biocore/redbiom issues and pull requests

#130 - Connection to qiita.ucsd.edu timed out.

Issue - State: open - Opened by kattweigh2 7 months ago - 14 comments

#129 - Installed Greengenes2 and redbiom in Qiime2 but getting a connection error

Issue - State: closed - Opened by waalkes 8 months ago - 4 comments

#128 - Updated code + tests

Pull Request - State: closed - Opened by charles-cowart about 1 year ago - 1 comment

#127 - Verify redbiom test suite works with Redis 7

Issue - State: open - Opened by charles-cowart about 1 year ago - 4 comments

#126 - Latin1 bug

Pull Request - State: closed - Opened by wasade over 1 year ago

#125 - Discrepancy between metadata search results & piped fetch results

Issue - State: open - Opened by nvpatin over 1 year ago - 4 comments

#124 - metadata search by study id not working

Issue - State: closed - Opened by nvpatin over 1 year ago - 5 comments

#123 - Fetch qiita-study --md5 should be is_flag

Issue - State: open - Opened by wasade over 1 year ago

#122 - WIP: Closing out a few issues

Pull Request - State: closed - Opened by wasade almost 2 years ago - 1 comment

#121 - Error message fetch-samples

Issue - State: closed - Opened by sscansan almost 2 years ago

#120 - PyPi version 0.3.8 is 37.9 MB in size

Issue - State: closed - Opened by ElDeveloper over 2 years ago - 1 comment

#119 - Allow for resolution of ambiguities while retaining the artifact ID

Issue - State: closed - Opened by wasade over 2 years ago

#118 - ping!

Pull Request - State: closed - Opened by antgonza over 2 years ago

#117 - A particular sample always crashes for me

Issue - State: closed - Opened by BenKaehler over 2 years ago - 3 comments

#116 - It would be nice to have an easy option to pull a specific qiita study

Issue - State: closed - Opened by wasade over 2 years ago

#115 - add msgpack

Pull Request - State: closed - Opened by wasade almost 3 years ago

#114 - API/PERF: allow avoiding fetch of taxonomy

Pull Request - State: closed - Opened by wasade almost 3 years ago

#113 - Force json

Pull Request - State: closed - Opened by wasade almost 3 years ago

#112 - Release items

Pull Request - State: closed - Opened by wasade about 3 years ago

#111 - tentative py3738 support

Pull Request - State: closed - Opened by wasade about 3 years ago

#110 - Updates for py37 and py38

Pull Request - State: closed - Opened by wasade about 3 years ago - 1 comment

#109 - Bug in Querying for public microbiome data in Qiita using redbiom tutorial

Issue - State: closed - Opened by AlohaPropolis about 3 years ago - 1 comment

#108 - Code inversion for ambiguities solving in fetch?

Issue - State: closed - Opened by cotillau about 3 years ago - 1 comment

#107 - Bug in version up on pip and conda

Issue - State: closed - Opened by BenKaehler about 3 years ago - 5 comments

#106 - Expand on test failure

Pull Request - State: closed - Opened by wasade over 3 years ago

#105 - Create main.yml

Pull Request - State: closed - Opened by wasade over 3 years ago - 1 comment

#104 - CI first pass

Pull Request - State: closed - Opened by wasade over 3 years ago

#103 - Support for large numbers of features

Pull Request - State: closed - Opened by wasade over 3 years ago - 2 comments

#102 - How to get ITS amplicon environmental samples

Issue - State: closed - Opened by hotblast about 4 years ago - 2 comments

#101 - CTX for ITS data?

Issue - State: closed - Opened by hotblast about 4 years ago - 1 comment

#100 - Pulling all available Qiita metadata as a single table

Issue - State: closed - Opened by adamklie about 4 years ago - 1 comment

#99 - ran the example, got following errors.

Issue - State: closed - Opened by hotblast about 4 years ago - 5 comments

#98 - Fetching many samples is slower than batching externally

Issue - State: closed - Opened by wasade about 4 years ago

#97 - Defined Constant to resolve as Str or Num for AST expression eval

Pull Request - State: closed - Opened by ryanc16 over 4 years ago - 1 comment

#96 - Remark Python 3.5-3.6

Pull Request - State: closed - Opened by wasade over 4 years ago - 2 comments

#95 - Tickle

Pull Request - State: closed - Opened by wasade over 4 years ago

#94 - Searching commands are incompatible with python 3.8+

Issue - State: closed - Opened by ryanc16 over 4 years ago - 4 comments

#93 - Possible regression in ambiguity reporting

Issue - State: closed - Opened by wasade over 4 years ago

#92 - Resolution of ambiguities on fetch sample-metadata can trigger an AttributeError

Issue - State: closed - Opened by wasade over 4 years ago

#91 - Bump version

Pull Request - State: closed - Opened by wasade almost 5 years ago

#90 - Resolve ambiguities

Pull Request - State: closed - Opened by wasade almost 5 years ago

#89 - MAINT: allow extracting specific metadata columns

Pull Request - State: closed - Opened by wasade almost 5 years ago

#88 - Escape periods

Pull Request - State: closed - Opened by wasade almost 5 years ago

#87 - Encode variable values for use over URLs

Pull Request - State: closed - Opened by wasade about 5 years ago - 3 comments

#86 - Stable column ordering on test

Pull Request - State: closed - Opened by wasade about 5 years ago

#85 - Illogical results from redbiom summarize metadata-category

Issue - State: closed - Opened by rahel31 about 5 years ago - 4 comments

#84 - add md5 feature output for biom

Pull Request - State: closed - Opened by antgonza about 5 years ago - 3 comments

#83 - Add API method to obtain the loaded tags

Issue - State: closed - Opened by wasade about 5 years ago - 1 comment

#82 - ENH: allow for storing timestamps

Pull Request - State: closed - Opened by wasade about 5 years ago - 1 comment

#81 - Differentiate empty from already loaded

Pull Request - State: closed - Opened by wasade about 5 years ago - 1 comment

#80 - Pandas fix

Pull Request - State: closed - Opened by wasade over 5 years ago

#79 - adding python 3.6

Pull Request - State: closed - Opened by antgonza over 5 years ago

#78 - Obtain the tags associated with samples in a context

Pull Request - State: closed - Opened by wasade over 5 years ago

#77 - All public samples not being searched?

Issue - State: closed - Opened by adswafford over 5 years ago - 4 comments

#76 - added a conda recipe

Pull Request - State: closed - Opened by BenKaehler over 5 years ago - 2 comments

#75 - create a command to generate figure 2A of MS

Issue - State: closed - Opened by antgonza over 5 years ago - 1 comment

#74 - ENH/API: add in minimum count filtering on search

Pull Request - State: closed - Opened by wasade over 5 years ago

#73 - Doc update

Pull Request - State: closed - Opened by jwdebelius over 5 years ago

#72 - Pull down based on sample id

Issue - State: closed - Opened by jwdebelius over 5 years ago - 4 comments

#71 - Allow select samples from metadata to support cross-context queries

Issue - State: open - Opened by ElDeveloper over 5 years ago

#70 - should some of the output be optional in redbiom.fetch.data_from_samples

Issue - State: closed - Opened by antgonza over 5 years ago - 5 comments
Labels: question

#69 - contexts parameter as a list of str

Issue - State: closed - Opened by antgonza over 5 years ago - 4 comments
Labels: enhancement

#68 - Remap IDs to simplify storage for taxonomy, and simplify structures used for taxonomy

Pull Request - State: closed - Opened by wasade almost 6 years ago

#67 - Get representative subset for a metadata category

Issue - State: closed - Opened by cuttlefishh almost 6 years ago - 1 comment

#66 - Tag fetch

Pull Request - State: closed - Opened by wasade about 6 years ago - 9 comments

#65 - It would be nice to get the list of features in samples

Issue - State: open - Opened by wasade over 6 years ago

#64 - Contexts should optionally store machine readable processing information

Issue - State: open - Opened by wasade over 6 years ago

#63 - It should be possible to guess a context

Issue - State: open - Opened by wasade over 6 years ago - 1 comment

#62 - support for randomly sampling

Issue - State: closed - Opened by antgonza over 6 years ago - 1 comment

#61 - parallel support via joblib

Issue - State: open - Opened by antgonza over 6 years ago

#60 - Uniquify

Issue - State: open - Opened by wasade over 6 years ago

#59 - Allow testing where a metadata value is None

Pull Request - State: closed - Opened by wasade over 6 years ago

#58 - On fetch, it should be possible to retain a non-ambiguous set

Issue - State: closed - Opened by wasade over 6 years ago

#57 - `redbiom search metadata` should support finding samples where a category is not null

Issue - State: closed - Opened by wasade over 6 years ago - 1 comment

#56 - fetch specific metadata categories

Issue - State: closed - Opened by wasade over 6 years ago

#55 - Ambiguous was backwards

Pull Request - State: closed - Opened by wasade over 6 years ago

#54 - Query a context for contained features or samples

Pull Request - State: closed - Opened by wasade over 6 years ago - 2 comments

#53 - PERF: sortedset to list for feature and sample data

Pull Request - State: closed - Opened by wasade over 6 years ago - 1 comment

#52 - If context creation fails, error gracefully

Issue - State: closed - Opened by wasade almost 7 years ago

#51 - Remove whole contexts

Issue - State: open - Opened by wasade almost 7 years ago
Labels: server-side-support

#50 - search for phrases

Issue - State: closed - Opened by antgonza about 7 years ago

#49 - Changing version number

Pull Request - State: closed - Opened by josenavas about 7 years ago

#48 - expose tag admin-load_sample_data

Pull Request - State: closed - Opened by antgonza about 7 years ago - 1 comment

#47 - [WIP] Initial JS API

Pull Request - State: closed - Opened by josenavas about 7 years ago

#46 - Fixing instructions in readme

Issue - State: closed - Opened by antgonza about 7 years ago - 1 comment

#45 - On fetch, use HMGET

Issue - State: open - Opened by wasade over 7 years ago

#44 - redbiom search metadata NUMBER should fail gracefully

Issue - State: closed - Opened by ElDeveloper over 7 years ago - 2 comments

#43 - redbiom summarize taxonomy should handle no hits gracefully

Issue - State: closed - Opened by wasade over 7 years ago

#42 - It should be possible to easily discover the metadata categories for a set of samples

Issue - State: open - Opened by wasade over 7 years ago

#41 - Where queries should support "in" correctly when the left hand is a string

Issue - State: closed - Opened by wasade over 7 years ago

#40 - Discrepancy between metadata search and stored metadata

Issue - State: open - Opened by wasade over 7 years ago - 1 comment
Labels: server-side-support

#39 - Let "redbiom fetch sample-metadata" print to stdout

Issue - State: open - Opened by ElDeveloper over 7 years ago

#38 - pypi updates

Pull Request - State: closed - Opened by wasade over 7 years ago - 3 comments

#34 - Feedback mechanism for when metadata appear funky

Issue - State: closed - Opened by wasade over 7 years ago - 1 comment

#28 - substring matching via SCAN

Issue - State: open - Opened by wasade over 7 years ago
Labels: server-side-support

#27 - `redbiom search observations` should search all contexts if one is not provided

Issue - State: open - Opened by wasade over 7 years ago - 1 comment
Labels: server-side-support

#23 - Support a default context

Issue - State: open - Opened by wasade over 7 years ago - 1 comment
Labels: server-side-support

GitHub / biocore/redbiom issues and pull requests