charite.christo.metannogen
Class UploadDatasets

java.lang.Object
  charite.christo.metannogen.UploadDatasets

All Implemented Interfaces:

ChRunnable

public class UploadDatasets
extends Object
implements ChRunnable

HELP A Metannogen datasets contain a biochemical equation and expert opinion edited by the curator. The datasets can be stored in a local file on the PC or on a central HTTP server such that several investigators can work on the same data. For a central data repository, a PERL script needs to be installed on the server in the cgi-bin directory:

   http://www.charite.de/bioinf/strap/metannogen/metannogen.pl.txt.
    

JCOMPONENT:MetannogenMain#newPnlServer()

The top of the PERL file contains two variables which need to be customized:

use constant  DIR =>        "/var/www/bioinf/strap/metannogen/hoppe_datasets";
use constant  PASSWORD =>   "secret password";
    

If the password is kept empty ("") as for the demo database then there is no access control. Anyone can modify the datasets. The constant variable DIR gives the directory on the server. It should be a directory which is visible through HTTP. This is the case if it is located in the /htdocs/ -branch.

Entering the server URL and password: When Metannogen is started with GUI the start dialog appears. The top panel of the start dialog has three input text fields to enter the server data.

Server address: The multi-line text-field holds the URL of the PERL-script. The first valid URL is the master server. Optional, secondary URLs in text lines below may serve as Backup servers, as they receive the same data from Metannogen. The server can be tested with the Web-browser: Visiting this address in the Web-browser should show a file with all datasets. For example visit the demo server address:

STRING:MetannogenStatics#DEMO_SERVER

Lines that are commented out by a leading "#" are ignored.
Address of one single dataset The server address may optionally be followed in the same line by an expression denoting the URL for single datasets. The asterisk of this mask stands for the dataset ID. The URL of a single dataset is formed by replacing the asterisk by the ID. For example consider the URL mask of the demo server:

STRING:MetannogenStatics#DEMO_URL_SINGLE

Replace the asterisk by a dataset ID such as "R08689" and visit the resulting address in the Web-browser: This address allows Metannogen to observe the "Last-Modified" and "Date" attributes of the current dataset. If a dataset is uploaded by another investigator while it is modified, a warning message appears. The goal is to prevent data loss when datasets are modified simultaneously by different users.

Password: If the password is not matching the password written in the PERL script, the user is not allowed to change datasets.

Field Summary

static int	BACKGROUND
static int	DONOT_ASK
static String	HTTP_PARAM_DATASETS
static String	HTTP_PARAM_PATHWAY
static String	HTTP_PARAM_SCIENTIST
static int	ONLY_CHANGED

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Method Summary

static void	batchUpload(URL url, ByteArray datasets, String passwd)
static boolean	checkDataset(Dataset d, StringBuffer sb)
static int	currentTimeFromServerResponseSec(ByteArray ba)
static void	datasetsToServer(int mode, Dataset... dd0)
static void	delDatasetIDsOnSrv(int mode, String... ids)
static void	deleteDatasetsOnServer(Dataset[] dd, int mode)
static File	logResponseSrv(URL url)
static File	logSentToSrv(URL url)
Object	run(String id, Object arg)
static void	setPasswd(String s)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DONOT_ASK

public static final int DONOT_ASK

See Also:

Constant Field Values

BACKGROUND

public static final int BACKGROUND

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Constant Field Values

ONLY_CHANGED

public static final int ONLY_CHANGED

See Also:

Constant Field Values

HTTP_PARAM_DATASETS

public static final String HTTP_PARAM_DATASETS

See Also:

Constant Field Values

HTTP_PARAM_SCIENTIST

public static final String HTTP_PARAM_SCIENTIST

See Also:

Constant Field Values

HTTP_PARAM_PATHWAY

public static final String HTTP_PARAM_PATHWAY

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Constant Field Values

Method Detail

setPasswd

public static void setPasswd(String s)

batchUpload

public static void batchUpload(URL url,
                               ByteArray datasets,
                               String passwd)

currentTimeFromServerResponseSec

public static int currentTimeFromServerResponseSec(ByteArray ba)

logSentToSrv

public static File logSentToSrv(URL url)

logResponseSrv

public static File logResponseSrv(URL url)

run

public Object run(String id,
                  Object arg)

Specified by:

run in interface ChRunnable

deleteDatasetsOnServer

public static void deleteDatasetsOnServer(Dataset[] dd,
                                          int mode)

delDatasetIDsOnSrv

public static void delDatasetIDsOnSrv(int mode,
                                      String... ids)

checkDataset

public static boolean checkDataset(Dataset d,
                                   StringBuffer sb)

datasetsToServer

public static void datasetsToServer(int mode,
                                    Dataset... dd0)