source: trunk/uk/ac/scri/batchimporter/README.txt @ 238

Last change on this file since 238 was 238, checked in by mbayer, 15 years ago

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1GENERAL INFO
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3The BatchDataImporter plugin imports a batch of individual data files into an experiment chosen by the user. It is set up to be invoked from the detail view of a single Experiment where an import tab lets the user select a zip file that contains all the data files. On invocation it proceeds to create a new subdirectory in the directory where the file is currently located -- this subdirectory is named after the zip file minus the extension plus a timestamp in the format ddMMyy_hhmmss. The zip file is unzipped into this directory. For each file in the directory, a single RawBioAssay object is then created, and once all the data files have been processed in this way, the RawBioAssay objects just created are attached to the Experiment where the import is run from.
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5It is assumed that all the data files are of the same data type and format -- the import will fail otherwise. It is also assumed that a suitable import configuration for the data exists already.
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7In the case of non-Affy data, the raw data will be added to the RawBioAssay objects by physically importing it into the database. For Affy data, the cel file will be attached to the RawBioAssay objects but no actual data is imported into the database -- the raw data stays in the cel files. Affy data imports also assume that a new ArrayDesign needs to be created and this is done with the cdf file which needs to be included in the zip file with the data files. The Arraydesign object is then set on each RawBioAssay created.
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9============================================================
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11INSTALLATION
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13- Place batchimporter.jar into the www/plugins directory of your BASE2 installation.
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15- Create a new plugin definition:
161. In the BASE web client, go to Administrate -> Plugins -> Definitions.
172. Click New.
183. In the dialog that opens, enter "sbrn.base.BatchDataImporter" under Class.
194. Under Path, enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/batchimporter.jar
205. Click Save.
21The new plugin appears under the name "Batch Data Importer" in the plugins list and is now ready to use.
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23Bear in mind that if you install plugins as an administrator you will have still have to share them to the appropriate users by manually setting the permissions on the item.
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25============================================================
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27USE
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291. Zip up into a single file the data files that make up your experiment. If your data files are Affy format (cel files) the zip file also needs to include the cdf file for your chip. Upload this file to your account on BASE (go to View -> Files -> Upload File).
302. Create a new Experiment in the BASE web client. Make sure it is of the same data type as the data in the files you want to import.
313. Open the detail view of the newly created experiment and click on the import tab.
324. In the dialog that opens, leave the settings for Plugin and File format on auto-detect and click Next.
335. On the next screen, select the zip file that contains your data files and click Next.
346. The next screen reviews what the plugin knows about your setup so far, and does not need to be modified -- click Next.
357. The next screen gives you an option for entering a job name and description but you can also go with the defaults -- click Finish. You will then be shown the progress of the batch import in the dialog, with the page refreshing itself regularly.
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37For long imports you can close the dialog, and even log out of BASE and shut down your browser or even your computer. The Job information is stored persistently on the server and your job will execute independently of this. You can check its status by going back to the View -> Jobs menu item in the web client.
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39When the import has finished, you can check the detail view of your experiment -- the raw bioassays that have been created should be listed at the bottom of the page.
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41============================================================
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43AUTHOR
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45Micha Bayer - Plant Bioinformatics Group, Scottish Crop Research Institute
46email: sbrn@scri.ac.uk
47web: http://www.scri.ac.uk and http://www.scri.sari.ac.uk/MichaBayer.htm
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