Adding sequence records, and cleaning up reference records.

src/main/resources/avro/referencemethods.avdl

@@ -161,67 +161,4 @@ GAReference getReference(
     */
     string id) throws GAException;
 
-/****************  /references/{id}/bases  *******************/
-/**
-The query parameters for a request to `GET /references/{id}/bases`, for
-example:
-
-`GET /references/{id}/bases?start=100&end=200`
-*/
-record GAListReferenceBasesRequest {
-  /**
-  The start position (0-based) of this query. Defaults to 0.
-  Genomic positions are non-negative integers less than reference length.
-  Requests spanning the join of circular genomes are represented as
-  two requests one on each side of the join (position 0).
-  */
-  long start = 0;
-
-  /**
-  The end position (0-based, exclusive) of this query. Defaults
-  to the length of this `GAReference`.
-  */
-  union { null, long } end = null;
-
-  /**
-  The continuation token, which is used to page through large result sets.
-  To get the next page of results, set this parameter to the value of
-  `nextPageToken` from the previous response.
-  */
-  union { null, string } pageToken = null;
-}
-
-/** The response from `GET /references/{id}/bases` expressed as JSON. */
-record GAListReferenceBasesResponse {
-  /**
-  The offset position (0-based) of the given `sequence` from the start of this
-  `GAReference`. This value will differ for each page in a paginated request.
-   */
-  long offset = 0;
-
-  /**
-  A substring of the bases that make up this reference. Bases are represented
-  as IUPAC-IUB codes; this string matches the regexp `[ACGTMRWSYKVHDBN]*`.
-  */
-  string sequence;
-
-  /**
-  The continuation token, which is used to page through large result sets.
-  Provide this value in a subsequent request to return the next page of
-  results. This field will be empty if there aren't any additional results.
-  */
-  union { null, string } nextPageToken = null;
-}
-
-/**
-Lists `GAReference` bases by ID and optional range.
-`GET /references/{id}/bases` will return a JSON version of
-`GAListReferenceBasesResponse`.
-*/
-GAListReferenceBasesResponse getReferenceBases(
-    /** The ID of the `GAReference`. */
-    string id,
-    /** Additional request parameters to restrict the query. */
-    GAListReferenceBasesRequest request) throws GAException;
-
 }

src/main/resources/avro/references.avdl

@@ -11,18 +11,23 @@ record GAReference {
   /** The reference ID. Unique within the repository. */
   string id;
 
+  /** The ID of the reference set that contains this reference contig. */
+  string referenceSetId;
+
   /** The length of this reference's sequence. */
   long length;
 
+  /** The ID of the assembled sequence of this contig. */
+  string sequenceId;
+
   /**
   MD5 of the upper-case sequence excluding all whitespace characters
   (this is equivalent to SQ:M5 in SAM).
   */
   string md5checksum;
 
   /**
-  The name of this reference. (e.g. '22') Also see the
-  `names` field on the parent `GAReferenceSet`.
+  The name of this reference. (e.g. '22').
   */
   string name;
 
@@ -44,17 +49,19 @@ record GAReference {
   is sufficiently small. Two sequences derived from the same official
   sequence share the same coordinates and annotations, and
   can be replaced with the official sequence for certain use cases.
+
+  This field contains the IDs of the references that this reference is derived
+  from. If this reference sequence is not derived from any other reference sequences,
+  this array should be empty.
   */
-  boolean isDerived = false;
+  array<string> derivedFrom = [];
 
   /**
   The `sourceDivergence` is the fraction of non-indel bases that do not match the
-  reference this record was derived from.
+  reference this record was derived from. This array should have the same length
+  as the derivedFrom array.
   */
-  union { null, float } sourceDivergence = null;
-
-  /** ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human). */
-  union { null, int } ncbiTaxonId = null;
+  array<float> sourceDivergence = [];
 }
 
 /**
@@ -66,17 +73,6 @@ record GAReferenceSet {
   /** The reference set ID. Unique in the repository. */
   string id;
 
-  /** The IDs of the `GAReference` objects that are part of this set. */
-  array<string> referenceIds = [];
-
-  /**
-  Order-independent MD5 checksum which identifies this `GAReferenceSet`. The
-  checksum is computed by sorting all `reference.md5checksum` (for all
-  `reference` in this set) in ascending lexicographic order, concatenating,
-  and taking the MD5 of that value.
-  */
-  string md5checksum;
-
   /**
   ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating
   the species which this assembly is intended to model. Note that contained
@@ -101,14 +97,14 @@ record GAReferenceSet {
   All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
   with a version number, e.g. `NC_000001.11`.
   */
-  array<string> sourceAccessions;
+  array<string> sourceAccessions = [];
 
   /**
-  A reference set may be derived from a source if it contains
-  additional sequences, or some of the sequences within it are derived
-  (see the definition of `isDerived` in `GAReference`).
+  The IDs of the reference sets that this reference set is derived from.
+  If this reference set is not derived from another reference set, this
+  field should be empty.
   */
-  boolean isDerived = false;
+  array<string> derivedFrom = [];
 }
 
 }

src/main/resources/avro/sequencemethods.avdl

@@ -0,0 +1,133 @@
+@namespace("org.ga4gh")
+protocol GAReferenceMethods {
+
+import idl "common.avdl";
+import idl "sequences.avdl";
+
+/****************  /sequences/search  *******************/
+/**
+This request maps to the body of `POST /sequences/search`
+as JSON.
+*/
+record GASearchSequencesRequest {
+  /** If present, the names of the sequences to search for. */
+  array<string> names = [];
+
+  /**
+  The continuation token, which is used to page through large result sets.
+  To get the next page of results, set this parameter to the value of
+  `nextPageToken` from the previous response.
+  */
+  union { null, string } pageToken = null;  
+}
+
+/**
+This is the response from `POST /sequences/search` expressed as JSON.
+*/
+record GASearchSequencesResponse {
+  /** The list of matching sequences. */
+  array<GASequence> sequences = [];
+
+  /**
+  The continuation token, which is used to page through large result sets.
+  Provide this value in a subsequent request to return the next page of
+  results. This field will be empty if there aren't any additional results.
+  */
+  union { null, string } nextPageToken = null;
+}
+
+/**
+Gets a list of `GASequence` matching the search criteria.
+
+`POST /sequences/search` must accept a JSON version of
+`GASearchSequencesRequest` as the post body and will return a JSON
+version of `GASearchSequencesResponse`
+*/
+GASearchSequencesResponse searchSequences(
+    /**
+    This request maps to the body of `POST /sequences/search` as JSON.
+    */
+    GASearchSequencesRequest request) throws GAException;
+
+/****************  /sequences/{id}  *******************/
+/**
+Gets a `GASequence` by ID. `GET /sequences/{id}` will return a
+JSON version of `GASequence`.
+*/
+GASequence getSequence(
+    /**
+    The ID of the `GASequence`.
+    */
+    string id) throws GAException;
+
+/****************  /sequencefragments/search  *******************/
+/**
+This request maps to the body of `POST /sequencefragments/search`
+as JSON.
+*/
+record GASearchSequenceFragmentsRequest {
+  /** If present, the IDs of the sequences to search for. */
+  array<string> sequenceIds = [];
+
+  /**
+  The start position (0-based) of this query. Defaults to 0.
+  Genomic positions are non-negative integers less than reference length.
+  Requests spanning the join of circular genomes are represented as
+  two requests one on each side of the join (position 0).
+  */
+  long start = 0;
+
+  /**
+  The end position (0-based, exclusive) of this query. Defaults
+  to the length of this `GAReference`.
+  */
+  union { null, long } end = null;
+
+  /**
+  The continuation token, which is used to page through large result sets.
+  To get the next page of results, set this parameter to the value of
+  `nextPageToken` from the previous response.
+  */
+  union { null, string } pageToken = null;  
+}
+
+/**
+This is the response from `POST /sequencefragments/search` expressed as JSON.
+*/
+record GASearchSequenceFragmentsResponse {
+  /** The list of matching sequence fragments. */
+  array<GASequenceFragment> sequenceFragments = [];
+
+  /**
+  The continuation token, which is used to page through large result sets.
+  Provide this value in a subsequent request to return the next page of
+  results. This field will be empty if there aren't any additional results.
+  */
+  union { null, string } nextPageToken = null;
+}
+
+/**
+Gets a list of `GASequenceFragments` matching the search criteria.
+
+`POST /sequencefragments/search` must accept a JSON version of
+`GASearchSequenceFragmentsRequest` as the post body and will return a JSON
+version of `GASearchSequenceFragmentsResponse`
+*/
+GASearchSequenceFragmentsResponse searchSequenceFragments(
+    /**
+    This request maps to the body of `POST /sequencefragments/search` as JSON.
+    */
+    GASearchSequenceFragmentsRequest request) throws GAException;
+
+/****************  /sequencefragments/{id}  *******************/
+/**
+Gets a `GASequenceFragment` by ID. `GET /sequencefragments/{id}` will return a
+JSON version of `GASequenceFragment`.
+*/
+GASequenceFragment getSequenceFragment(
+    /**
+    The ID of the `GASequenceFragment`.
+    */
+    string id) throws GAException;
+
+}

src/main/resources/avro/sequences.avdl

@@ -0,0 +1,61 @@
+@namespace("org.ga4gh")
+
+protocol GASequences {
+
+/**
+A `GASequence` is a contiguous sequence of bases, which is made up by a
+set of `GASequenceFragments`. A `GASequence` could correspond to a
+reference contig, bases from a de novo assembly, etc.
+*/
+record GASequence {
+
+  /** The sequence ID. Unique within the repository. */
+  string id;
+
+  /** The name of the sequence. */
+  union { null, string } name = null;
+
+  /** A description of the sequence. */
+  union { null, string } description = null;
+
+  /**
+  The IDs of the data sources from which this sequence is generated. 
+  This can include IDs for any combination of the following (and more):
+
+  * A GAReadSet (if the sequence was de novo assembled from reads)
+  * A GAReference (if the sequence was taken from a reference assembly)
+  * A GAVariantSet (if variants were spliced in to a reference assembly)
+  */
+  array<string> sourceIds = [];
+
+  /**
+  The length of this sequence. Sequences are assumed to start at 0.
+  */
+  long length;
+}
+
+/**
+A `GASequenceFragment` represents a subsection of a sequence.
+*/
+record GASequenceFragment {
+
+  /** The ID of this sequence fragment. Unique within the repository. */
+  string id;
+
+  /**
+  The bases in this sequence. Bases are represented as IUPAC-IUB codes;
+  this string matches the regexp `[ACGTMRWSYKVHDBN]*`.
+  */
+  string bases;
+
+  /**
+  The start position of this fragment, within the sequence. The fragment's
+  end position will be `start + len(bases)`.
+  */
+  long start;
+
+  /** The ID of the sequence which contains this fragment. */
+  string sequenceId;
+}
+
+}