bwalsh · November 21, 2016 18:21 · bwalsh · Nov 20, 2016
diff --git a/swagger.yml b/swagger.yml
 info:
  title: YA-DMS  API description
  description: |-
    ### "Yet Another Data Management Service"
    ##### Key endpoints

    ![image](https://cloud.githubusercontent.com/assets/47808/20463919/517044ca-aef2-11e6-8d8a-3b1a1f24a1f4.png)



  version: '0.1'
 paths:
  /files:
    get:
      summary: Searches resources and associated meta data.
      responses:
        '200':
          description: Document fetched successfully
          schema:
            $ref: '#/definitions/SearchResponse'
      parameters:
        - $ref: '#/parameters/filter'
        - $ref: '#/parameters/sort'
        - $ref: '#/parameters/fields'
        - $ref: '#/parameters/size'
        - $ref: '#/parameters/from'
        - $ref: "#/parameters/Authorization"

      tags:
        - Researcher
        - Informatician
        - Biospecimen
        - Search

      description: |+

        See this [overview from GDC](https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#files-endpoint).



    post:
      summary: Creates a File document, updates search index
      description: |-
        It is necessary to describe files `independently of project submission`.  For example, a `reference genome` resource is used across all projects.   This entry point allows Administrator and Informaticians to create files outside of the `Project` context.   Files created in this manner are also  returned in `Search`.
      responses:
        '201':
          description: File document created successfully
      parameters:
        - in: body
          name: File
          required: true
          schema:
            $ref: '#/definitions/File'
        - $ref: "#/parameters/Authorization"
      tags:
        - File
        - Administrator
        - Informatician

  /files/summary:
    get:
      summary: Provides aggregated results of the current search.
      description: Histograms of [age_at_diagnosis, project_code, individual, sample, file]
      responses:
        '200':
          description: Document fetched successfully
          schema:
            $ref: '#/definitions/SearchResponse'
      parameters:
        - $ref: '#/parameters/filter'
        - $ref: "#/parameters/Authorization"


      tags:
        - Researcher
        - Informatician
        - Biospecimen
        - Search

  '/files/{_id}':
    patch:
      summary: Updates a File document, updates search index
      description: |-
        Administrator and Informaticians can update files `created outside of project submission` can be updated
      responses:
        '200':
          description: File document updated successfully
      parameters:
        - $ref: '#/parameters/File__id'
        - in: body
          name: File
          required: true
          schema:
            $ref: '#/definitions/File'
        - $ref: "#/parameters/Authorization"
      tags:
        - File
        - Administrator
        - Informatician

    delete:
      summary: Deletes a File document, removes from search index
      responses:
        '200':
          description: File document deleted successfully
      parameters:
        - $ref: '#/parameters/File__id'
        - $ref: "#/parameters/Authorization"
      tags:
        - File
        - Administrator
        - Informatician

  '/submission/{program_name}/{project_code}/{_id}':
    get:
      summary: >-
        Retrieves one or more submission objects.
      responses:
        '200':
          description: >-
            An array of submission objects.
          schema:
            items:
              $ref: '#/definitions/Submission'
            type: array
      parameters:
        - $ref: '#/parameters/program_name'
        - $ref: '#/parameters/project_code'
        - $ref: '#/parameters/submission_id'
        - $ref: "#/parameters/Authorization"
      tags:
        - Submission
        - Informatician

      description: |+

        * /submission/XXX     - returns all submissions for all projects in program 'XXX'
        * /submission/XXX/YYY - returns all submissions program 'XXX', project 'YYY'
        * /submission/XXX/YYY/nnnn - returns submission  program 'XXX', project 'YYY', id 'nnnnn'

    delete:
      summary: >-
        Deletes all submissions and their associated entities
      parameters:
        - $ref: '#/parameters/program_name'
        - $ref: '#/parameters/project_code'
        - $ref: '#/parameters/submission_id'
        - $ref: "#/parameters/Authorization"

      responses:
        '200':
          description: operation has been successful
      tags:
        - Submission
        - Informatician

    patch:
      summary: Updates a Submission document
      responses:
        '200':
          description: Submission document updated successfully
      parameters:
        - $ref: '#/parameters/program_name'
        - $ref: '#/parameters/project_code'
        - $ref: '#/parameters/submission_id'
        - in: body
          name: Submission
          required: true
          schema:
            $ref: '#/definitions/Submission'
      tags:
        - Submission
        - Informatician

  '/submission/{program_name}/{project_code}':
    post:
      summary: >-
        Stores one or more submissions and child entities
      parameters:
        - in: body
          name: Submission
          required: true
          schema:
            $ref: '#/definitions/Submission'
        - $ref: '#/parameters/program_name'
        - $ref: '#/parameters/project_code'
        - $ref: "#/parameters/Authorization"
      responses:
        '200':
          description: operation has been successful
      tags:
        - Submission
        - Informatician
      description: |+
        Validate that project and program exist before submission
        Validate and save associated entities
        see [here for more](https://gdc-docs.nci.nih.gov/API/Users_Guide/Submission/#making-requests-to-the-submission-api)


  '/programs':
    get:
      summary: Retrieves one or more programs
      parameters:
        - $ref: "#/parameters/Authorization"
      responses:
        '200':
          description: An array of programs
          schema:
            items:
              $ref: '#/definitions/Program'
            type: array
      tags:
        - Program
        - Administrator

    post:
      summary: Stores one or more programs
      parameters:
        - in: body
          name: Program
          required: true
          schema:
            $ref: '#/definitions/Program'
        - $ref: "#/parameters/Authorization"
      responses:
        '200':
          description: operation has been successful
      tags:
        - Program
        - Administrator
    delete:
      summary: Deletes all programs
      parameters:
        - $ref: "#/parameters/Authorization"
      responses:
        '200':
          description: operation has been successful
      tags:
        - Program
        - Administrator

  '/programs/{programId}':
    get:
      summary: Retrieves a Program document
      responses:
        '200':
          description: Program document fetched successfully
          schema:
            $ref: '#/definitions/Program'
      parameters:
        - $ref: '#/parameters/Program__id'
        - $ref: "#/parameters/Authorization"
      tags:
        - Program
        - Administrator

    patch:
      summary: Updates a Program document
      responses:
        '200':
          description: Program document updated successfully
      parameters:
        - $ref: '#/parameters/Program__id'
        - in: body
          name: Program
          required: true
          schema:
            $ref: '#/definitions/Program'
        - $ref: "#/parameters/Authorization"
      tags:
        - Program
        - Administrator
    delete:
      summary: Deletes a Program document
      responses:
        '200':
          description: Program document deleted successfully
      parameters:
        - $ref: '#/parameters/Program__id'
        - $ref: "#/parameters/Authorization"
      tags:
        - Program
        - Administrator

  '/projects':
    get:
      summary: Retrieves one or more projects
      parameters:
        - $ref: "#/parameters/Authorization"
      responses:
        '200':
          description: An array of projects
          schema:
            items:
              $ref: '#/definitions/Project'
            type: array
      tags:
        - Project
        - Administrator

  '/projects/{projectId}':
    get:
        summary: Retrieves one or more projects
        parameters:
          - $ref: '#/parameters/Project__id'
          - $ref: "#/parameters/Authorization"
        responses:
          '200':
            description: Project document fetched successfully
            schema:
              $ref: '#/definitions/Project'
        tags:
          - Project
          - Administrator



  '/login':
    post:
      summary: Authenticates user, returns token
      parameters:
        - in: body
          name: Login
          required: true
          schema:
            $ref: '#/definitions/Login'
      responses:
        '200':
          description: Schema document fetched successfully
        '401':
          description: |-
            `{'message': 'Invalid user/password'}`
      tags:
        - Administrator
        - Informatician
        - Utility
        - Development

  '/logout':
    post:
      summary: De-authenticates user
      parameters:
        - $ref: "#/parameters/Authorization"
      responses:
        '200':
          description: |-
            `{'message': 'development user logged out'}`
      tags:
        - Administrator
        - Informatician
        - Utility
        - Development

  '/schemas':
    get:
      summary: Retrieves current schemas
      responses:
        '200':
          description: Schema document fetched successfully
      tags:
        - Administrator
        - Informatician
        - Utility
        - Development


  '/status':
    get:
      summary: retrieves current build & configuration information
      responses:
        '200':
          description: Status document fetched successfully
      tags:
        - Administrator
        - Informatician
        - Utility
        - Development

  '/static':
    get:
      summary: Retrieves static content - currently  `/static/swagger.yml`
      description: |-
        *NOTE:* this is an absolute path it is _not_ proceeded with api version.
      responses:
        '200':
          description: Static document fetched successfully
      tags:
        - Administrator
        - Informatician
        - Utility
        - Development


 schemes:
  - http
 parameters:
  File__id:
    in: path
    name: _id
    required: true
    description: 'unique id of the resource'
    type: string
    format: objectid
  Program__id:
    in: path
    name: programId
    required: true
    description: ''
    type: string
    format: objectid
  Project__id:
    in: path
    name: projectId
    required: true
    description: ''
    type: string
    format: objectid
  program_name:
    in: path
    name: program_name
    required: true
    description: 'unique name of the program, assigned by admin'
    type: string
  project_code:
    in: path
    name: project_code
    required: true
    description: 'unique name of the project, assigned by informatician'
    type: string
  submission_id:
    in: path
    name: _id
    required: true
    description: 'unique id of the submission, assigned by system'
    type: string
  Authorization:
    in: header
    name: authorization
    type: string
    required: true
    description: JSON Web Tokens are an open standard for representing claims securely between two parties.
  filter:
    in: query
    name: filter
    type: string
    required: false
    description: |+
      Filter parameter passed to backend.  Note:  The [GDC Spec](https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query) is specific their graphql backend. We diverge from the GDC spec here and use a google search like [syntax](https://github.com/Intel-HSS/CCC_DMS/blob/api5/doc/query_syntax.md)
  sort:
    name: sort
    in: query
    description: |+
      The sort query parameter sorts the results by a specific field, and with the sort direction specified using the :asc (ascending) or :desc (descending) prefix, e.g. sort=field:desc. [more](https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#sort)

    required: false
    type: string

  fields:
    name: fields
    in: query
    description: |+
      This query parameter specifies which fields are to be included in the API response. [more](https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#fields)

    required: false
    type: string

  size:
    name: size
    in: query
    description: |+
      The size query parameter specifies the maximum number of results to return. Default size is 10. If the number of query results is greater than size, only some of the results will be returned.

    required: false
    type: integer
  from:
    name: from
    in: query
    description: |+
      The from query parameter specifies the first record to return out of the set of results. For example, if there are 20 cases returned from the cases endpoint, then setting from to 11 will return results 11 to 20. The from parameter can be used in conjunction with the size parameter to return a specific subset of results.

    required: false
    type: integer


 produces:
  - application/json
 basePath: /v0
 tags:

  - name: File
    description: |-
      `Entity` aka "Resource". "A set of related records (either file or api) identified by a url. Other attributes include mimetype, size, description, checksum (NCIt C42883)."  It is necessary to describe files `independently of project submission`.  For example, a `reference genome` resource is used across all projects.   This entry point allows Administrator and Informaticians to create files outside of the `Project` context.   Files created in this manner are also  returned in `Search`.

  - name: Search
    description: |-
      `Operation`
      The CCC Search provides users with web-based access to data from cancer genomics studies. Key features include:

      * Open, granular access to information about all datasets available in the CCC
      * Advanced search and visualization-assisted filtering of data files
      * A resource centric view for browsing available harmonized focused on resources(files) and their associated meta data

      The files endpoint `/v0/files` enables search and retrieval of information relating to files stored in the DMS, including file properties such as file_name, md5sum, data_format, and others.  Users can search using attributes of the file or any of its associated entitities. A standardized, pagable response returns variable content depending on the hits found.

  - name: Submission
    description: |-
      `Operation`
      The CCC will accept submissions of cancer genomic and clinical data from researchers around the world who wish to share their data broadly.
      The Submission endpoint is a platform that allows researchers to submit and release data to CCC. The key features of the GDC Data Submission Portal are:
        * Upload and Validate Data: Project data can be uploaded and registered with the CCC. The API will validate the data against the data model.
        * Harmonization: While preserving the submitter's data model, key fields and attributes are standardized to enable cross project search and aggregation.  This responsibility is shared between the API and the ccc_client.
          * Meta data relationships - biospecimen entitities are associcated with resources for searching and aggregations
          * Vocabulary alignment - a small number of fields are cross referenced based on the GA4GH metadata schema.
          * The data model is flexible and imposes very few technical limits on adjusting the entities and relationships. However there may be effects on quality control, reporting, accounting and user interface/experience.
        * Quality Control: Submitted metadata relationships are checked for data integrity, the links between metadata.

        The API accepts project metadata in JSON formats for the purpose
        of creating entities in the Data Model. This includes clinical
        and biospecimen metadata such as disease name and stage,
        patient age, sample type, and certain details about the types of
        data collected. Upon successful data submission this metadata is indexed
        and becomes available for queries by data users via the /v0/files endpoint.
        The user can submit several entity types all linked by user submitted ids. [files, slide, aliquot, analyte, portion, samples, cases, projects ]
        See [here](https://gdc-docs.nci.nih.gov/API/Users_Guide/Submission/#submission) for more.

        The goal of the CCC submittal process is to support active experiements and workflows.  The CCC submission process is an abbreviated workflow when compared to [others](https://gdc-docs.nci.nih.gov/Data_Submission_Portal/Users_Guide/Submission_Workflow/) in that the CCC is not geared for data publication and "release".

  - name: Program
    description: Administrative `Entity`. Program has many Projects. "A broad framework of goals to be achieved. (NCIt C52647)."  Created by Informatician during submission.

  - name: Project
    description: Administrative `Entity`. Belongs to Program, has many Cases. "Any specifically defined piece of work that is undertaken or attempted to meet a single requirement. (NCIt C47885)"

  - name: Case
    description:  Administrative `Entity`. Belongs to Project. "The collection of all data related to a specific subject in the  context of a specific project."

  - name: Biospecimen
    description: |-
      `Entity category`. Biospecimen data refers to information associated with the physical sample taken from a participant and its processing down to the aliquot level for sequencing experiments. This data falls into several key entities `[slide, aliquot, analyte, portion, samples]`  forming the chain of meta data between resource(file) and case(individual)

  - name: Informatician
    description: |-
      `Role`. Execute, test and roll out project specific solutions. More specifically, develops and manages pipelines (genomic, imaging,etc.) for their projects, including managing data.

  - name: Researcher
    description: |-
      `Role`. CCC researchers will be able to integrate genetic and clinical data, such as cancer imaging and histological data, with information on the molecular profiles of tumors as well as treatment response. From this perspective, the CCC would become an important resource for generating potentially actionable information that ultimately contributes to scientific progress.

  - name: Administrator
    description: |-
      `Role`. Effective provisioning, installation/configuration, operation, and maintenance of systems software and related infrastructure.

  - name: Utility
    description: |-
      ` Operation Category`. Useful endpoints for general use.

  - name: Development
    description: |-
      ` Operation Category`. Useful endpoints for development, will change frequently and may be deprecated.

 host: '192.168.99.100:8000'
 definitions:
  File:
    type: object
    properties:
      mimeType:
        type: string
      info:
        type: object
      description:
        type: string
      name:
        type: string
      format:
        type: string
      checksum:
        type: string
      created:
        type: string
      class:
        type: string
      gid:
        type: string
      location:
        type: string
      _id:
        type: string
        format: objectid
      type:
        type: string
      id:
        type: string
      datasetID:
        type: string
      size:
        type: integer
    description: |-
      Entity aka Resource. "A set of related records (either file or api) identified by a url. Other attributes include mimetype, size, description, checksum (NCIt C42883)."

  Submission:
    type: object
    properties:
      submitter_id:
        type: string
      id:
        type: string
      program_name:
        type: string
      _id:
        type: string
        format: objectid
      type:
        type: string
      project_code:
        type: string
    description: |-

          The API accepts project metadata in JSON formats for the purpose
          of creating entities in the Data Model. This includes clinical
          and biospecimen metadata such as disease name and stage,
          patient age, sample type, and certain details about the types of
          data collected. Upon successful data submission this metadata is indexed
          and becomes available for queries by data users via the /v0/files endpoint.

  Project:
    required:
      - code
      - name
    type: object
    properties:
      code:
        type: string
      _id:
        type: string
        format: objectid
      id:
        type: string
      name:
        type: string
    description: Any specifically defined piece of work that is undertaken or attempted to meet a single requirement. (NCIt C47885)


  Program:
    required:
      - code
      - name
    type: object
    properties:
      code:
        type: string
      _id:
        type: string
        format: objectid
      id:
        type: string
      name:
        type: string
    description: A broad framework of goals to be achieved. (NCIt C52647)

  SearchResponse:
    type: object
    properties:
      data:
        type: object
        properties:
          hits:
            description: Array of objects.  Type of object returned depends on entities searched.
            type: array
            items:
              type: object
              properties:
                id:
                  type: string
                type:
                  type: string
          pagination:
            type: object
            properties:
              count:
                type: integer
              sort:
                type: string
              from:
                type: integer
              pages:
                type: integer
              total:
                type: integer
              page:
                type: integer
              size:
                type: integer
      warnings:
        type: object
        properties: {}
    description: |-
          The files Endpoint https://gdc-api.nci.nih.gov/files enables search and retrieval of information relating to files stored in the GDC, including file properties such as file_name, md5sum, data_format, and others.


  Login:
    required:
      - user
      - password
    type: object
    properties:
      user:
        type: string
      password:
        type: string
    description: authenticate user

 swagger: '2.0'
 consumes:
  - application/json
	info:
	title: YA-DMS API description
	description: \|-
	### "Yet Another Data Management Service"
	##### Key endpoints

	![image](https://cloud.githubusercontent.com/assets/47808/20463919/517044ca-aef2-11e6-8d8a-3b1a1f24a1f4.png)



	version: '0.1'
	paths:
	/files:
	get:
	summary: Searches resources and associated meta data.
	responses:
	'200':
	description: Document fetched successfully
	schema:
	$ref: '#/definitions/SearchResponse'
	parameters:
	- $ref: '#/parameters/filter'
	- $ref: '#/parameters/sort'
	- $ref: '#/parameters/fields'
	- $ref: '#/parameters/size'
	- $ref: '#/parameters/from'
	- $ref: "#/parameters/Authorization"

	tags:
	- Researcher
	- Informatician
	- Biospecimen
	- Search

	description: \|+

	See this [overview from GDC](https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#files-endpoint).



	post:
	summary: Creates a File document, updates search index
	description: \|-
	It is necessary to describe files `independently of project submission`. For example, a `reference genome` resource is used across all projects. This entry point allows Administrator and Informaticians to create files outside of the `Project` context. Files created in this manner are also returned in `Search`.
	responses:
	'201':
	description: File document created successfully
	parameters:
	- in: body
	name: File
	required: true
	schema:
	$ref: '#/definitions/File'
	- $ref: "#/parameters/Authorization"
	tags:
	- File
	- Administrator
	- Informatician

	/files/summary:
	get:
	summary: Provides aggregated results of the current search.
	description: Histograms of [age_at_diagnosis, project_code, individual, sample, file]
	responses:
	'200':
	description: Document fetched successfully
	schema:
	$ref: '#/definitions/SearchResponse'
	parameters:
	- $ref: '#/parameters/filter'
	- $ref: "#/parameters/Authorization"


	tags:
	- Researcher
	- Informatician
	- Biospecimen
	- Search

	'/files/{_id}':
	patch:
	summary: Updates a File document, updates search index
	description: \|-
	Administrator and Informaticians can update files `created outside of project submission` can be updated
	responses:
	'200':
	description: File document updated successfully
	parameters:
	- $ref: '#/parameters/File__id'
	- in: body
	name: File
	required: true
	schema:
	$ref: '#/definitions/File'
	- $ref: "#/parameters/Authorization"
	tags:
	- File
	- Administrator
	- Informatician

	delete:
	summary: Deletes a File document, removes from search index
	responses:
	'200':
	description: File document deleted successfully
	parameters:
	- $ref: '#/parameters/File__id'
	- $ref: "#/parameters/Authorization"
	tags:
	- File
	- Administrator
	- Informatician

	'/submission/{program_name}/{project_code}/{_id}':
	get:
	summary: >-
	Retrieves one or more submission objects.
	responses:
	'200':
	description: >-
	An array of submission objects.
	schema:
	items:
	$ref: '#/definitions/Submission'
	type: array
	parameters:
	- $ref: '#/parameters/program_name'
	- $ref: '#/parameters/project_code'
	- $ref: '#/parameters/submission_id'
	- $ref: "#/parameters/Authorization"
	tags:
	- Submission
	- Informatician

	description: \|+

	* /submission/XXX - returns all submissions for all projects in program 'XXX'
	* /submission/XXX/YYY - returns all submissions program 'XXX', project 'YYY'
	* /submission/XXX/YYY/nnnn - returns submission program 'XXX', project 'YYY', id 'nnnnn'

	delete:
	summary: >-
	Deletes all submissions and their associated entities
	parameters:
	- $ref: '#/parameters/program_name'
	- $ref: '#/parameters/project_code'
	- $ref: '#/parameters/submission_id'
	- $ref: "#/parameters/Authorization"

	responses:
	'200':
	description: operation has been successful
	tags:
	- Submission
	- Informatician

	patch:
	summary: Updates a Submission document
	responses:
	'200':
	description: Submission document updated successfully
	parameters:
	- $ref: '#/parameters/program_name'
	- $ref: '#/parameters/project_code'
	- $ref: '#/parameters/submission_id'
	- in: body
	name: Submission
	required: true
	schema:
	$ref: '#/definitions/Submission'
	tags:
	- Submission
	- Informatician

	'/submission/{program_name}/{project_code}':
	post:
	summary: >-
	Stores one or more submissions and child entities
	parameters:
	- in: body
	name: Submission
	required: true
	schema:
	$ref: '#/definitions/Submission'
	- $ref: '#/parameters/program_name'
	- $ref: '#/parameters/project_code'
	- $ref: "#/parameters/Authorization"
	responses:
	'200':
	description: operation has been successful
	tags:
	- Submission
	- Informatician
	description: \|+
	Validate that project and program exist before submission
	Validate and save associated entities
	see [here for more](https://gdc-docs.nci.nih.gov/API/Users_Guide/Submission/#making-requests-to-the-submission-api)


	'/programs':
	get:
	summary: Retrieves one or more programs
	parameters:
	- $ref: "#/parameters/Authorization"
	responses:
	'200':
	description: An array of programs
	schema:
	items:
	$ref: '#/definitions/Program'
	type: array
	tags:
	- Program
	- Administrator

	post:
	summary: Stores one or more programs
	parameters:
	- in: body
	name: Program
	required: true
	schema:
	$ref: '#/definitions/Program'
	- $ref: "#/parameters/Authorization"
	responses:
	'200':
	description: operation has been successful
	tags:
	- Program
	- Administrator
	delete:
	summary: Deletes all programs
	parameters:
	- $ref: "#/parameters/Authorization"
	responses:
	'200':
	description: operation has been successful
	tags:
	- Program
	- Administrator

	'/programs/{programId}':
	get:
	summary: Retrieves a Program document
	responses:
	'200':
	description: Program document fetched successfully
	schema:
	$ref: '#/definitions/Program'
	parameters:
	- $ref: '#/parameters/Program__id'
	- $ref: "#/parameters/Authorization"
	tags:
	- Program
	- Administrator

	patch:
	summary: Updates a Program document
	responses:
	'200':
	description: Program document updated successfully
	parameters:
	- $ref: '#/parameters/Program__id'
	- in: body
	name: Program
	required: true
	schema:
	$ref: '#/definitions/Program'
	- $ref: "#/parameters/Authorization"
	tags:
	- Program
	- Administrator
	delete:
	summary: Deletes a Program document
	responses:
	'200':
	description: Program document deleted successfully
	parameters:
	- $ref: '#/parameters/Program__id'
	- $ref: "#/parameters/Authorization"
	tags:
	- Program
	- Administrator

	'/projects':
	get:
	summary: Retrieves one or more projects
	parameters:
	- $ref: "#/parameters/Authorization"
	responses:
	'200':
	description: An array of projects
	schema:
	items:
	$ref: '#/definitions/Project'
	type: array
	tags:
	- Project
	- Administrator

	'/projects/{projectId}':
	get:
	summary: Retrieves one or more projects
	parameters:
	- $ref: '#/parameters/Project__id'
	- $ref: "#/parameters/Authorization"
	responses:
	'200':
	description: Project document fetched successfully
	schema:
	$ref: '#/definitions/Project'
	tags:
	- Project
	- Administrator



	'/login':
	post:
	summary: Authenticates user, returns token
	parameters:
	- in: body
	name: Login
	required: true
	schema:
	$ref: '#/definitions/Login'
	responses:
	'200':
	description: Schema document fetched successfully
	'401':
	description: \|-
	`{'message': 'Invalid user/password'}`
	tags:
	- Administrator
	- Informatician
	- Utility
	- Development

	'/logout':
	post:
	summary: De-authenticates user
	parameters:
	- $ref: "#/parameters/Authorization"
	responses:
	'200':
	description: \|-
	`{'message': 'development user logged out'}`
	tags:
	- Administrator
	- Informatician
	- Utility
	- Development

	'/schemas':
	get:
	summary: Retrieves current schemas
	responses:
	'200':
	description: Schema document fetched successfully
	tags:
	- Administrator
	- Informatician
	- Utility
	- Development


	'/status':
	get:
	summary: retrieves current build & configuration information
	responses:
	'200':
	description: Status document fetched successfully
	tags:
	- Administrator
	- Informatician
	- Utility
	- Development

	'/static':
	get:
	summary: Retrieves static content - currently `/static/swagger.yml`
	description: \|-
	NOTE: this is an absolute path it is _not_ proceeded with api version.
	responses:
	'200':
	description: Static document fetched successfully
	tags:
	- Administrator
	- Informatician
	- Utility
	- Development


	schemes:
	- http
	parameters:
	File__id:
	in: path
	name: _id
	required: true
	description: 'unique id of the resource'
	type: string
	format: objectid
	Program__id:
	in: path
	name: programId
	required: true
	description: ''
	type: string
	format: objectid
	Project__id:
	in: path
	name: projectId
	required: true
	description: ''
	type: string
	format: objectid
	program_name:
	in: path
	name: program_name
	required: true
	description: 'unique name of the program, assigned by admin'
	type: string
	project_code:
	in: path
	name: project_code
	required: true
	description: 'unique name of the project, assigned by informatician'
	type: string
	submission_id:
	in: path
	name: _id
	required: true
	description: 'unique id of the submission, assigned by system'
	type: string
	Authorization:
	in: header
	name: authorization
	type: string
	required: true
	description: JSON Web Tokens are an open standard for representing claims securely between two parties.
	filter:
	in: query
	name: filter
	type: string
	required: false
	description: \|+
	Filter parameter passed to backend. Note: The [GDC Spec](https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query) is specific their graphql backend. We diverge from the GDC spec here and use a google search like [syntax](https://github.com/Intel-HSS/CCC_DMS/blob/api5/doc/query_syntax.md)
	sort:
	name: sort
	in: query
	description: \|+
	The sort query parameter sorts the results by a specific field, and with the sort direction specified using the :asc (ascending) or :desc (descending) prefix, e.g. sort=field:desc. [more](https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#sort)

	required: false
	type: string

	fields:
	name: fields
	in: query
	description: \|+
	This query parameter specifies which fields are to be included in the API response. [more](https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#fields)

	required: false
	type: string

	size:
	name: size
	in: query
	description: \|+
	The size query parameter specifies the maximum number of results to return. Default size is 10. If the number of query results is greater than size, only some of the results will be returned.

	required: false
	type: integer
	from:
	name: from
	in: query
	description: \|+
	The from query parameter specifies the first record to return out of the set of results. For example, if there are 20 cases returned from the cases endpoint, then setting from to 11 will return results 11 to 20. The from parameter can be used in conjunction with the size parameter to return a specific subset of results.

	required: false
	type: integer


	produces:
	- application/json
	basePath: /v0
	tags:

	- name: File
	description: \|-
	`Entity` aka "Resource". "A set of related records (either file or api) identified by a url. Other attributes include mimetype, size, description, checksum (NCIt C42883)." It is necessary to describe files `independently of project submission`. For example, a `reference genome` resource is used across all projects. This entry point allows Administrator and Informaticians to create files outside of the `Project` context. Files created in this manner are also returned in `Search`.

	- name: Search
	description: \|-
	`Operation`
	The CCC Search provides users with web-based access to data from cancer genomics studies. Key features include:

	* Open, granular access to information about all datasets available in the CCC
	* Advanced search and visualization-assisted filtering of data files
	* A resource centric view for browsing available harmonized focused on resources(files) and their associated meta data

	The files endpoint `/v0/files` enables search and retrieval of information relating to files stored in the DMS, including file properties such as file_name, md5sum, data_format, and others. Users can search using attributes of the file or any of its associated entitities. A standardized, pagable response returns variable content depending on the hits found.

	- name: Submission
	description: \|-
	`Operation`
	The CCC will accept submissions of cancer genomic and clinical data from researchers around the world who wish to share their data broadly.
	The Submission endpoint is a platform that allows researchers to submit and release data to CCC. The key features of the GDC Data Submission Portal are:
	* Upload and Validate Data: Project data can be uploaded and registered with the CCC. The API will validate the data against the data model.
	* Harmonization: While preserving the submitter's data model, key fields and attributes are standardized to enable cross project search and aggregation. This responsibility is shared between the API and the ccc_client.
	* Meta data relationships - biospecimen entitities are associcated with resources for searching and aggregations
	* Vocabulary alignment - a small number of fields are cross referenced based on the GA4GH metadata schema.
	* The data model is flexible and imposes very few technical limits on adjusting the entities and relationships. However there may be effects on quality control, reporting, accounting and user interface/experience.
	* Quality Control: Submitted metadata relationships are checked for data integrity, the links between metadata.

	The API accepts project metadata in JSON formats for the purpose
	of creating entities in the Data Model. This includes clinical
	and biospecimen metadata such as disease name and stage,
	patient age, sample type, and certain details about the types of
	data collected. Upon successful data submission this metadata is indexed
	and becomes available for queries by data users via the /v0/files endpoint.
	The user can submit several entity types all linked by user submitted ids. [files, slide, aliquot, analyte, portion, samples, cases, projects ]
	See [here](https://gdc-docs.nci.nih.gov/API/Users_Guide/Submission/#submission) for more.

	The goal of the CCC submittal process is to support active experiements and workflows. The CCC submission process is an abbreviated workflow when compared to [others](https://gdc-docs.nci.nih.gov/Data_Submission_Portal/Users_Guide/Submission_Workflow/) in that the CCC is not geared for data publication and "release".

	- name: Program
	description: Administrative `Entity`. Program has many Projects. "A broad framework of goals to be achieved. (NCIt C52647)." Created by Informatician during submission.

	- name: Project
	description: Administrative `Entity`. Belongs to Program, has many Cases. "Any specifically defined piece of work that is undertaken or attempted to meet a single requirement. (NCIt C47885)"

	- name: Case
	description: Administrative `Entity`. Belongs to Project. "The collection of all data related to a specific subject in the context of a specific project."

	- name: Biospecimen
	description: \|-
	`Entity category`. Biospecimen data refers to information associated with the physical sample taken from a participant and its processing down to the aliquot level for sequencing experiments. This data falls into several key entities `[slide, aliquot, analyte, portion, samples]` forming the chain of meta data between resource(file) and case(individual)

	- name: Informatician
	description: \|-
	`Role`. Execute, test and roll out project specific solutions. More specifically, develops and manages pipelines (genomic, imaging,etc.) for their projects, including managing data.

	- name: Researcher
	description: \|-
	`Role`. CCC researchers will be able to integrate genetic and clinical data, such as cancer imaging and histological data, with information on the molecular profiles of tumors as well as treatment response. From this perspective, the CCC would become an important resource for generating potentially actionable information that ultimately contributes to scientific progress.

	- name: Administrator
	description: \|-
	`Role`. Effective provisioning, installation/configuration, operation, and maintenance of systems software and related infrastructure.

	- name: Utility
	description: \|-
	` Operation Category`. Useful endpoints for general use.

	- name: Development
	description: \|-
	` Operation Category`. Useful endpoints for development, will change frequently and may be deprecated.

	host: '192.168.99.100:8000'
	definitions:
	File:
	type: object
	properties:
	mimeType:
	type: string
	info:
	type: object
	description:
	type: string
	name:
	type: string
	format:
	type: string
	checksum:
	type: string
	created:
	type: string
	class:
	type: string
	gid:
	type: string
	location:
	type: string
	_id:
	type: string
	format: objectid
	type:
	type: string
	id:
	type: string
	datasetID:
	type: string
	size:
	type: integer
	description: \|-
	Entity aka Resource. "A set of related records (either file or api) identified by a url. Other attributes include mimetype, size, description, checksum (NCIt C42883)."

	Submission:
	type: object
	properties:
	submitter_id:
	type: string
	id:
	type: string
	program_name:
	type: string
	_id:
	type: string
	format: objectid
	type:
	type: string
	project_code:
	type: string
	description: \|-

	The API accepts project metadata in JSON formats for the purpose
	of creating entities in the Data Model. This includes clinical
	and biospecimen metadata such as disease name and stage,
	patient age, sample type, and certain details about the types of
	data collected. Upon successful data submission this metadata is indexed
	and becomes available for queries by data users via the /v0/files endpoint.

	Project:
	required:
	- code
	- name
	type: object
	properties:
	code:
	type: string
	_id:
	type: string
	format: objectid
	id:
	type: string
	name:
	type: string
	description: Any specifically defined piece of work that is undertaken or attempted to meet a single requirement. (NCIt C47885)


	Program:
	required:
	- code
	- name
	type: object
	properties:
	code:
	type: string
	_id:
	type: string
	format: objectid
	id:
	type: string
	name:
	type: string
	description: A broad framework of goals to be achieved. (NCIt C52647)

	SearchResponse:
	type: object
	properties:
	data:
	type: object
	properties:
	hits:
	description: Array of objects. Type of object returned depends on entities searched.
	type: array
	items:
	type: object
	properties:
	id:
	type: string
	type:
	type: string
	pagination:
	type: object
	properties:
	count:
	type: integer
	sort:
	type: string
	from:
	type: integer
	pages:
	type: integer
	total:
	type: integer
	page:
	type: integer
	size:
	type: integer
	warnings:
	type: object
	properties: {}
	description: \|-
	The files Endpoint https://gdc-api.nci.nih.gov/files enables search and retrieval of information relating to files stored in the GDC, including file properties such as file_name, md5sum, data_format, and others.


	Login:
	required:
	- user
	- password
	type: object
	properties:
	user:
	type: string
	password:
	type: string
	description: authenticate user

	swagger: '2.0'
	consumes:
	- application/json