https://wiki.bgbm.org/rebind_documentation/index.php?title=Special:NewPages&feed=atom&hideredirs=1&limit=50&offset=&namespace=0&username=&tagfilter=reBiND Documentation - New pages [en]2024-03-28T14:22:10ZFrom reBiND DocumentationMediaWiki 1.28.2https://wiki.bgbm.org/rebind_documentation/index.php/Creating_new_rebind_projectCreating new rebind project2015-01-14T14:58:52Z<p>AgnesKirchhoff: Created page with "= Uploading data to the reBiND portal = The previous data preparation step ensures the data is in ABCD format. Once the data has been prepared an XML file (conforming to the..."</p>
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<div>= Uploading data to the reBiND portal =<br />
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The previous data preparation step ensures the data is in ABCD format. Once the data has been prepared an XML file (conforming to the ABCD schema) can be exported from the Biocase Provider software. It should be noted that ABCD files can be prepared using any software. There are other types of software that use a metadata-based approach to extract data from CSV and relational databases and enable transformation into XML format, for example [http://community.pentaho.com/projects/data-integration/ Pentaho Kettle]. Furthermore the reBiND software has been designed to work with any XML file, not just ABCD, providing there is an associated XML schema available.<br />
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In addition to at least one XML data file the project should also contain a metadata file. Additional files can also uploaded, such as the original data file (from which the XML data file was generated), images, other multimedia objects or PDF files. For the sake of clarity image and multimedia objects should be placed into special sub-collections within the data project collection, like ''images/''. A data project could also contain more than one XML data document, however only one metadata file. <br />
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The figures below show a step-by-step guide to the process of uploading data to the reBiND portal. Once these steps are completed the user can continue to the the [[Validation_and_Corrections|validation and automated correction]] steps.<br />
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== Logging onto reBiND ==<br />
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The homepage of the reBiND portal has links to the published data-sets and to further information on the project web-site. In figure 1 below the left-hand margin shows the login form. Login is required in order to submit data to the reBiND system. For information on how to set up user accounts for login see this page.<br />
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[[File:Rebind_portal_logon.PNG|border]]<br />
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== Creating and viewing unpublished projects ==<br />
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After logging into the reBiND portal the user is presented with a left-hand side panel which lists the 'Unpublished' and 'Published' projects. An icon 'Create Project' which is used to create a new unpublished project to which XML files and other data can be imported. In the screenshot below the unpublished project 'ClemensHBG' has been selected and the summary of the files associated with this project can be seen in the right-hand panel. Below this are icons to upload further data.<br />
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[[File:ReBIND_portal_project_overview.PNG|border]]<br />
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To create an entirely new project the user should click 'Create Project' in the left-hand side panel and in the pop up form supply a unique name for the new project. The project should have a clear descriptive name, but must not contain special characters, digits, spaces or dashes. In the figure below we have used 'Puffinus' to identify the project - data on the ''Puffinus Creatopus'' - the pink-footed Shearwater.<br />
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[[File:ReBIND_portal_project_create_project.PNG|border]]</div>AgnesKirchhoffhttps://wiki.bgbm.org/rebind_documentation/index.php/Exporting_XML_files_from_BPSExporting XML files from BPS2015-01-14T12:41:43Z<p>AgnesKirchhoff: </p>
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<div>===Uploading large data files from BPS to reBiND===<br />
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After the mapping of the data to the ABCD elements (http://wiki.bgbm.org/bps/index.php/ABCD2Mapping) the data needs to be either exported as XML files from BPS or uploaded directly to reBiND (see the following sections for details).<br />
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When the XML data files are large (> 1000 records or abcd:Units) it is currently necessary to export multiple files from the BPS and run an xquery script to join them into a single ABCD file. <br />
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====The following steps describe how to do this:====<br />
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1. export the data from BPS using ABCD2 search. After the mapping is complete within the BPS then select the "QueryForms" on the top menu as shown in the screenshot below:<br />
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[[File:BPS_ABCD_mapping.PNG|border]]<br />
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After selecting "QueryForms" click on "ABCD2 search" from the list below the textfield, see the screenshot below. After selecting the "ABCD2 search" the field is automatically filled with the Query tags for the ABCD search. Please remove the <filter> element from the text as shown in the screenshot. Then set the limit to 999 in the following tag: <responseFormat start='0' limit='998'> (the default limit is set to 10). Click the "submit" button. An XML file is displayed in the browser.<br />
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[[File:BPS_ABCD_query.PNG|border]]<br />
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2. Save the file as {dataset name}_1.xml. <br />
For the next file click on the "back" button on your browser to return to the query form and modify the tag to <responseFormat start='999' limit='998'> . This retrieves the next block of data records. Press the "submit" button again and then save the XML file as {dataset name}_2.xml ...<br />
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3. Continue to export XML files as in step 2, in each case modifying the start (1998, 2997, 3996 and so on). When saving the file naming it with a sequential suffix (_1, _2, _3 ...) until their are no further records. In each step you retrieve 999 records.<br />
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4. Create a new project in rebind (see also the instructions [[Data_upload_to_rebind_framework#Creating_and_viewing_unpublished_projects|here]]) and name it with a unique name e.g. HBGnummeriert (dataset name) and then create a collection called ‘abcd’ by pressing 'New collection'. Click on 'abcd' to navigate into the new collection. Store all of the individual ABCD files in the 'abcd' collection by pressing 'Upload File' and selecting each file - one at a time until all files are uploaded: e.g. HBGnummeriert _1.XML, HBGnummeriert_2.XML etc. <br />
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5. Open another browser tab, enter the URL below. <br />
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http://data-rebind.bgbm.org/rebind/join_abcd.xquery?coll=HBGnummeriert<br />
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''Replace the final part of the URL with the name of your collection e.g. if your collection is called HBGnummeriert then the URL should end with coll=HBGnummeriert.''<br />
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After pressing 'enter' the browser should show a white screen, once the script has run.<br />
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6. Going back to the reBiND browser, click on your new project in the left hand panel and you see only one XML file (all of the individual XML files are now combined into one single), as in the screenshot below.<br />
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[[File:ReBIND_portal_project_overview.PNG|border]]</div>AgnesKirchhoff