OpenTreeOfLife/phylesystem-api issues and pull requests

#100 - Improved error messages, waiver/license changes to match opentree

Pull Request - State: closed - Opened by jimallman over 10 years ago

#99 - RESTful API methods sometimes return cryptic errors

Issue - State: closed - Opened by jimallman over 10 years ago - 2 comments

#98 - Two minor fixes for production (Bos)

Pull Request - State: closed - Opened by jimallman over 10 years ago - 1 comment

#97 - Restore simple functionality of RESTful study creation and updates

Issue - State: open - Opened by jimallman over 10 years ago - 1 comment
Labels: bug

#96 - Lag time between "local" and GitHub phylesystem repos is very confusing

Issue - State: open - Opened by jimallman over 10 years ago - 7 comments
Labels: question

#95 - working dir will appear to be way ahead of GitHub until we start pulling.

Issue - State: open - Opened by mtholder over 10 years ago

#94 - Master fixing v1

Pull Request - State: closed - Opened by mtholder over 10 years ago

#93 - study aliasing confusion

Issue - State: closed - Opened by mtholder over 10 years ago - 1 comment

#92 - Treesource

Pull Request - State: closed - Opened by mtholder over 10 years ago

#91 - Tweak URLs for repo to match current name

Pull Request - State: closed - Opened by jar398 over 10 years ago

#90 - Could not connect to Redis at 127.0.0.1:6379: Connection refused

Issue - State: open - Opened by jar398 over 10 years ago

#89 - oti nudge not getting new studies

Issue - State: open - Opened by mtholder over 10 years ago - 3 comments

#88 - Match UI in same-named branch

Pull Request - State: closed - Opened by jimallman over 10 years ago

#87 - need to change the name of this repo

Issue - State: closed - Opened by mtholder over 10 years ago - 2 comments

#86 - need to pass all NeXML inputs through the TreeBase NeXML processor

Issue - State: closed - Opened by mtholder over 10 years ago - 2 comments

#85 - need to allow POST with new ID

Issue - State: closed - Opened by mtholder over 10 years ago - 1 comment

#84 - Modified study creation

Pull Request - State: closed - Opened by jimallman over 10 years ago

#83 - Get version history (also includes celery and webhooks)

Pull Request - State: closed - Opened by jimallman over 10 years ago

#82 - External urls

Pull Request - State: closed - Opened by mtholder over 10 years ago

#81 - clean up phylesystem repos to deal with stricter NexSON validation

Issue - State: closed - Opened by mtholder over 10 years ago

#80 - install redis on deployment

Issue - State: closed - Opened by mtholder over 10 years ago - 2 comments
Labels: wontfix

#79 - Adding study removal (and mini-documentation) to oti webhook

Pull Request - State: closed - Opened by jimallman over 10 years ago

#78 - Add prompt for managing GitHub webhooks.

Pull Request - State: closed - Opened by jimallman over 10 years ago

#77 - Code cleanup and comments

Pull Request - State: closed - Opened by jimallman over 10 years ago

#76 - Fixes for oti nudge, added OPENTREE_DOCSTORE_URL on config file

Pull Request - State: closed - Opened by jimallman over 10 years ago

#75 - More diagnostics to web2py console.

Pull Request - State: closed - Opened by jimallman over 10 years ago

#74 - typo

Pull Request - State: closed - Opened by jimallman over 10 years ago

#73 - Isolate study IDs in GitHub payload (after push)

Pull Request - State: closed - Opened by jimallman over 10 years ago

#72 - list WIPs on GET

Issue - State: closed - Opened by mtholder over 10 years ago - 1 comment

#71 - Initial test of GitHub webhook

Pull Request - State: closed - Opened by jimallman over 10 years ago

#70 - Skip non-standard license metatag (no '@property')

Pull Request - State: closed - Opened by jimallman over 10 years ago

#69 - Simplify CC-0 license as a single metatag.

Pull Request - State: closed - Opened by jimallman over 10 years ago - 1 comment

#68 - Record CC-0 license in NexSON as pseudo-RDF/XML

Pull Request - State: closed - Opened by jimallman over 10 years ago - 6 comments

#67 - Unicode handling and create from reference string.

Pull Request - State: closed - Opened by jimallman over 10 years ago

#66 - Read incoming DOI and find matching study metadata

Pull Request - State: closed - Opened by jimallman over 10 years ago

#65 - Populate new study NexSON

Pull Request - State: closed - Opened by jimallman over 10 years ago

#64 - SHA bookkeeepping

Pull Request - State: closed - Opened by jimallman over 10 years ago - 3 comments

#63 - AttributeError: 'GitData' object has no attribute 'return_study'

Issue - State: closed - Opened by jimallman over 10 years ago - 14 comments

#62 - Pga

Pull Request - State: closed - Opened by snacktavish over 10 years ago

#61 - Finalize IDs of ad-hoc rooting elements when PUTting a study

Issue - State: open - Opened by jimallman over 10 years ago - 16 comments
Labels: enhancement

#60 - Merging Nexson translation and validation

Pull Request - State: closed - Opened by jimallman over 10 years ago

#59 - GET operation should return a version identifier

Issue - State: closed - Opened by mtholder over 10 years ago - 1 comment

#58 - Write operations should take a SHA argument that identifies their parent

Issue - State: closed - Opened by mtholder over 10 years ago - 1 comment
Labels: bug

#57 - local mirror of master on deployment machine

Issue - State: closed - Opened by mtholder over 10 years ago - 8 comments
Labels: nice commentary

#56 - Getting a study happens on the current branch (not chosen)

Issue - State: closed - Opened by jimallman over 10 years ago - 4 comments
Labels: bug

#55 - minimize time that repo-level lock is held

Issue - State: closed - Opened by mtholder over 10 years ago - 1 comment
Labels: enhancement

#54 - avoid os.chdir in git operations

Issue - State: closed - Opened by mtholder over 10 years ago - 2 comments
Labels: enhancement

#53 - support for multiple repos

Issue - State: closed - Opened by mtholder over 10 years ago - 2 comments
Labels: enhancement

#52 - modified study on the wrong WIP

Issue - State: closed - Opened by mtholder over 10 years ago - 2 comments
Labels: bug

#51 - default controller do_commit does pull, commit, and push

Issue - State: closed - Opened by mtholder almost 11 years ago - 2 comments
Labels: enhancement

#50 - refactored to add __finish_write_verb to reduce code duplication. Added ...

Pull Request - State: closed - Opened by mtholder almost 11 years ago

#49 - Logging module

Pull Request - State: closed - Opened by mtholder almost 11 years ago

#48 - Prepare for using oti search from a different server

Issue - State: closed - Opened by jimallman almost 11 years ago - 2 comments

#47 - Some thoughts on the OTL API

Issue - State: open - Opened by sckott almost 11 years ago - 7 comments
Labels: nice commentary

#46 - Support pure JSON or text requests in PUT (update) method

Issue - State: closed - Opened by jimallman almost 11 years ago - 15 comments

#45 - API URL to receive Github post-receive hooks and ask OTI to reindex studies

Issue - State: closed - Opened by leto almost 11 years ago - 10 comments
Labels: enhancement

#44 - Support prefixed study ids

Issue - State: closed - Opened by jar398 almost 11 years ago - 4 comments
Labels: enhancement

#43 - API call to list all available studies

Issue - State: closed - Opened by leto almost 11 years ago - 10 comments
Labels: enhancement

#42 - Rewrite history to remove accidental commit of study data

Issue - State: closed - Opened by leto almost 11 years ago - 1 comment

#41 - Remove hard-wired references to treenexus repo

Issue - State: closed - Opened by jar398 almost 11 years ago - 2 comments

#40 - API documentation update needed

Issue - State: closed - Opened by jar398 almost 11 years ago - 1 comment

#39 - Change 'OTOL' to 'open tree' or 'Open Tree' or 'Open Tree of Life'

Issue - State: closed - Opened by jar398 almost 11 years ago

#38 - Delete remote WIP branches

Pull Request - State: closed - Opened by leto almost 11 years ago

#37 - Pull from upstream before committing changes to studies

Issue - State: closed - Opened by jimallman almost 11 years ago - 14 comments
Labels: bug

#36 - Return raised errors as JSON (versus HTML pages)

Issue - State: closed - Opened by jimallman almost 11 years ago - 3 comments

#35 - Remove merged WIP branches from Github

Issue - State: closed - Opened by leto almost 11 years ago

#34 - Use a local git repo instead of the Github API

Pull Request - State: closed - Opened by leto almost 11 years ago

#33 - Implement search controller which uses OTI

Pull Request - State: closed - Opened by leto almost 11 years ago

#32 - Storage and retrieval of supporting files

Issue - State: closed - Opened by jimallman about 11 years ago - 2 comments

#31 - Forward study-creation request to a (long-running?) call to treemachine

Issue - State: open - Opened by jimallman about 11 years ago - 6 comments
Labels: nice commentary

#30 - Shifting API functions to RESTful HTTP methods

Pull Request - State: closed - Opened by jimallman about 11 years ago

#29 - Use conventional HTTP methods for a RESTful API

Issue - State: closed - Opened by jimallman about 11 years ago - 3 comments

#28 - Github File contents API only supports files up to 1MB in size

Issue - State: closed - Opened by leto about 11 years ago - 9 comments

#27 - Assign alphabetic prefix to study IDs

Issue - State: closed - Opened by jimallman about 11 years ago - 1 comment

#26 - Support for CORS (cross-domain requests)

Issue - State: closed - Opened by jimallman about 11 years ago - 2 comments

#25 - Add org/repo of datastore to configuration file

Issue - State: closed - Opened by leto about 11 years ago - 1 comment

#24 - Implement searching for a property across multiple NexSON files

Issue - State: closed - Opened by leto about 11 years ago - 1 comment

#23 - Run validation code on POSTed NexSON

Issue - State: closed - Opened by leto about 11 years ago - 10 comments

#22 - Simple fix for "literal" JSON from treenexus

Pull Request - State: closed - Opened by jimallman about 11 years ago

#21 - Retry on a Github API 502

Issue - State: closed - Opened by leto about 11 years ago - 1 comment

#20 - Allow override of HTTP verb (in POST requests)

Issue - State: closed - Opened by jimallman about 11 years ago - 9 comments
Labels: enhancement

#19 - Github client module

Pull Request - State: closed - Opened by jimallman about 11 years ago - 5 comments

#18 - Cleanup of generic JSON(P) views

Pull Request - State: closed - Opened by jimallman about 11 years ago

#17 - Define and spec authentication needs

Issue - State: closed - Opened by leto about 11 years ago - 3 comments
Labels: question

#16 - Add this API to the main opentree AWS deployment script

Issue - State: closed - Opened by leto about 11 years ago - 2 comments

#15 - Implement API endpoint which searches across studies

Issue - State: closed - Opened by leto about 11 years ago - 6 comments

#14 - Implement the deletion of a given study_id

Issue - State: closed - Opened by leto about 11 years ago - 7 comments

#13 - Use PyGithub

Issue - State: closed - Opened by leto about 11 years ago - 2 comments

#12 - Add instructions for updating treenexus submodule

Issue - State: closed - Opened by leto about 11 years ago - 1 comment

#11 - Remove web2py

Issue - State: closed - Opened by leto about 11 years ago - 1 comment

#10 - Added generic view for JSONP, modified GET method.

Pull Request - State: closed - Opened by jimallman about 11 years ago

#9 - Support for JSONP (cross-domain API calls)

Issue - State: closed - Opened by jimallman about 11 years ago - 2 comments

#8 - libgit2 prereq. needs to be exposed to travis

Issue - State: closed - Opened by mtholder about 11 years ago - 1 comment

#7 - Convert to BSD license

Issue - State: closed - Opened by leto about 11 years ago - 1 comment

#6 - Branches and pull requests for pending changes

Issue - State: closed - Opened by jimallman about 11 years ago - 2 comments
Labels: enhancement

#5 - Tagged releases of OTOL data repo

Issue - State: closed - Opened by jimallman about 11 years ago - 2 comments
Labels: enhancement

#4 - Allow for partial updates to a study

Issue - State: open - Opened by jimallman about 11 years ago - 7 comments
Labels: enhancement

#3 - Can we authenticate the user, for proper attribution in the datastore?

Issue - State: closed - Opened by jimallman about 11 years ago - 2 comments
Labels: question

#2 - Implement POST /v1/study/N.json

Issue - State: closed - Opened by leto about 11 years ago - 3 comments

#1 - Implement GET /v1/study/N.json

Issue - State: closed - Opened by leto about 11 years ago - 1 comment

GitHub / OpenTreeOfLife/phylesystem-api issues and pull requests