Swagger generated server

Overview

This server was generated by the swagger-codegen project. By using the OpenAPI-Spec from a remote server, you can easily generate a server stub. This is an example of building a swagger-enabled Flask server.

This example uses the Connexion library on top of Flask.

Requirements

Python 3.5.2+

Usage

To run the server, please execute the following from the root directory:

pip3 install -r requirements.txt
export PYTHONPATH=./
python swagger_server/server.py

and open your browser to here:

http://localhost:8090/v2/ui/

Your Swagger definition lives here:

http://localhost:8090/v2/swagger.json

Running with Docker

To run the server on a Docker container, please execute the following from the root directory:

# building the image
docker build -t swagger_server .

# starting up a container
docker run -p 8090:8090 swagger_server

Adding new Templates

Templates are a predefine structure for the SDRF, with fields that the user or community have agreed that needs to be provided. For example, the default-ms.yaml is the template for mass spectrometry data including properties to encode post-translational modifications, tolerances, instruments.

The structure of the template is like:

template:
  name: Default Mass Spectrometry Template
  type: Data
  description: The default sample metadata template for any type of omics submission
  columns:
    assay name:
      type: None
      searchable: false
    fraction identifier:
      type: comment
      ontology_accession: "MS:1000858"
      ontology: MS
      ols_uri: http://purl.obolibrary.org/obo/MS_1000858
      searchable: false
    label:
      type: comment
      ontology_accession: "PRIDE:0000514"
      ontology: PRIDE
      ols_uri: http://www.ebi.ac.uk/pride/PRIDE_0000514
      searchable: true
    modification parameters:
      type: comment
      ontology_accession: "MS:1001055"
      ontology: MS
      ols_uri: http://purl.obolibrary.org/obo/MS_1001055
      searchable: true
      otherSearchTerm:
        - ontology_accession: "UNIMOD:0"
          ontology: UNIMOD
          name: "unimod root node"
          ols_uri: http://purl.obolibrary.org/obo/UNIMOD_0

It includes the following fields:

• name: Name of the template
• type: Type of the template (Data or Sample), templates related with sample organize the way the sample is capture and annotated, while templates related with Data capture the way data is annotated.
• description: Additional description of the template.
• columns: A list of columns annotated as ontology terms.

If the user/community wants to add a new template, you should do a PR in the repository and the core contributors and curators of the API will review the PR and merged into the master branch. The new changes will be automatically deploy.

Adding additional terms

In many cases new terms are added to the SDRF that they are not included in any Template. This can be considered "additional" to annotate the Sample or the Data. If the community/user wants to add terms into the application, it should perform a Pull request in the application modifying the following file other_terms.yaml

The structure of the other_terms.yaml file is:

terms:
  bait:
    type: characteristics
    ontology_accession: "OBI:0100026"
    ontology: MI
    ols_uri: http://purl.obolibrary.org/obo/MI_0496
    searchable: false
  concentration of:
    type: characteristics
    ontology_accession: "PATO:0000033"
    ontology: PATO
    ols_uri: http://purl.obolibrary.org/obo/PATO_0000033
    searchable: false
  protein_coding_gene:
    type: characteristics
    ontology_accession: "SO:0001217"
    ontology: SO
    ols_uri:  http://purl.obolibrary.org/obo/SO_0001217
    searchable: false
  precursor mass tolerance:
    type: comment
    ontology_accession: "PRIDE:0000575"
    ontology: PRIDE
    ols_uri:  http://purl.obolibrary.org/obo/PRIDE_0000575
    searchable: false