Mercurial > repos > iuc > hmmer_hmmalign
Help: internals.wireprotocolv2
Wire Protocol Version 2
**Experimental and under active development**
This section documents the wire protocol commands exposed to transports using the frame-based protocol. The set of commands exposed through these transports is distinct from the set of commands exposed to legacy transports.
The frame-based protocol uses CBOR to encode command execution requests. All command arguments must be mapped to a specific or set of CBOR data types.
The response to many commands is also CBOR. There is no common response format: each command defines its own response format.
TODOs
- Add "node namespace" support to each command. In order to support SHA-1 hash transition, we want servers to be able to expose different "node namespaces" for the same data. Every command operating on nodes should specify which "node namespace" it is operating on and responses should encode the "node namespace" accordingly.
Commands
The sections below detail all commands available to wire protocol version 2.
branchmap
Obtain heads in named branches.
Receives no arguments.
The response is a map with bytestring keys defining the branch name. Values are arrays of bytestring defining raw changeset nodes.
capabilities
Obtain the server's capabilities.
Receives no arguments.
This command is typically called only as part of the handshake during initial connection establishment.
The response is a map with bytestring keys defining server information.
The defined keys are:
- commands
- A map defining available wire protocol commands on this server.
Keys in the map are the names of commands that can be invoked. Values are maps defining information about that command. The bytestring keys are:
- args
- (map) Describes arguments accepted by the command.
Keys are bytestrings denoting the argument name.
Values are maps describing the argument. The map has the following bytestring keys:
- default
- (varied) The default value for this argument if not specified. Only present if "required" is not true.
- required
- (boolean) Whether the argument must be specified. Failure to send required arguments will result in an error executing the command.
- type
- (bytestring) The type of the argument. e.g. "bytes" or "bool".
- validvalues
- (set) Values that are recognized for this argument. Some arguments only allow a fixed set of values to be specified. These arguments may advertise that set in this key. If this set is advertised and a value not in this set is specified, the command should result in error.
- permissions
- An array of permissions required to execute this command.
- *
- (various) Individual commands may define extra keys that supplement generic command metadata. See the command definition for more.
- framingmediatypes
- An array of bytestrings defining the supported framing protocol media types. Servers will not accept media types not in this list.
- pathfilterprefixes
- (set of bytestring) Matcher prefixes that are recognized when performing path filtering. Specifying a path filter whose type/prefix does not match one in this set will likely be rejected by the server.
- rawrepoformats
- An array of storage formats the repository is using. This set of requirements can be used to determine whether a client can read a *raw* copy of file data available.
- redirect
- A map declaring potential *content redirects* that may be used by this server. Contains the following bytestring keys:
- targets
- (array of maps) Potential redirect targets. Values are maps describing this target in more detail. Each map has the following bytestring keys:
- name
- (bytestring) Identifier for this target. The identifier will be used by clients to uniquely identify this target.
- protocol
- (bytestring) High-level network protocol. Values can be "http", "'https", "ssh", etc.
- uris
- (array of bytestrings) Representative URIs for this target.
- snirequired (optional)
- (boolean) Indicates whether Server Name Indication is required to use this target. Defaults to False.
- tlsversions (optional)
- (array of bytestring) Indicates which TLS versions are supported by this target. Values are "1.1", "1.2", "1.3", etc.
- hashes
- (array of bytestring) Indicates support for hashing algorithms that are used to ensure content integrity. Values include "sha1", "sha256", etc.
changesetdata
Obtain various data related to changesets.
The command accepts the following arguments:
- revisions
- (array of maps) Specifies revisions whose data is being requested. Each value in the array is a map describing revisions. See the *Revisions Specifiers* section below for the format of this map.
Data will be sent for the union of all revisions resolved by all revision specifiers.
Only revision specifiers operating on changeset revisions are allowed.
- fields
- (set of bytestring) Which data associated with changelog revisions to fetch. The following values are recognized:
- bookmarks
- Bookmarks associated with a revision.
- parents
- Parent revisions.
- phase
- The phase state of a revision.
- revision
- The raw, revision data for the changelog entry. The hash of this data will match the revision's node value.
The response bytestream starts with a CBOR map describing the data that follows. This map has the following bytestring keys:
- totalitems
- (unsigned integer) Total number of changelog revisions whose data is being transferred. This maps to the set of revisions in the requested node range, not the total number of records that follow (see below for why).
Following the map header is a series of 0 or more CBOR values. If values are present, the first value will always be a map describing a single changeset revision.
If the "fieldsfollowing" key is present, the map will immediately be followed by N CBOR bytestring values, where N is the number of elements in "fieldsfollowing". Each bytestring value corresponds to a field denoted by "fieldsfollowing".
Following the optional bytestring field values is the next revision descriptor map, or end of stream.
Each revision descriptor map has the following bytestring keys:
- node
- (bytestring) The node value for this revision. This is the SHA-1 hash of the raw revision data.
- bookmarks (optional)
- (array of bytestrings) Bookmarks attached to this revision. Only present if "bookmarks" data is being requested and the revision has bookmarks attached.
- fieldsfollowing (optional)
- (array of 2-array) Denotes what fields immediately follow this map. Each value is an array with 2 elements: the bytestring field name and an unsigned integer describing the length of the data, in bytes.
If this key isn't present, no special fields will follow this map.
The following fields may be present:
- revision
- Raw, revision data for the changelog entry. Contains a serialized form of the changeset data, including the author, date, commit message, set of changed files, manifest node, and other metadata.
Only present if the "revision" field was requested.
- parents (optional)
- (array of bytestrings) The nodes representing the parent revisions of this revision. Only present if "parents" data is being requested.
- phase (optional)
- (bytestring) The phase that a revision is in. Recognized values are "secret", "draft", and "public". Only present if "phase" data is being requested.
The set of changeset revisions emitted may not match the exact set of changesets requested. Furthermore, the set of keys present on each map may vary. This is to facilitate emitting changeset updates as well as new revisions.
For example, if the request wants "phase" and "revision" data, the response may contain entries for each changeset in the common nodes set with the "phase" key and without the "revision" key in order to reflect a phase-only update.
TODO support different revision selection mechanisms (e.g. non-public, specific revisions) TODO support different hash "namespaces" for revisions (e.g. sha-1 versus other) TODO support emitting obsolescence data TODO support filtering based on relevant paths (narrow clone) TODO support hgtagsfnodes cache / tags data TODO support branch heads cache TODO consider unify query mechanism. e.g. as an array of "query descriptors" rather than a set of top-level arguments that have semantics when combined.
filedata
Obtain various data related to an individual tracked file.
The command accepts the following arguments:
- fields
- (set of bytestring) Which data associated with a file to fetch. The following values are recognized:
- linknode
- The changeset node introducing this revision.
- parents
- Parent nodes for the revision.
- revision
- The raw revision data for a file.
- haveparents
- (bool) Whether the client has the parent revisions of all requested nodes. If set, the server may emit revision data as deltas against any parent revision. If not set, the server MUST only emit deltas for revisions previously emitted by this command.
False is assumed in the absence of any value.
- nodes
- (array of bytestrings) File nodes whose data to retrieve.
- path
- (bytestring) Path of the tracked file whose data to retrieve.
TODO allow specifying revisions via alternate means (such as from changeset revisions or ranges)
The response bytestream starts with a CBOR map describing the data that follows. It has the following bytestream keys:
- totalitems
- (unsigned integer) Total number of file revisions whose data is being returned.
Following the map header is a series of 0 or more CBOR values. If values are present, the first value will always be a map describing a single changeset revision.
If the "fieldsfollowing" key is present, the map will immediately be followed by N CBOR bytestring values, where N is the number of elements in "fieldsfollowing". Each bytestring value corresponds to a field denoted by "fieldsfollowing".
Following the optional bytestring field values is the next revision descriptor map, or end of stream.
Each revision descriptor map has the following bytestring keys:
Each map has the following bytestring keys:
- node
- (bytestring) The node of the file revision whose data is represented.
- deltabasenode
- (bytestring) Node of the file revision the following delta is against.
Only present if the "revision" field is requested and delta data follows this map.
- fieldsfollowing
- (array of 2-array) Denotes extra bytestring fields that following this map. See the documentation for "changesetdata" for semantics.
The following named fields may be present:
- "delta"
- The delta data to use to construct the fulltext revision.
Only present if the "revision" field is requested and a delta is being emitted. The "deltabasenode" top-level key will also be present if this field is being emitted.
- "revision"
- The fulltext revision data for this manifest. Only present if the "revision" field is requested and a fulltext revision is being emitted.
- parents
- (array of bytestring) The nodes of the parents of this file revision.
Only present if the "parents" field is requested.
When "revision" data is requested, the server chooses to emit either fulltext revision data or a delta. What the server decides can be inferred by looking for the presence of the "delta" or "revision" keys in the "fieldsfollowing" array.
filesdata
Obtain various data related to multiple tracked files for specific changesets.
This command is similar to "filedata" with the main difference being that individual requests operate on multiple file paths. This allows clients to request data for multiple paths by issuing a single command.
The command accepts the following arguments:
- fields
- (set of bytestring) Which data associated with a file to fetch. The following values are recognized:
- linknode
- The changeset node introducing this revision.
- parents
- Parent nodes for the revision.
- revision
- The raw revision data for a file.
- haveparents
- (bool) Whether the client has the parent revisions of all requested nodes.
- pathfilter
- (map) Defines a filter that determines what file paths are relevant.
See the *Path Filters* section for more.
If the argument is omitted, it is assumed that all paths are relevant.
- revisions
- (array of maps) Specifies revisions whose data is being requested. Each value in the array is a map describing revisions. See the *Revisions Specifiers* section below for the format of this map.
Data will be sent for the union of all revisions resolved by all revision specifiers.
Only revision specifiers operating on changeset revisions are allowed.
The response bytestream starts with a CBOR map describing the data that follows. This map has the following bytestring keys:
- totalpaths
- (unsigned integer) Total number of paths whose data is being transferred.
- totalitems
- (unsigned integer) Total number of file revisions whose data is being transferred.
Following the map header are 0 or more sequences of CBOR values. Each sequence represents data for a specific tracked path. Each sequence begins with a CBOR map describing the file data that follows. Following that map is N CBOR values describing file revision data. The format of this data is identical to that returned by the "filedata" command.
Each sequence's map header has the following bytestring keys:
- path
- (bytestring) The tracked file path whose data follows.
- totalitems
- (unsigned integer) Total number of file revisions whose data is being transferred.
The "haveparents" argument has significant implications on the data transferred.
When "haveparents" is true, the command MAY only emit data for file revisions introduced by the set of changeset revisions whose data is being requested. In other words, the command may assume that all file revisions for all relevant paths for ancestors of the requested changeset revisions are present on the receiver.
When "haveparents" is false, the command MUST assume that the receiver has no file revisions data. This means that all referenced file revisions in the queried set of changeset revisions will be sent.
TODO we want a more complicated mechanism for the client to specify which ancestor revisions are known. This is needed so intelligent deltas can be emitted and so updated linknodes can be sent if the client needs to adjust its linknodes for existing file nodes to older changeset revisions. TODO we may want to make linknodes an array so multiple changesets can be marked as introducing a file revision, since this can occur with e.g. hidden changesets.
heads
Obtain DAG heads in the repository.
The command accepts the following arguments:
- publiconly (optional)
- (boolean) If set, operate on the DAG for public phase changesets only. Non-public (i.e. draft) phase DAG heads will not be returned.
The response is a CBOR array of bytestrings defining changeset nodes of DAG heads. The array can be empty if the repository is empty or no changesets satisfied the request.
TODO consider exposing phase of heads in response
known
Determine whether a series of changeset nodes is known to the server.
The command accepts the following arguments:
- nodes
- (array of bytestrings) List of changeset nodes whose presence to query.
The response is a bytestring where each byte contains a 0 or 1 for the corresponding requested node at the same index.
TODO use a bit array for even more compact response
listkeys
List values in a specified "pushkey" namespace.
The command receives the following arguments:
- namespace
- (bytestring) Pushkey namespace to query.
The response is a map with bytestring keys and values.
TODO consider using binary to represent nodes in certain pushkey namespaces.
lookup
Try to resolve a value to a changeset revision.
Unlike "known" which operates on changeset nodes, lookup operates on node fragments and other names that a user may use.
The command receives the following arguments:
- key
- (bytestring) Value to try to resolve.
On success, returns a bytestring containing the resolved node.
manifestdata
Obtain various data related to manifests (which are lists of files in a revision).
The command accepts the following arguments:
- fields
- (set of bytestring) Which data associated with manifests to fetch. The following values are recognized:
- parents
- Parent nodes for the manifest.
- revision
- The raw revision data for the manifest.
- haveparents
- (bool) Whether the client has the parent revisions of all requested nodes. If set, the server may emit revision data as deltas against any parent revision. If not set, the server MUST only emit deltas for revisions previously emitted by this command.
False is assumed in the absence of any value.
- nodes
- (array of bytestring) Manifest nodes whose data to retrieve.
- tree
- (bytestring) Path to manifest to retrieve. The empty bytestring represents the root manifest. All other values represent directories/trees within the repository.
TODO allow specifying revisions via alternate means (such as from changeset revisions or ranges) TODO consider recursive expansion of manifests (with path filtering for narrow use cases)
The response bytestream starts with a CBOR map describing the data that follows. It has the following bytestring keys:
- totalitems
- (unsigned integer) Total number of manifest revisions whose data is being returned.
Following the map header is a series of 0 or more CBOR values. If values are present, the first value will always be a map describing a single manifest revision.
If the "fieldsfollowing" key is present, the map will immediately be followed by N CBOR bytestring values, where N is the number of elements in "fieldsfollowing". Each bytestring value corresponds to a field denoted by "fieldsfollowing".
Following the optional bytestring field values is the next revision descriptor map, or end of stream.
Each revision descriptor map has the following bytestring keys:
- node
- (bytestring) The node of the manifest revision whose data is represented.
- deltabasenode
- (bytestring) The node that the delta representation of this revision is computed against. Only present if the "revision" field is requested and a delta is being emitted.
- fieldsfollowing
- (array of 2-array) Denotes extra bytestring fields that following this map. See the documentation for "changesetdata" for semantics.
The following named fields may be present:
- "delta"
- The delta data to use to construct the fulltext revision.
Only present if the "revision" field is requested and a delta is being emitted. The "deltabasenode" top-level key will also be present if this field is being emitted.
- "revision"
- The fulltext revision data for this manifest. Only present if the "revision" field is requested and a fulltext revision is being emitted.
- parents
- (array of bytestring) The nodes of the parents of this manifest revision. Only present if the "parents" field is requested.
When "revision" data is requested, the server chooses to emit either fulltext revision data or a delta. What the server decides can be inferred by looking for the presence of "delta" or "revision" in the "fieldsfollowing" array.
Servers MAY advertise the following extra fields in the capabilities descriptor for this command:
- recommendedbatchsize
- (unsigned integer) Number of revisions the server recommends as a batch query size. If defined, clients needing to issue multiple "manifestdata" commands to obtain needed data SHOULD construct their commands to have this many revisions per request.
pushkey
Set a value using the "pushkey" protocol.
The command receives the following arguments:
- namespace
- (bytestring) Pushkey namespace to operate on.
- key
- (bytestring) The pushkey key to set.
- old
- (bytestring) Old value for this key.
- new
- (bytestring) New value for this key.
TODO consider using binary to represent nodes is certain pushkey namespaces. TODO better define response type and meaning.
rawstorefiledata
Allows retrieving raw files used to store repository data.
The command accepts the following arguments:
- files
- (array of bytestring) Describes the files that should be retrieved.
The meaning of values in this array is dependent on the storage backend used by the server.
The response bytestream starts with a CBOR map describing the data that follows. This map has the following bytestring keys:
- filecount
- (unsigned integer) Total number of files whose data is being transferred.
- totalsize
- (unsigned integer) Total size in bytes of files data that will be transferred. This is file on-disk size and not wire size.
Following the map header are N file segments. Each file segment consists of a CBOR map followed by an indefinite length bytestring. Each map has the following bytestring keys:
- location
- (bytestring) Denotes the location in the repository where the file should be written. Values map to vfs instances to use for the writing.
- path
- (bytestring) Path of file being transferred. Path is the raw store path and can be any sequence of bytes that can be tracked in a Mercurial manifest.
- size
- (unsigned integer) Size of file data. This will be the final written file size. The total size of the data that follows the CBOR map will be greater due to encoding overhead of CBOR.
TODO this command is woefully incomplete. If we are to move forward with a stream clone analog, it needs a lot more metadata around how to describe what files are available to retrieve, other semantics.
Revision Specifiers
A *revision specifier* is a map that evaluates to a set of revisions.
A *revision specifier* has a "type" key that defines the revision selection type to perform. Other keys in the map are used in a type-specific manner.
The following types are defined:
- changesetexplicit
- An explicit set of enumerated changeset revisions.
The "nodes" key MUST contain an array of full binary nodes, expressed as bytestrings.
- changesetexplicitdepth
- Like "changesetexplicit", but contains a "depth" key defining the unsigned integer number of ancestor revisions to also resolve. For each value in "nodes", DAG ancestors will be walked until up to N total revisions from that ancestry walk are present in the final resolved set.
- changesetdagrange
- Defines revisions via a DAG range of changesets on the changelog.
The "roots" key MUST contain an array of full, binary node values representing the *root* revisions.
The "heads" key MUST contain an array of full, binary nodes values representing the *head* revisions.
The DAG range between "roots" and "heads" will be resolved and all revisions between will be used. Nodes in "roots" are not part of the resolved set. Nodes in "heads" are. The "roots" array may be empty. The "heads" array MUST be defined.
Path Filters
Various commands accept a *path filter* argument that defines the set of file paths relevant to the request.
A *path filter* is defined as a map with the bytestring keys "include" and "exclude". Each is an array of bytestring values. Each value defines a pattern rule (see 'hg help patterns') that is used to match file paths.
A path matches the path filter if it is matched by a rule in the "include" set but doesn't match a rule in the "exclude" set. In other words, a path matcher takes the union of all "include" patterns and then substracts the union of all "exclude" patterns.
Patterns MUST be prefixed with their pattern type. Only the following pattern types are allowed: "path:", "rootfilesin:".
If the "include" key is omitted, it is assumed that all paths are relevant. The patterns from "exclude" will still be used, if defined.
An example value is "path:tests/foo", which would match a file named "tests/foo" or a directory "tests/foo" and all files under it.