Org Mode Reflex Bibliography Template


9.1.3 Capture templates

You can use templates for different types of capture items, and for different target locations. The easiest way to create such templates is through the customize interface.

Customize the variable .

Before we give the formal description of template definitions, let’s look at an example. Say you would like to use one template to create general TODO entries, and you want to put these entries under the heading ‘’ in your file . Also, a date tree in the file should capture journal entries. A possible configuration would look like:

(setq org-capture-templates '(("t" "Todo" entry (file+headline "~/org/gtd.org" "Tasks") "* TODO %?\n %i\n %a") ("j" "Journal" entry (file+olp+datetree "~/org/journal.org") "* %?\nEntered on %U\n %i\n %a")))

If you then press , Org will prepare the template for you like this:

* TODO [[file:]]

During expansion of the template, has been replaced by a link to the location from where you called the capture command. This can be extremely useful for deriving tasks from emails, for example. You fill in the task definition, press and Org returns you to the same place where you started the capture process.

To define special keys to capture to a particular template without going through the interactive template selection, you can create your key binding like this:

(define-key global-map "\C-cx" (lambda () (interactive) (org-capture nil "x")))

What is Reflex?

Reflex is an environment that provides an easy and flexible way to reduce VLT/VLTI science data using the ESO pipelines. Its top-level functionalities are:
  • Reflex allows to graphically specify the sequence in which the data reduction steps are executed, including conditional stops, loops and conditional branches.
  • Reflex makes it easy to inspect the intermediate and final data products and to repeat selected processing steps to optimize the data reduction.
  • The data organization necessary to reduce the data is built into the system and is fully automatic.
  • Advanced users can plug-in their own modules and steps into the data reduction sequence.
  • Reflex supports the development of data reduction workflows based on the ESO Common Pipeline Library.

Reflex is based on the concept of a scientific workflow, whereby the data reduction cascade is rendered graphically and data seamlessly flow from one processing step to the next. It is distributed with a number of complete test datasets so that users can immediately start experimenting and familiarize themselves with the system.

For further information, please, refer to the latest Reflex User Manual.

Reflex is based on the open source workflow engine Kepler.

If you make use of Reflex or Reflex workflows in a scientific publication, please consider citing Reflex. You may reference the following paper: Automated Data Reduction Workflows for Astronomy: The ESO Reflex Environment, 2013, Freudling, W., et al., Astron.Astrophys., 559, A96 (Bibtex entry)

Reflex Latest Public Version

The latest public version of Reflex is 2.8

Officially Supported Pipelines

Reflex can be used with any CPL-based pipeline. Some pipelines provide Reflex-based workflows in their public releases. Please refer to this table for information about supported modes, tutorials, example data sets and user manuals.

Reflex System Requirements

Reflex is written in Java and is known to work in the following systems:
  • Fedora 18 64 bits
  • Fedora 20 64 bits
  • Fedora 22 64 bits
  • Scientific Linux 6.4 64bits
  • Ubuntu 14.04 64 bits
  • OS X 10.8
  • OS X 10.9
Any recent Linux distribution should be compatible with Reflex out of the box.

Additionally, some Reflex-based workflows might have extra software requirements (most notably python modules). Check Reflex-based workflows release notes for more information.

Installing and running Reflex

Prerequisites

Reflex 2.8 requires a Java Runtime Environment (JRE) version 7, it is recommended to use at least update 45.
NOTE: On OS X you need to install the JDK instead, you can download it from here
Workflows may have other requirements, please refer to the workflow tutorial and to the pipeline user manual. There are two installation option: the automatic and the manual one.

Package managers for Fedora and OS X (recommended)

For Fedora 20/21/22 64 bits, it is strongly recommended to install it with our rpm repository. This repository includes both Reflex and the pipelines. Refer to the instructions provided here.

For Apple Mac OS X 10.9 or newer, it is strongly recommended to install it with MacPorts. This repository includes both Reflex and the pipelines. Refer to the instructions provided here.

Automatic Installation with installation script

A script is provided that takes care of all the required steps to install and run Reflex:
  • It downloads and installs a pipeline kit, that contains the workflows associated to the pipeline.
  • It downloads and installs some test data.
  • It donwloads and installs Reflex.
  • It configures Reflex to point to the installed pipeline.
If you want to use this method, check the software requirements in the release information of this table, download the script and follow the instructions.

Manual method

If you don't want to use the automatic method (e.g. because you want to use a specific version of the pipeline), you can manually download and install Reflex following these steps:
  • Install the pipeline kit you are interested in. Only the recipes present in the output of esorex --recipes will be available to Reflex.
  • Download the latest stable version for Linux or OS X.
  • Uncompress the package using gzip and tar.
  • Execute the reflex command in the bin directory under the distribution directory.

Reflex User Manual

Current Issue: 3.8

The Reflex User Manual is available for download in PDF format.

Reflex Workflow Development Guide

Current Issue: 1.0

The Reflex Workflow Development Guide is available for download in PDF format.

Bug Reports

If you experience an unexpected behavior of Reflex, please, first refer to the troubleshooting section in the User Manual. For any other issues or requests, please, send a report to the ESO User Support Department, describing:
  • the Reflex release you are using
  • the pipeline release you are using
  • the version of your OS
  • the exact sequence of actions you performed before the bug occurred
  • what were precisely the symptoms and the possible error message(s)
  • whether the bug is repeatable

 

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