The Computational Materials Repository

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58 Computational Materials RepositoryFigure 3.1: Data flow diagram of CMR. Blue: user interface components; purple arerepository components; db-files are denoted with red font; black: diverse. Light bluecolor signifies third-party components.CMR Python package that is accessible for other components as well. Db-filesgenerally store the data of a single calculation and are used within CMR as acontainer to transfer or store data. Since db-files are identified by their contentand not by their file names and directory locations they are collected in a singledirectory, the db-file repository (3.3.2.1). The data in the db-file repositoryhas normally two purposes: it is kept for long-term storage as a backup and itshould be accessible for further analysis. Since it is not very efficient to querya db-file repository, the files are uploaded to the (CMR) database (3.3.2.3).To allow queries to be executed efficiently, the data is rearranged in a bettersearchable way during the upload. As a consequence of this scheme the data isstored twice in the system: in the db-file repository as long-term storage and inthe database for fast access. The figure shows a local repository that is notconnected to a database as well. This is to show that CMR can also performbasic queries on the db-files as if they were located in a database - although theyare a bit slower.The user interfaces hide the complexity behind intuitive commands and functions.There are four user interfaces with different purposes: the command line interface(CLI) (3.3.1.1) is executed in a command shell, is the most basic interfaceand allows to create and administrate db-files locally as already described insection 3.3.1.1. The python user interface (PUI) (3.3.1.2) is the most powerfuland provides scriptable access to the local/third-party CMR databases, is able toretrieve data from the local/third-party PHP/HTML interfaces (3.3.1.3) as wellas providing basic scriptable access to a local db-file repository. The PUI can
3.3 System Components and Processes 59also use agent templates 3.3.3.1 like the GroupingAgent (2.2), but cannot writeto the database directly due to access restrictions. The most convenient accessto the data is to visit the PHP/HTML interface (PHPUI) (2.3,3.3.1.3) witha web browser. The user creates a query by selecting criteria. The PHPUIcan be programmed to perform more complex analysis [19],3.3.1.3. Because thePHPUI is not scriptable itself it provides a PUI script that executes the samequery (see Fig. 2.18) if possible. That script includes code that can be used forfurther analysis or to modify or download the complete data. The last interfaceis the HTML/JavaScript silo user interface (3.3.1.4) and is mentioned forcompleteness because it currently works only with the previous version of theCMR database. It is a workbench to analyze data in a web browser that allowsto create queries visually. It is capable of working offline with the data which isnot possible with the PHPUI. Agents (3.3.3.1) are processes that run in thebackground and perform tasks that normally take a little longer than regularqueries. For example some analysis could be performed on all data containedin the database. Currently the agents are used to prepare data needed by thePHPUI.3.3.1 User InterfacesThe user interfaces enable the user to work with data in a convenient way andhide the complexity of communicating with a repository behind well definedinterfaces. CMR features four user interfaces that access the data in differentways.3.3.1.1 Command line interface (CLI)Purpose: This interface enables to work with db-files (3.3.3.2) in a commandshell. It provides functionality to batch process operations like converting files todb-files, updating content, submitting data to the db-file repository and makesit thereby unnecessary to write programming code for these tasks.Usage: The command cmr enables to batch process files in a command shell.There are two ways to work with this tool. The first one is to use it directly withdb-files to create, modify, touch, validate, dump or submit them to the db-filerepository. The second mode is to use it to work with a dataset of original outputfiles (e.g. *.traj) that are going to be added to the CMR database. The first stepis to select/schedule the files during which they are converted (transparently) todb-files. In the next steps they can be attributed with keywords/fields/scriptindividually or as a group. When the files are ready they can be submitted. Ifat any later point more keywords are added they can simply be resubmitted.Usage example(s): Scheduling all *.traj to be uploaded to the database, addkeyword “adsorption” and send it to the db-file repository:$> cmr −a ∗ . t r a j$> cmr −m ∗ . t r a j
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