NCBI C++ ToolKit
Classes | Macros | Typedefs | Enumerations | Functions
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>
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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  )
Modified on Sun Mar 03 03:17:07 2024 by modify_doxy.py rev. 669887