Difference between revisions of "Data upload to rebind framework"

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(→‎Importing XML and other data files from file system)
 
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= Uploading data to the reBiND portal =
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== Importing XML and other data files from file system ==
  
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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. The validation and correction tools can be configured to work with any XML file, providing there is an associated XML schema available.
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After creating the new project the project name (in this example 'Puffinus') should appear in the list of un-published projects in the left-hand side panel.
  
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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.
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Clicking on the project name takes you to the list of files associated with the project. In this case there are no files yet associated with the project as it is a new empty project.  
  
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== Logging onto reBiND ==
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'Upload from BioCASE' enables the user to connect to a specific ABCD file stored in the Biocase Provider software, if the URL is known. However this is currently restricted to files below a certain size (a maximum of 1000 records / abcd:Units).
  
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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.
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The 'Upload File' can be used to upload any file type from the file system. Several files of various file types (e.g. XML, PDF and images) and folders can be added to a project. Other XML files, which don't conform to the ABCD Schema can be uploaded. PDF files containing associated publications and images can also be uploaded with this button. This option is also used for ABCD XML files larger than 1000 units [[Exporting_XML_files_from_BPS|(see that section for details)]].
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[[File:Rebind_portal_logon.PNG|border]]
 
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== Creating and viewing unpublished projects ==
 
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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 slected 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.
 
  
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[[File:ReBIND_portal_project_new_project.PNG|border]]
  
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[[File:ReBIND_portal_project_overview.PNG|border]]
 
  
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For ABCD files smaller than 1000 ABCD units the 'Upload from BioCASE' button directly retrieves the XML data from BioCASE and stores it in reBiND.
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Clicking on the 'Upload from BioCASE' button opens a form shown in the screenshot below.
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You need to enter a URL of your dataset. Please open the BPS (home: http://ww3.bgbm.org/biocase/index.cgi), click on your dataset in the list. A new screen opens, which shows a URL under the headline 'access point'. Copy this URL and paste it into the URL field shown in the screenshot below. Under 'Store as:' give the file a name and enter the extension ".xml".
  
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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. In the figure below we have used 'Puffinus' to identify the project - data on the ''Puffinus Creatopus'' - the pink-footed Shearwater.
 
  
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[[File:Upload_data_biocase.PNG|border]]
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[[File:ReBIND_portal_project_create_project.PNG|border]]
 
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== Importing XML and other data files from file system ==
 
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After creating the new project the project name (in this example 'Puffinus') should appear in the list of un-published projects in the left-hand side panel.
 
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Clicking on the project name takes you to the list of files associated with the project. In this case there are no files yet associated with the project as it is a new empty project. The 'Upload File' can be used to upload any file type from the file system. Several files of various file types (e.g. XML, PDF and images) and folders can be added to a project. 'Connect to BioCASE' enables the user to connect to a spacfic ABCD file stored in a Biocase if the URL is know. However this is currently restricted to files below a certain size (a maximum of 500 records / abcd:Units).
 
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[[File:ReBIND_portal_project_new_project.PNG|border]]
 
  
  

Latest revision as of 16:25, 14 January 2015

Importing XML and other data files from file system

After creating the new project the project name (in this example 'Puffinus') should appear in the list of un-published projects in the left-hand side panel.

Clicking on the project name takes you to the list of files associated with the project. In this case there are no files yet associated with the project as it is a new empty project.

'Upload from BioCASE' enables the user to connect to a specific ABCD file stored in the Biocase Provider software, if the URL is known. However this is currently restricted to files below a certain size (a maximum of 1000 records / abcd:Units).

The 'Upload File' can be used to upload any file type from the file system. Several files of various file types (e.g. XML, PDF and images) and folders can be added to a project. Other XML files, which don't conform to the ABCD Schema can be uploaded. PDF files containing associated publications and images can also be uploaded with this button. This option is also used for ABCD XML files larger than 1000 units (see that section for details).

ReBIND portal project new project.PNG


For ABCD files smaller than 1000 ABCD units the 'Upload from BioCASE' button directly retrieves the XML data from BioCASE and stores it in reBiND. Clicking on the 'Upload from BioCASE' button opens a form shown in the screenshot below. You need to enter a URL of your dataset. Please open the BPS (home: http://ww3.bgbm.org/biocase/index.cgi), click on your dataset in the list. A new screen opens, which shows a URL under the headline 'access point'. Copy this URL and paste it into the URL field shown in the screenshot below. Under 'Store as:' give the file a name and enter the extension ".xml".


Upload data biocase.PNG


Depending on the file type different options are offered for the current file. All file types have the option to view/download the file in its native form. Text based file types have the option to edit the file online. XML files can be validated against their schema (if it is registered with the reBiND Software) and can be corrected or modified by running automated corrections on them. Below the details of the data file 'reBiND_Puffinus.xml' are shown and the list of available actions. 'View XML' and 'View Data' link to an XML view or a tabular view of the data respectively. In the next section we'll describe remaining actions in turn, going into detail of how to run the validation and correction actions.


ReBIND portal project upload file actions.PNG

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