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ucsd-ccbb / qiimp

Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints
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QIIMP

(Pronounced "chimp"!)

Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints

Note that this repository contains the full code necessary for QIIMP to function, which includes code that ccbb-ucsd did not write (contained in the "third-party" folder).

Requirements

Installation

  1. Create and source a conda environment for QIIMP

    conda create -n qiimp python=3 openpyxl tornado xlsxwriter PyYAML pandas git
source activate qiimp

  2. Install QIIMP from github.com

    pip install --upgrade git+git://github.com/ucsd-ccbb/qiimp.git

  3. Find the config.txt file

    • Find the location of your conda install's site-packages folder by running

      pip show qiimp

    • Look for the line in the output that starts with Location: and find the path it lists (for example, /Users/Me/Applications/miniconda3/envs/qiimp/lib/python3.6/site-packages). This will be referred to below as sitepackagespath.

    • The config.txt file will be at sitepackagespath/qiimp/settings/config.txt

  4. Edit the [DEPLOYED] section of the config.txt file to set the appropriate values for your installation

    • Set the main_url variable to the public hostname of the machine/instance (e.g., ec2-34-215-148-70.us-west-2.compute.amazonaws.com).
    • If you want the port used to be something other than the default (e.g., 8183),
      • If you want the user to access this port directly, add it to the main_url (e.g., ec2-34-215-148-70.us-west-2.compute.amazonaws.com:8183)
      • Regardless of whether you want the user to access the port directly or be redirected to it internally, set the listen_port variable to the desired port.
      • Be sure that public access to this port is enabled on your machine!

  5. Start the QIIMP server

    start_qiimp_server --deployed

    • If you are running QIIMP on your local host instead of on a publicly available host, run it without the --deployed switch. It will then use the settings in the [LOCAL] section of the config instead of the [DEPLOYED] section.

    • If you see UserWarnings like the examples below:

      /home/ec2-user/miniconda3/envs/qiimp/lib/python3.6/site-packages/qiimp/metadata_package_schema_builder.py:163: UserWarning: No filename specified for sample type 'sponge' in environment 'non-vertebrate'.
warnings.warn("No filename specified for {0}.".format(context_description))
      • ... this indicates that not all environments and/or sample types have schema files defined for them in the settings/environments.yaml file for the installation.
      • This is sometimes acceptable, specifically in cases in which the sample type or environment truly has no unique field definitions associated with it, such as the "other" sample type in the "base" environment.
      • However, it is more often an indication that not all expected configuration information for environment and sample type packages has been properly placed in the settings/packages directory.
      • Thus, each such warning should be checked to ensure that it is expected.

    • When the QIIMP server is accessible, a server ready message will be printed to STDOUT

  6. Access QIIMP through a browser at the URL of your instance + the port number, e.g. http://ec2-18-236-71-136.us-west-2.compute.amazonaws.com:8181/

  7. If desired (when done using it), stop the QIIMP server by typing Ctrl+c on the server command line