0.7.5

Features

• n/a

Improvements

• gracefully handle Zenodo API outage #266 so that other remotes can take a stab at resolving requested content
• look for updated anchors on [preston track] and [preston head]; relat… …ed to #256
• ignore 40x 50x return codes when querying remotes.

Bugs

• n/a

0.7.4

Features

• support for tracking/streaming records associated with biological associations kept in TaxonWorks. globalbioticinteractions/globalbioticinteractions#373 @mjy

Example 1. Tracking TaxonWorks Biological Associations records

preston track -u https://sfg.taxonworks.org 

or

preston track https://sfg.taxonworks.org/api/v1

Example 2. Streaming of TaxonWorks records into GloBI compatible json-lines

The tracked taxonworks content can be streamed into json-lines that express

preston track https://sfg.taxonworks.org/api/v1\
 | preston tw-stream

producing records such as:

{
  "http://www.w3.org/ns/prov#wasDerivedFrom": "hash://sha256/f1c123b38bdfab129d8a393b06842eddae823bf08a2c91b1100399940b582a9a",
  "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "application/vnd.taxonworks+json",
  "referenceId": "https://sfg.taxonworks.org/api/v1/sources/49013",
  "interactionId": "https://sfg.taxonworks.org/api/v1/biological_associations/84748",
  "taxonRootsResolved": 2,
  "referenceResolved": true,
  "referenceCitation": "@article{49013,\n  author = {Abate, T.},\n  booktitle = {Journal of Applied Entomology},\n  journal = {Journal of Applied Entomology},\n  month = {mar},\n  day = {31},\n  pages = {278-285},\n  title = {The bean fly <i>Ophiomyia phaseoli</i> Tryon (Diptera: Agromyzidae) and its parasitoids in Ethiopia.},\n  volume = {111(3)},\n  year = {1991},\n  stated_year = {1991},\n  year_suffix = {a},\n  issn = {0044-2240}\n}\n",
  "interactionTypeId": "gid://taxon-works/BiologicalRelationship/14",
  "interactionTypeName": "Primary host",
  "sourceTaxonName": "Eupelmus",
  "sourceTaxonId": "gid://taxon-works/TaxonName/456381",
  "sourceTaxonRank": "genus",
  "sourceTaxonAuthorship": "Dalman, 1820",
  "sourceTaxonPath": "Root | Animalia | Arthropoda | Insecta | Hymenoptera | Chalcidoidea | Eupelmidae | Eupelminae | Eupelmus",
  "sourceTaxonPathIds": "gid://taxon-works/TaxonName/455455 | gid://taxon-works/TaxonName/703648 | gid://taxon-works/TaxonName/703653 | gid://taxon-works/TaxonName/703658 | gid://taxon-works/TaxonName/455456 | gid://taxon-works/TaxonName/455458 | gid://taxon-works/TaxonName/455504 | gid://taxon-works/TaxonName/455506 | gid://taxon-works/TaxonName/456381",
  "sourceTaxonPathNames": "nomenclatural rank | kingdom | phylum | class | order | superfamily | family | subfamily | genus",
  "targetTaxonName": "Agromyzidae",
  "targetTaxonId": "gid://taxon-works/TaxonName/513569",
  "targetTaxonRank": "family",
  "targetTaxonAuthorship": "",
  "targetTaxonPath": "Root | Animalia | Arthropoda | Insecta | Diptera | Agromyzidae",
  "targetTaxonPathIds": "gid://taxon-works/TaxonName/455455 | gid://taxon-works/TaxonName/703648 | gid://taxon-works/TaxonName/703653 | gid://taxon-works/TaxonName/703658 | gid://taxon-works/TaxonName/513567 | gid://taxon-works/TaxonName/513569",
  "targetTaxonPathNames": "nomenclatural rank | kingdom | phylum | class | order | family"
}

Improvements

• n/a

Bugs

• n/a

0.7.3

Features

n/a

Improvements

• support streaming of "enriched" github issue metadata #156

Example, tracking #156 produces, via pandoc and jq:

preston track https://github.com/bio-guoda/preston/issues/156\
 | preston gh-stream\
 | jq --raw-output '.["body"]'\
 | pandoc -s --to=plain\
 | head

resulting in a plain text representation of the example issue body text. As the github issue json contains structured markdown as "body" of issues and their comments, pandoc can transform this into many different kinds of formats, including but not limited to pdf, html, docx, markdown, etc etc.

Traditionally, academic discourse happened through journal publications,
physical books, and lectures.

Today other forums are used to exchange and develop ideas. Slack is one
of them.

Suggest to extend Preston to track slack discussions and make them
citable.

Similar to https://github.com/bio-guoda/preston/issues/137 and desire to

Bugs

• n/a

0.7.2

Features

• add first pass at tracking github issues and related artifacts / issues. To track all issues (rate limits permitting) in https://github.com/globalbioticinteractions/globalbioticinteractions - #156 inspired by discussions with @PietrH @Daniel-Mietchen @matdillen @n8upham

preston track "https://github.com/mammaldiversity/mammaldiversity.github.io/issues" 

use export GITHUB_TOKEN=[some token] in sh/bash to make preston aware of your token. Also see, https://github.com/settings/tokens?type=beta . Note that in GitHub Actions workflows, a github token is generated on the fly with 1000 request. So, you should be able to track up to about 500 issues in on workflow, assuming that not many issues are referenced in the tracked issues.

• allow using OCI repositories as remotes #255 inspired by @cboettig @mbjones . With this release you can do things like (see also cboettig/contentid#94 (comment))

$ preston cat --remote https://ghcr.io/cboettig/content-store hash://sha256/9412325831dab22aeebdd674b6eb53ba6b7bdd04bb99a4dbb21ddff646287e37\
 | head -n5
*******************************************************************************
*** Historical CO2 Record from the Vostok Ice Core                          ***
***                                                                         ***
*** Source: J.M. Barnola                                                    ***
***         D. Raynaud                                                      ***

Improvements

• n/a

Bugs

• n/a

0.7.1

Features

n/a

Improvements

n/a

Bugs

• selecting only most recent alias; related to #252

0.7.0

Features

• allow retrieval of WikiMedia Commons content via their sha1 hash (#239)

Improvements

n/a

Bugs

• reduce logging caused by unsupported http cookies (59706a9)

0.6.5

Features

n/a

Improvements

n/a

Bugs

• only match GenBank Flat Files with accession number 6db9464
• take only GenBank accession numbers without white spaces, truncate otherwise 329d715
• disable automated decompression of gzipped content by embedded httpclient #249

0.6.4

Features

• introducing support for streaming GenBank Flat Files (see #246 and globalbioticinteractions/globalbioticinteractions#904)
  example:

preston track https://ftp.ncbi.nlm.nih.gov/genbank/gbpln1.seq.gz\
| preston gb-stream\
| head -n1\
| jq .

produces:

{
  "accession": "AB000001",
  "http://www.w3.org/2000/01/rdf-schema#seeAlso": "https://ncbi.nlm.nih.gov/nuccore/AB000001",
  "definition": "Rhizoctonia solani genes for 18S rRNA, 5.8S rRNA, 28S rRNA, partial and complete sequence, isolate: #1.",
  "organism": "Rhizoctonia solani",
  "db_xref": "taxon:456999",
  "http://www.w3.org/ns/prov#wasDerivedFrom": "line:gz:hash://sha256/510ea17a974eaf35504ca24ad57e9be708196d38189353487eb312426ed9f0b4!/L11-L58",
  "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "genbank-flatfile"
}

Improvements

• rename provenanceRoot -> provenance-root and provenanceAnchor -> prov… as suggested by @mielliott
• specify that Java-style regular are used in [preston grep] as suggest… as suggested by @mielliott
• Print trailing newlines for line: queries; #246 #128 thanks @mielliott
• include bash command completion in deb package; related to #247 as suggested by @mielliott

Bugs

• return expected content for alias when using preston cat [some alias] #248

0.6.3

Features

• allow for bashing commands from stdin related to #240

Improvements

• allow for tracking content via stdin #240

Bugs

• stop processing when asked to stop; fixes #238
• avoid pre-mature processing cancelation after finding an alias

0.6.2

Features

n/a

Improvements

• add sha1 support for dataone; related to #181 #236 @mbjones - example usage:

preston cat\
 --remote https://dataone.org\
 hash://sha1/c99e906eaa98f7e7a2b19161c3340218bbb994bc\
 > photo.jpg

with photo included and attached.

Bugs

n/a