParse
|
(package private) java.lang.String |
embossBin
|
(package private) java.lang.String |
embossData
|
(package private) java.lang.String |
embossPath
|
private java.lang.String[] |
env
|
private java.lang.String |
environ
|
private java.lang.String |
errorLog
|
private java.lang.String |
fs
|
(package private) JembossParams |
jp
|
private java.lang.String |
logFile
|
(package private) java.lang.String |
plplot
|
private java.lang.String |
ps
|
private java.lang.String |
tmproot
|
Constructor Summary | |
JembossAuthServer()
|
Method Summary | |
java.lang.String |
about()
|
java.lang.String |
abouturl()
|
private void |
appendToLogFile(java.lang.String logEntry,
java.lang.String logFileName)
Appends a log entry to the log file |
java.lang.String |
appversion()
|
java.util.Vector |
call_ajax(java.lang.String fileContent,
java.lang.String seqtype)
Uses JNI to calculate sequence attributes using EMBOSS library call. |
java.util.Vector |
call_ajax(java.lang.String fileContent,
java.lang.String seqtype,
java.lang.String userName,
byte[] passwd)
Uses JNI to calculate sequence attributes using EMBOSS library call. |
java.lang.Object |
clone()
|
java.util.Vector |
delete_saved_results(java.lang.String project,
java.lang.String cl,
java.lang.String userName,
byte[] passwd)
Private server Deletes a projects saved results. |
java.lang.String |
docurl()
|
private java.util.Hashtable |
getHashtable(java.util.Vector v)
|
java.util.Vector |
getWossname()
Returns the output of the EMBOSS utility wossname |
java.lang.String |
helpurl()
|
java.util.Vector |
list_saved_results(java.lang.String userName,
byte[] passwd)
Private Server List of the saved results on the server. |
private java.util.Vector |
loadFilesContent(Ajax aj,
java.lang.String userName,
byte[] passwd,
java.io.File projectDir,
java.lang.String project,
java.util.Vector result,
java.util.Hashtable inFiles)
Reads in files from EMBOSS output |
java.lang.String |
name()
|
private java.lang.String |
quoteMe(java.lang.String s)
Quote all tokens ready for shell scripts |
private java.util.Vector |
returnError(Ajax aj,
java.lang.String msg)
Report the stderr and stdout to error logs |
java.util.Vector |
run_prog(java.lang.String embossCommand,
java.lang.String options,
java.util.Hashtable inFiles,
java.lang.String userName,
byte[] passwd)
Private Authenticated Server Run an EMBOSS application |
java.util.Vector |
run_prog(java.lang.String embossCommand,
java.lang.String options,
java.util.Vector inFiles,
java.lang.String userName,
byte[] passwd)
|
private void |
runAsBatch(Ajax aj,
java.lang.String userName,
byte[] passwd,
java.lang.String project,
java.lang.String embossCommand)
|
private void |
runAsGNQSBatch(Ajax aj,
java.lang.String userName,
byte[] passwd,
java.lang.String project,
java.lang.String embossCommand)
Submit to a Generic NQS batch queue. |
private void |
runAsPBSBatch(Ajax aj,
java.lang.String userName,
byte[] passwd,
java.lang.String project,
java.lang.String embossCommand)
Submit to a OpenPBS batch queue. |
java.util.Vector |
save_project_file(java.lang.String project,
java.lang.String filename,
java.lang.String notes,
java.lang.String userName,
byte[] passwd)
Private server Save a file to a project directory on the server. |
java.util.Hashtable |
servicedesc()
|
java.util.Vector |
show_acd(java.lang.String appName)
Retrieves the ACD file of an application. |
java.util.Vector |
show_db()
Returns the databases held on the server |
java.util.Vector |
show_help(java.lang.String applName)
Returns the help for an application as given by 'tfm' |
java.util.Vector |
show_saved_results(java.lang.String project,
java.lang.String cl,
java.lang.String userName,
byte[] passwd)
Private Server Returns the results for a saved project. |
java.util.Vector |
update_result_status(java.lang.String prog,
java.lang.String opt,
java.util.Hashtable resToQuery,
java.lang.String userName,
byte[] passwd)
|
java.util.Vector |
update_result_status(java.lang.String prog,
java.lang.String opt,
java.util.Vector resToQuery,
java.lang.String userName,
byte[] passwd)
Used to provide information on the batch/background processes. |
private boolean |
verifyUser(Ajax aj,
java.lang.String userName,
byte[] passwd,
java.util.Vector res)
|
java.lang.String |
version()
|
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
private java.lang.String tmproot
private java.lang.String logFile
private java.lang.String errorLog
private java.lang.String fs
private java.lang.String ps
JembossParams jp
java.lang.String plplot
java.lang.String embossData
java.lang.String embossBin
java.lang.String embossPath
java.lang.String acdDirToParse
private java.lang.String[] env
private java.lang.String environ
Constructor Detail |
public JembossAuthServer()
Method Detail |
public java.lang.String name()
public java.lang.String version()
public java.lang.String appversion()
public java.lang.String about()
public java.lang.String helpurl()
public java.lang.String abouturl()
public java.lang.String docurl()
public java.util.Hashtable servicedesc()
public java.util.Vector show_acd(java.lang.String appName)
public java.util.Vector getWossname()
public java.util.Vector show_help(java.lang.String applName)
public java.util.Vector call_ajax(java.lang.String fileContent, java.lang.String seqtype, java.lang.String userName, byte[] passwd)
public java.util.Vector call_ajax(java.lang.String fileContent, java.lang.String seqtype)
public java.util.Vector show_db()
public java.util.Vector run_prog(java.lang.String embossCommand, java.lang.String options, java.util.Vector inFiles, java.lang.String userName, byte[] passwd)
private java.util.Hashtable getHashtable(java.util.Vector v)
public java.util.Vector run_prog(java.lang.String embossCommand, java.lang.String options, java.util.Hashtable inFiles, java.lang.String userName, byte[] passwd)
private java.lang.String quoteMe(java.lang.String s)
private void runAsPBSBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand)
private void runAsGNQSBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand)
private void runAsBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand)
public java.util.Vector show_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName, byte[] passwd)
public java.util.Vector save_project_file(java.lang.String project, java.lang.String filename, java.lang.String notes, java.lang.String userName, byte[] passwd)
public java.util.Vector delete_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName, byte[] passwd)
public java.util.Vector list_saved_results(java.lang.String userName, byte[] passwd)
private void appendToLogFile(java.lang.String logEntry, java.lang.String logFileName)
private java.util.Vector loadFilesContent(Ajax aj, java.lang.String userName, byte[] passwd, java.io.File projectDir, java.lang.String project, java.util.Vector result, java.util.Hashtable inFiles)
public java.util.Vector update_result_status(java.lang.String prog, java.lang.String opt, java.util.Vector resToQuery, java.lang.String userName, byte[] passwd)
public java.util.Vector update_result_status(java.lang.String prog, java.lang.String opt, java.util.Hashtable resToQuery, java.lang.String userName, byte[] passwd)
private boolean verifyUser(Ajax aj, java.lang.String userName, byte[] passwd, java.util.Vector res)
private java.util.Vector returnError(Ajax aj, java.lang.String msg)
public final java.lang.Object clone() throws java.lang.CloneNotSupportedException
clone
in class java.lang.Object
java.lang.CloneNotSupportedException
|
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