Modification in support of eventual Zarr support. #1259
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This is a set of changes to the way that URLs are handled as paths. This is in support of eventual Zarr support. The primary difference is to extract io handler information from the url. This will be used inside dispatchers that support multiple IO access methods (like file versus Zarr) to figure out what internal IO handler to use. Specific changes: 1. move url analyzer code from dfile.c to durlmodel.c 2. add code to walk the .daprc triples 3. NC_HDF5_finalize was not being properly called by nc_finalize(). 4. Fix minor bug in ncgen3.l 5. fix memory leak in nc4info.c 6. replace protocol= fragment tag with a more general mode= tag.
|
I am temporarily closing this until I can make further improvements. |
This PR has two purposes: 1. Try to centralize all the code that infers the dispatcher from various available pieces of information in the path, the mode flags, and in the dataset itself. 2. Modify URL handling in support of using S3 URLS for S3 reading and for Zarr. The goal is to make specific IO handling tags accessible inside dispatchers that support multiple IO access methods (like file versus Zarr) to figure out what internal IO handler to use. The primary code change is to create a new set of files libdispatch/dinfermodel.c and include/ncinfermodel.c to centralize the dispatcher inference code. Aside: the whole dispatcher inference mechanism needs serious fixing: it is way too ad hoc. Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag.
|
Re-opening with the changes as described in revised description |
|
Closing again permanently in favor of a later TBD pull request. |
|
@DennisHeimbigner I noticed this go by on my twitter feed, it may be of interest: "Earlier today, @rabernat gave a punchy little talk on his vision #zarr and #netcdf for cloud storage of geoscientific data." |
DennisHeimbigner
added a commit
that referenced
this pull request
Jan 2, 2019
re: issue #1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR #1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Modification in support of eventual Zarr support.
[Revised PR Description]
This PR has two purposes:
from various available pieces of information in the path,
the mode flags, and in the dataset itself.
reading and for Zarr. The goal is to make specific IO
handling tags accessible inside dispatchers that support
multiple IO access methods (like file versus Zarr) to figure
out what internal IO handler to use.
The primary code change is to create a new set of files
libdispatch/dinfermodel.c and include/ncinfermodel.c
to centralize the dispatcher inference code.
Aside: the whole dispatcher inference mechanism needs serious fixing:
it is way too ad hoc.
Other changes:
fragment tag with a more general mode= tag.