Kurator-Web User Documentation
- 1 Getting Started
- 2 Account Settings
- 3 Workflows
- 4 Workflow Runs
- 5 User Uploads
- 6 Admin/User Management
- 7 Workflow Builder
Running workflows using Kurator Web requires a user to login. Users that already have a registered account can login on the main page by clicking the "Login" navbar button or by following the link: http://kurator.acis.ufl.edu/kurator-web/login
The second image pictured to the right is the login form the user will be presented with after following the link above or clicking the "Login" nav bar entry to the upper right corner.
Register to obtain an account on a Kurator-web application deployment. An administrator will need to activate your account, usually within 24 hours. Once registered and activated, you'll receive an email notification at the address you used to sign up with further instructions and you can log in and use the web application.
If you've forgotten the password you used to sign up, use the "Forgot Password" link on the login form pictured to the right to request a password reset. Enter your username and the email you used to sign up and submit receive a temporary password via email that you can use to login.
Later you can change the temporary password to one of your choosing on the user settings page described below
You can report issues with Kurator-web or Kurator-web workflows on github.
You can report issues or ask for help on the Kurator project public mailing list.
Logged in users can update their password via the user settings page accessible via the dropdown menu for the currently logged in user to the right of the nav bar.
Select settings from the menu pictured above and enter your current password and a new password you wish to change to on the settings page. Click "Update" to change the password and use the new password next time you login
Available Canned Workflows
Once logged in, you can navigate from the home page to the workflows page to see a list of available pre-built workflows. Each workflow has a name and a brief description and the i Info icon links out to a page that documents the workflow.
Click the Run Workflow button to run a workflow. This will display a form where you can provide the workflow with a data set to run on and any other parameters that it needs.
The documentation for the set of pre-built workflows which is linked to from the workflows page can also be accessed directly on the kurator GitHub wiki pages here: https://github.com/kurator-org/kurator-validation/wiki
Picking a Workflow
The current set of workflows can be divided in two ways, by what you want to accomplish, and by what form of input you have.
The workflows, for the most part, start with "CSV" or "Darwin Core Archive". CSV workflows run on CSV files, usually in flat DarwinCore form, that you upload to the Kurator-Web environment. Darwin Core Archive workflows run on a Darwin Core Archive downloaded from a URI that you provide (usually a Darwin Core Archive produced by an IPT instance or by Symbiota).
Some of the workflows (in particular some of the CSV workflows) are intended for preparing data for publishing to aggregators (in an IPT instance). Others of the workflows are intended to check the quality of your data and report on compliance or non-compliance with standard vocabularies or tests. Some of the data quality workflows (e.g. CSV/Darwin Core Archive Geography Assessor) simply report on how much of your data conforms with expectations, others (e.g. CSV/ Darwin Core Archive Geography Cleaner) propose amendments that could be made to your data to improve its quality for particular uses.
The "Validator" workflows (e.g. CSV File Georeference Validator or Darwin Core Archive Date Validator) provide reports on data quality in terms of a developing TDWG framework for reporting on data fitness for use. Their output includes an .xls spreadsheet containing the input data, the input data with amendments applied, and sets of data quality Measures, Validations, and Amendments on those data.
The "Counter", "Assessor", and "Cleaner" workflows provide reports on distinct values of terms (e.g. higher geography names) found in the input data. The Assessor and Cleaner workflows compare those distinct values to controlled vocabularies.
Some of the workflows, in particular the CSV File Darwinizer and the CSV File Aggregator, are intended for preparing data for publication to aggregators, but in general, the workflows could be run at any point in the data life cycle.
Detailed descriptions of each of the canned workflows can be found at: https://github.com/kurator-org/kurator-validation/wiki and the "i" button in front of each workflow links to the documentation for that workflow there on the kurator wiki on github.
Running a Workflow
When you click the Run link on the list of workflows you will be taken to a dialog where you can enter the information needed by that workflow. This may be the URI at which a Darwin Core archive can be found, or may be an option to upload a data file. Some workflows may take other configuration parameters as well.
When you have provided the information the workflow needs, click the Run Workflow button. This will start the workflow. After some period of time, your browser will redirect to the home page where you will now see the workflow you just launched in the list of running workflows. You can also click on Home to go to the home page to see the running workflows, or you can navigate elsewhere, your workflow will be running in the background on the server.
Depending on the nature of the workflow and the size of your dataset, the workflow may take some time to complete.
Below the list of available workflows on the home page is a list of your workflow runs.
Workflows may be running, may have completed successfully, or may have failed with an error.
For a workflow which has completed successfully, click the Document icon for a popup dialog from which you can download some or all of the result files produced by the workflow.
The workflow result artifacts dialog displays some metadata about the run (time started/ended, name of the workflow) and allows you to either download all files as an archive or to browse and download only specific artifacts.
Click on the Download Archive link to obtain a zip archive containing all of the workflow results, or click on the links to download individual files. Click on the "Download YAML Config" link to obtain the workflow definition file (which you can edit and run locally with an installation of Kurator-validation).
Each artifact listed has a name and a short description as well as a link to Download the file. The individual artifacts listed on this dialog are separated into two tiers, result files and other files. Clicking the tiers will toggle between the two of them.
The result files, which are displayed by default, are files produced as the outputs of the workflow and the other files tier includes the intermediate files used by the workflow when producing those results.
In addition to uploading files at workflow run time, Kurator Web supports staging of input files through the use of the user uploads feature. The this feature can be accessed by clicking the "Upload" item from the sidebar on the Workflows page.
Upload a File
Use the form on this page to upload a new file to your user account by first clicking the "Browse" button to select a file from your local machine. Once you have selected a file, click the green "Upload File" button to upload the file.
All files previously uploaded via this feature are displayed in the list on this page and can be selected from a dropdown as input when running workflows. Users can download a copy of the uploaded file by clicking the "Download" button next to the entry in the list or remove the files from their account by clicking the "Remove" button.
The table on the user management page lists all current users by username along with profile data associated with their account such as their full name, email address, affiliation, date the account was created and date the user was last active.
Activation and Role Assignment
The "Role and "Active" columns contain buttons for changing the user's role and a toggle button for switching between active and inactive. Clicking the user activation toggle button will activate the user and send them an email notification containing a link to login.
Add to Group
To the very left of each entry of the users table is a drag and drop handle icon that enables an admin to drag a user and drop on one of the groups listed in the treeview. When the admin drags a row to a group that user is assigned to that group. Selecting the group in the treeview to filter will show the users currently assigned to that group.
The table view on the admin page lists all of the current users by default. Also supported is filtering of users by activation status (Active, Inactive), role (ADMIN, USER) and user groups.
Clicking one of the nodes in the tree view will activate filtering. For example, to see only the users that are currently inactive click the "Inactive" label in the hierarchical tree view and the users table will update to show only the inactive users.
NOTE: this feature is currently in development
The workflow builder will enable users of the Web App to construct their own custom workflows through the use of a graphical tool. Using the builder a user would be able to drag and drop from a set of "actors" onto a canvas and draw connections between their inputs and outputs to compose a workflow. Once the user has assembled the actors, the workflow can be saved and accessed along with the set of canned workflows or exported in the form of a yaml config file for use with the command-line implementation of Kurator.