psg_client.hpp File Reference

#include <corelib/ncbimisc.hpp>
#include <corelib/ncbitime.hpp>
#include <corelib/ncbi_url.hpp>
#include <corelib/request_ctx.hpp>
#include <connect/services/json_over_uttp.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqsplit/ID2S_Seq_annot_Info.hpp>
#include <optional>
#include <unordered_map>

Include dependency graph for psg_client.hpp:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes
class	CPSG_Exception
struct	SPSG_UserArgs
	Arbitrary request URL arguments. More...
class	CPSG_Request
	Request to the PSG server (see "CPSG_Request_*" below) More...
class	CPSG_BioId
	Bio-id (such as accession) More...
class	CPSG_DataId
	Blob data unique ID. More...
class	CPSG_BlobId
	Blob unique ID. More...
class	CPSG_ChunkId
	Chunk unique ID. More...
class	CPSG_Request_Biodata
	Request to the PSG server (by bio-id, for a biodata specific info and data) More...
class	CPSG_Request_Resolve
	Request to the PSG server (by bio-id, for a biodata specific info and data) More...
class	CPSG_Request_Blob
	Request to the PSG server (by blob-id, for a particular blob of data) More...
class	CPSG_Request_NamedAnnotInfo
	Request meta-information for the named annotations which are defined on the bioseq. More...
class	CPSG_Request_Chunk
	Request blob data chunk. More...
class	CPSG_Request_IpgResolve
	Request IPG resolve. More...
struct	SPSG_Message
class	CPSG_ReplyItem
	A self-containing part of the reply, e.g. a meta-data or a data blob. More...
class	CPSG_BlobData
	Blob data. More...
class	CPSG_BlobInfo
	Blob data meta information. More...
class	CPSG_SkippedBlob
	Skipped blob. More...
class	CPSG_BioseqInfo
	Bio-sequence metainfo – result of the bio-id resolution. More...
class	CPSG_NamedAnnotInfo
	Named Annotations (NAs) metainfo – reply to CPSG_Request_NamedAnnotInfo. More...
class	CPSG_NamedAnnotStatus
	Named Annotations (NAs) status – reply to CPSG_Request_NamedAnnotInfo. More...
class	CPSG_PublicComment
	Public comment. More...
class	CPSG_Processor
	Processor event. More...
class	CPSG_IpgInfo
	Ipg info – result of the IPG resolution. More...
class	CPSG_Reply
	PSG reply – corresponds to a PSG request. More...
class	CPSG_Queue
	A queue to retrieve data (accession resolution info; bio-sequence; annotation blobs) from the storage. More...
class	CPSG_EventLoop
	A class derived from the queue class that additionally allows to run event loop. More...

Macros
#define	HAVE_PSG_CLIENT   1

Typedefs
using	CPSG_BioIds = vector< CPSG_BioId >

Enumerations
enum class	EPSG_AccSubstitution { Default , Limited , Never }
	Whether and how to substitute version-less primary seq-ids with the "more unique" secondary seq-ids. More...
enum class	EPSG_BioIdResolution { Resolve , NoResolve }
	Whether to try to resolve provided seq-ids before use. More...
enum class	EPSG_Status {   eSuccess , eInProgress , eNotFound , eCanceled ,   eForbidden , eError }
	Retrieval result. More...

Functions
	DECLARE_SAFE_FLAGS (CPSG_Request::EFlags)
	DECLARE_SAFE_FLAGS (CPSG_Request_Resolve::EIncludeInfo)

Macro Definition Documentation

HAVE_PSG_CLIENT

#define HAVE_PSG_CLIENT   1

Definition at line 50 of file psg_client.hpp.

Typedef Documentation

CPSG_BioIds

using CPSG_BioIds = vector<CPSG_BioId>

Definition at line 206 of file psg_client.hpp.

Enumeration Type Documentation

EPSG_AccSubstitution

enum EPSG_AccSubstitution

strong

Whether and how to substitute version-less primary seq-ids with the "more unique" secondary seq-ids.

Enumerator
Default	Substitute always (default)
Limited	Substitute only if the resolved record's seq_id_type is GI(12)
Never	No substitution whatsoever - return exact raw accession info.

Definition at line 290 of file psg_client.hpp.

EPSG_BioIdResolution

enum EPSG_BioIdResolution

strong

Whether to try to resolve provided seq-ids before use.

Enumerator
Resolve	Try to resolve provided seq-ids.
NoResolve	Use provided seq-ids as is.

Definition at line 299 of file psg_client.hpp.

EPSG_Status

enum EPSG_Status

strong

Retrieval result.

See also

GetStatus

Enumerator
eSuccess	Successfully retrieved.
eInProgress	Retrieval is not finalized yet, more info may come.
eNotFound	Not found.
eCanceled	Request canceled.
eForbidden	User is not authorized for the retrieval.
eError	An error was encountered while trying to send request or to read and to process the reply. If PSG server sends a message with severity: Error, Critical or Fatal – this status will be set, and any data data in the reply item must be considered invalid; such messages will also be logged by the client API with severity Error. Trace, Info or Warning – are considered to be informational, so these do NOT affect the status; such messages however will still be logged by the client API with the same (T, I or W) severity.

Definition at line 626 of file psg_client.hpp.

Function Documentation

DECLARE_SAFE_FLAGS() [1/2]

DECLARE_SAFE_FLAGS

(

CPSG_Request::EFlags

)

DECLARE_SAFE_FLAGS() [2/2]

DECLARE_SAFE_FLAGS

(

CPSG_Request_Resolve::EIncludeInfo

)