Mercurial > repos > q2d2 > qiime2__vsearch__cluster_features_open_reference
Help: internals.revlogs
Revision Logs
Revision logs - or *revlogs* - are an append only data structure for storing discrete entries, or *revisions*. They are the primary storage mechanism of repository data.
Revlogs effectively model a directed acyclic graph (DAG). Each node has edges to 1 or 2 *parent* nodes. Each node contains metadata and the raw value for that node.
Revlogs consist of entries which have metadata and revision data. Metadata includes the hash of the revision's content, sizes, and links to its *parent* entries. The collective metadata is referred to as the *index* and the revision data is the *data*.
Revision data is stored as a series of compressed deltas against ancestor revisions.
Revlogs are written in an append-only fashion. We never need to rewrite a file to insert nor do we need to remove data. Rolling back in-progress writes can be performed by truncating files. Read locks can be avoided using simple techniques. This means that references to other data in the same revlog *always* refer to a previous entry.
Revlogs can be modeled as 0-indexed arrays. The first revision is revision #0 and the second is revision #1. The revision -1 is typically used to mean *does not exist* or *not defined*.
File Format
A revlog begins with a 32-bit big endian integer holding version info and feature flags. This integer overlaps with the first four bytes of the first revision entry.
This integer is logically divided into 2 16-bit shorts. The least significant half of the integer is the format/version short. The other short holds feature flags that dictate behavior of the revlog.
The following values for the format/version short are defined:
- 0
- The original revlog version.
- 1
- RevlogNG (*next generation*). It replaced version 0 when it was implemented in 2006.
- 2
- In-development version incorporating accumulated knowledge and missing features from 10+ years of revlog version 1.
- 57005 (0xdead)
- Reserved for internal testing of new versions. No defined format beyond 32-bit header.
The feature flags short consists of bit flags. Where 0 is the least significant bit. The bit flags vary by revlog version.
Version 0 revlogs have no defined flags and the presence of a flag is considered an error.
Version 1 revlogs have the following flags at the specified bit offsets:
- 0
- Store revision data inline.
- 1
- Generaldelta encoding.
Version 2 revlogs have the following flags at the specified bit offsets:
- 0
- Store revision data inline.
The following header values are common:
- 00 00 00 01
- v1
- 00 01 00 01
- v1 + inline
- 00 02 00 01
- v1 + generaldelta
- 00 03 00 01
- v1 + inline + generaldelta
Following the 32-bit header is the remaining 60 bytes of the first index entry. Following that are additional *index* entries. Inlined revision data is possibly located between index entries. More on this inlined layout is described below.
Version 1 Format
Version 1 (RevlogNG) begins with an index describing the revisions in the revlog. If the "inline" flag is set, revision data is stored inline, or between index entries (as opposed to in a separate container).
Each index entry is 64 bytes. The byte layout of each entry is as follows, with byte 0 being the first byte (all data stored as big endian):
- 0-3 (4 bytes) (rev 0 only)
- Revlog header
- 0-5 (6 bytes)
- Absolute offset of revision data from beginning of revlog.
- 6-7 (2 bytes)
- Bit flags impacting revision behavior. The following bit offsets define:
0: REVIDX_ISCENSORED revision has censor metadata, must be verified.
1: REVIDX_ELLIPSIS revision hash does not match its data. Used by narrowhg
2: REVIDX_EXTSTORED revision data is stored externally.
- 8-11 (4 bytes)
- Compressed length of revision data / chunk as stored in revlog.
- 12-15 (4 bytes)
- Uncompressed length of revision data. This is the size of the full revision data, not the size of the chunk post decompression.
- 16-19 (4 bytes)
- Base or previous revision this revision's delta was produced against. This revision holds full text (as opposed to a delta) if it points to itself. For generaldelta repos, this is the previous revision in the delta chain. For non-generaldelta repos, this is the base or first revision in the delta chain.
- 20-23 (4 bytes)
- A revision this revision is *linked* to. This allows a revision in one revlog to be forever associated with a revision in another revlog. For example, a file's revlog may point to the changelog revision that introduced it.
- 24-27 (4 bytes)
- Revision of 1st parent. -1 indicates no parent.
- 28-31 (4 bytes)
- Revision of 2nd parent. -1 indicates no 2nd parent.
- 32-63 (32 bytes)
- Hash of revision's full text. Currently, SHA-1 is used and only the first 20 bytes of this field are used. The rest of the bytes are ignored and should be stored as \0.
If inline revision data is being stored, the compressed revision data (of length from bytes offset 8-11 from the index entry) immediately follows the index entry. There is no header on the revision data. There is no padding between it and the index entries before and after.
If revision data is not inline, then raw revision data is stored in a separate byte container. The offsets from bytes 0-5 and the compressed length from bytes 8-11 define how to access this data.
The 6 byte absolute offset field from the first revlog entry overlaps with the revlog header. That is, the first 6 bytes of the first revlog entry can be split into four bytes containing the header for the revlog file and an additional two bytes containing the offset for the first entry. Since this is the offset from the beginning of the file for the first revision entry, the two bytes will always be set to zero.
Version 2 Format
(In development. Format not finalized or stable.)
Version 2 is identical to version 1 with the following differences.
There is no dedicated *generaldelta* revlog format flag. Instead, the feature is implied enabled by default.
Delta Chains
Revision data is encoded as a chain of *chunks*. Each chain begins with the compressed original full text for that revision. Each subsequent *chunk* is a *delta* against the previous revision. We therefore call these chains of chunks/deltas *delta chains*.
The full text for a revision is reconstructed by loading the original full text for the base revision of a *delta chain* and then applying *deltas* until the target revision is reconstructed.
*Delta chains* are limited in length so lookup time is bound. They are limited to ~2x the length of the revision's data. The linear distance between the base chunk and the final chunk is also limited so the amount of read I/O to load all chunks in the delta chain is bound.
Deltas and delta chains are either computed against the previous revision in the revlog or another revision (almost certainly one of the parents of the revision). Historically, deltas were computed against the previous revision. The *generaldelta* revlog feature flag (enabled by default in Mercurial 3.7) activates the mode where deltas are computed against an arbitrary revision (almost certainly a parent revision).
File Storage
Revlogs logically consist of an index (metadata of entries) and revision data. This data may be stored together in a single file or in separate files. The mechanism used is indicated by the "inline" feature flag on the revlog.
Mercurial's behavior is to use inline storage until a revlog reaches a certain size, at which point it will be converted to non-inline. The reason there is a size limit on inline storage is to establish an upper bound on how much data must be read to load the index. It would be a waste to read tens or hundreds of extra megabytes of data just to access the index data.
The actual layout of revlog files on disk is governed by the repository's *store format*. Typically, a ".i" file represents the index revlog (possibly containing inline data) and a ".d" file holds the revision data.
Revision Entries
Revision entries consist of an optional 1 byte header followed by an encoding of the revision data. The headers are as follows:
- \0 (0x00)
- Revision data is the entirety of the entry, including this header.
- ( (0x28)
- zstd https://github.com/facebook/zstd
- u (0x75)
- Raw revision data follows.
- x (0x78)
- zlib (RFC 1950) data.
The 0x78 value is actually the first byte of the zlib header (CMF byte).
Hash Computation
The hash of the revision is stored in the index and is used both as a primary key and for data integrity verification.
Currently, SHA-1 is the only supported hashing algorithm. To obtain the SHA-1 hash of a revision:
- Hash the parent nodes
- Hash the fulltext of the revision
The 20 byte node ids of the parents are fed into the hasher in ascending order.
Changed Files side-data
(This feature is in active development and its behavior is not frozen yet. It should not be used in any production repository)
When the 'exp-copies-sidedata-changeset' requirement is in use, information related to the changed files will be stored as "side-data" for every changeset in the changelog.
These data contains the following information:
- set of files actively added by the changeset
- set of files actively removed by the changeset
- set of files actively merged by the changeset
- set of files actively touched by he changeset
- mapping of copy-source, copy-destination from first parent (p1)
- mapping of copy-source, copy-destination from second parent (p2)
The block itself is big-endian data, formatted in three sections: header, index, and data. See below for details:
Header:
4 bytes: unsigned integer
total number of entry in the index
Index:
The index contains an entry for every involved filename. It is sorted by filename. The entry use the following format:
1 byte: bits field
This byte hold two different bit fields:
The 2 lower bits carry copy information:
'00': file has not copy information, '10': file is copied from a p1 source, '11': file is copied from a p2 source.
The 3 next bits carry action information.
'000': file was untouched, it exist in the index as copy source, '001': file was actively added '010': file was actively merged '011': file was actively removed '100': reserved for future use '101': file was actively touched in any other way
(The last 2 bites are unused)
4 bytes: unsigned integer
Address (in bytes) of the end of the associated filename in the data block. (This is the address of the first byte not part of the filename)
The start of the filename can be retrieve by reading that field for the previous index entry. The filename of the first entry starts at zero.
4 bytes: unsigned integer
Index (in this very index) of the source of the copy (when a copy is happening). If no copy is happening the value of this field is irrelevant and could have any value. It is set to zero by convention
Data:
raw bytes block containing all filename concatenated without any separator.