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Allele profile routes.
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@kjolley
kjolley committed Apr 2, 2015
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201 changes: 161 additions & 40 deletions rest.rst
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Expand Up @@ -22,13 +22,14 @@ Resources
* :ref:`/db/{database}<db>`
* :ref:`/db/{database}/loci<db_loci>`
* :ref:`/db/{database}/loci/{locus}<db_loci_locus>`
* :ref:`/db/{database}/alleles/{locus}<db_alleles_locus>`
* :ref:`/db/{database}/alleles/{locus}/{allele_id}<db_alleles_locus_allele_id>`
* :ref:`/db/{database}/alleles_fasta/{locus}<db_alleles_fasta_locus>`
* /db/{database}/schemes
* /db/{database}/schemes/{scheme_id}
* /db/{database}/schemes/{scheme_id}/fields/{field}
* /db/{database}/schemes/{scheme_id}/profiles
* :ref:`/db/{database}/loci/{locus}/alleles<db_loci_locus_alleles>`
* :ref:`/db/{database}/loci/{locus}/alleles_fasta<db_loci_locus_alleles_fasta>`
* :ref:`/db/{database}/loci/{locus}/alleles/{allele_id}<db_loci_locus_alleles_allele_id>`
* :ref:`/db/{database}/schemes<db_schemes>`
* :ref:`/db/{database}/schemes/{scheme_id}<db_schemes_scheme_id>`
* :ref:`/db/{database}/schemes/{scheme_id}/fields/{field}<db_schemes_scheme_id_fields_field>`
* :ref:`/db/{database}/schemes/{scheme_id}/profiles<db_schemes_scheme_id_profiles>`
* /db/{database}/schemes/{scheme_id}/profiles_csv
* /db/{database}/schemes/{scheme_id}/profiles/{profile_id}
* /db/{database}/isolates
* /db/{database}/isolates/{isolate_id}
Expand Down Expand Up @@ -88,7 +89,7 @@ database.

**Supported methods:** GET, POST

**Required query parameter:** {database}: Database configuration name [string]
**Required query parameter:** {database} - Database configuration name [string]

**Optional parameters:** None

Expand All @@ -113,7 +114,7 @@ Lists loci defined within specified database configuration.

**Supported methods:** GET, POST

**Required query parameter:** {database}: Database configuration name [string]
**Required query parameter:** {database} - Database configuration name [string]

**Optional parameters:** page [integer], page_size [integer]. Set very large
page size to return all results in one go.
Expand Down Expand Up @@ -144,8 +145,8 @@ seqdef databases).
**Supported methods:** GET, POST

**Required query parameters:**
* {database}: Database configuration name [string]
* {locus}: Locus name [string]
* {database} - Database configuration name [string]
* {locus} - Locus name [string]

**Optional parameters:** None

Expand All @@ -171,9 +172,9 @@ seqdef databases).
* max_length [integer] (seqdef databases) - maximum length for variable length
loci
* alleles [string] (seqdef databases) - :ref:`URI to list of allele records
<db_alleles_locus>`
<db_loci_locus_alleles>`
* alleles_fasta [string] (seqdef databases) - :ref:`URI to FASTA file of all
alleles of locus<db_alleles_fasta_locus>`
alleles of locus<db_loci_locus_alleles_fasta>`
* curators [array] (seqdef databases) - list of URIs to user records of
curators of the locus
* publications [array] (seqdef databases) - list of PubMed id numbers of papers
Expand All @@ -194,31 +195,31 @@ seqdef databases).

* genome_position [integer] (isolate databases)

.. _db_alleles_locus:
.. _db_loci_locus_alleles:

.. index::
single: API resources; /db/{database}/alleles/{locus}
single: API resources; /db/{database}/loci/{locus}/alleles

/db/{database}/alleles/{locus}
==============================
/db/{database}/loci/{locus}/alleles
===================================
Lists alleles defined for specific locus.

**Supported methods:** GET, POST

**Required query parameters:**
* {database}: Database configuration name [string]
* {locus}: Locus name [string]
* {database} - Database configuration name [string]
* {locus} - Locus name [string]

**Optional parameters:** page [integer], page_size [integer]. Set very large
page size to return all results in one go.

**Example request URI:**
http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/alleles/abcZ
http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/loci/abcZ/alleles

**Response:** Object containing:

* alleles [array] - List of :ref:`URIs to defined allele records
<db_alleles_locus_allele_id>`.
<db_loci_locus_alleles_allele_id>`.
Pages are 100 records by default. Page size can be modified using the
page_size parameter.
* paging [object] - Some or all of the following:
Expand All @@ -227,25 +228,46 @@ http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/alleles/abcZ
* first - URI to first page of results
* last - URI to last page of results

.. _db_alleles_locus_allele_id:
.. _db_loci_locus_alleles_fasta:

.. index::
single: API resources; /db/{database}/loci/{locus}/alleles_fasta

/db/{database}/loci/{locus}/alleles_fasta
=========================================
Provides all alleles defined for a locus in FASTA format.

**Supported methods:** GET, POST

**Required query parameters:**
* {database} - Database configuration name [string]
* {locus} - Locus name [string]

**Optional parameters:** None

**Example request URI:** http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/loci/abcZ/alleles_fasta

**Response:** FASTA format file of alleles sequences

.. _db_loci_locus_alleles_allele_id:

.. index::
single: API resources; /db/{database}/alleles/{locus}/{allele_id}
single: API resources; /db/{database}/loci/{locus}/alleles/{allele_id}

/db/{database}/alleles/{locus}/{allele_id}
==========================================
/db/{database}/loci/{locus}/alleles/{allele_id}
===============================================
Provides information about an allele including its sequence.

**Supported methods:** GET, POST

**Required query parameters:**
* {database}: Database configuration name [string]
* {locus}: Locus name [string]
* {allele_id}: Allele identifier [string]
* {database} - Database configuration name [string]
* {locus} - Locus name [string]
* {allele_id} - Allele identifier [string]

**Optional parameters:** None

**Example request URI:** http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/alleles/abcZ/5
**Example request URI:** http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/loci/abcZ/alleles/5

**Response:** Object containing the following key/value pairs:

Expand All @@ -259,26 +281,125 @@ Provides information about an allele including its sequence.
* date_entered [string] - record creation date (ISO 8601 format)
* datestamp [string] - last updated date (ISO 8601 format)

.. _db_alleles_fasta_locus:
.. _db_schemes:

.. index::
single: API resources; /db/{database}/alleles_fasta/{locus}
single: API resources; /db/{database}/schemes

/db/{database}/alleles_fasta/{locus}
====================================
Provides all alleles defined for a locus in FASTA format.
/db/{database}/schemes
======================

Lists schemes defined within specified database configuration.

**Supported methods:** GET, POST

**Required query parameter:** {database} - Database configuration name [string]

**Optional parameters:** None

**Example request URI:** http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/schemes

**Response:** List of scheme objects, each containing:

* scheme [string] - URI to scheme information
* description [string]

.. _db_schemes_scheme_id:

.. index::
single: API resources; /db/{database}/schemes/{scheme_id}

/db/{database}/schemes/{scheme_id}
==================================

Provides information about a scheme, including links to allelic profiles (in
seqdef databases, if appropriate).

**Supported methods:** GET, POST

**Required query parameters:**
* {database}: Database configuration name [string]
* {locus}: Locus name [string]
* {database} - Database configuration name [string]
* {scheme_id} - Scheme id number [integer]

**Optional parameters:** None

**Example request URI:** http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/alleles_fasta/abcZ
**Example request URI:** http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/schemes/1

**Response:** FASTA format file of alleles sequences
**Response:** Object containing a subset of the following key/value pairs:

* id [integer]
* description [string]
* locus_count [integer] - number of loci belonging to scheme
* loci [array] - list of :ref:`URIs to locus descriptions<db_loci_locus>`
* has_primary_key_field [boolean]
* fields [array] - list of :ref:`URIs to scheme field descriptions
<db_schemes_scheme_id_fields_field>`
* primary_key_field [string] - :ref:`URI to primary key field description
<db_schemes_scheme_id_fields_field>`
* profile_count [integer] - number of defined profiles (only for schemes with
primary keys defined - only seqdef databases)
* profiles [array] - URI to list of profile definitions (only seqdef databases)
* profiles_csv [string] - URI to tab-delimited file of all scheme profiles


.. _db_schemes_scheme_id_fields_field:

.. index::
single: API resources; /db/{database}/schemes/{scheme_id}/fields/{field}

/db/{database}/schemes/{scheme_id}/fields/{field}
=================================================

Provides information about scheme fields.

**Supported methods:** GET, POST

**Required query parameters:**
* {database} - Database configuration name [string]
* {scheme_id} - Scheme id number [integer]
* {field} - Field name [string]

**Optional parameters:** None

**Example request URI:** http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/schemes/1/fields/ST

**Response:** Object containing the following key/value pairs:

* field [string] - field name
* type [string] - data type of field (integer or text)
* primary_key [boolean] - true if field is the scheme primary key

.. _db_schemes_scheme_id_profiles:

.. index::
single: API resources; /db/{database}/schemes/{scheme_id}/profiles

/db/{database}/schemes/{scheme_id}/profiles
===========================================
Lists allelic profiles defined for a specific scheme.

**Supported methods:** GET, POST

**Required query parameters:**
* {database} - Database configuration name [string]
* {scheme_id} - Scheme id [integer]

**Optional parameters:** page [integer], page_size [integer]. Set very large
page size to return all results in one go.

**Example request URI:**
http://rest.pubmlst.org/db/pubmlst_neisseria_seqdef/schemes/1/profiles

**Response:** Object containing:

* profiles [array] - List of URIs to defined profile records.
Pages are 100 records by default. Page size can be modified using the
page_size parameter.
* paging [object] - Some or all of the following:
* previous - URI to previous page of results
* next - URI to next page of results
* first - URI to first page of results
* last - URI to last page of results

.. _db_users_user_id:

Expand All @@ -292,8 +413,8 @@ Provides information about data senders and curators.
**Supported methods:** GET, POST

**Required query parameters:**
* {database}: Database configuration name [string]
* {user_id}: User id number [integer]
* {database} - Database configuration name [string]
* {user_id} - User id number [integer]

**Optional parameters:** None

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