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Merge pull request #630 from PecanProject/develop
release 5.1.0
2 parents 23859dd + 7e6c58a commit 822d5ad

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‎.zenodo.json‎

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{
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"metadata": {
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"access_right": "open",
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"creators": [{
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"affiliation": "University of Illinois",
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"name": "Scott Rohde"
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},
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{
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"name": "Carl Crott"
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},
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{
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"affiliation": "University of Illinois",
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"name": "David LeBauer"
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},
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{
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"name": "Patrick Mulrooney"
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},
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{
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"affiliation": "National Center for Supercomputing Applications",
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"name": "Rob Kooper"
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},
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{
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"name": "Jeremy Kemball"
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},
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{
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"name": "Jimmy Chen"
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},
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{
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"name": "Andrew Shirk"
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},
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{
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"name": "Zhengqi Yang"
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},
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{
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"affiliation": "National Center for Supercomputing Applications",
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"name": "Max Burnette"
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},
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{
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"name": "Haotian Jiang"
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},
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{
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"name": "Yilin Dong"
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},
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{
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"name": "Uday Saraf"
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},
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{
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"affiliation": "Boston University",
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"name": "Michael Dietze"
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},
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{
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"name": "Chris Black"
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}
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],
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"language": "eng",
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"license": {
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"id": "NCSA"
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"access_right": "open",
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"creators": [{
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"affiliation": "University of Illinois",
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"name": "Scott Rohde"
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},
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"references": [
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"LeBauer, D., Kooper, R., Mulrooney, P., Rohde, S., Wang, D., Long, S. P., & Dietze, M. C. (2018). BETYdb: a yield, trait, and ecosystem service database applied to second\u2010generation bioenergy feedstock production. GCB Bioenergy, 10(1), 61-71",
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"LeBauer, David, Michael Dietze, Rob Kooper, Steven Long, Patrick Mulrooney, Gareth Scott Rohde, Dan Wang (2010). Biofuel Ecophysiological Traits and Yields Database (BETYdb), Energy Biosciences Institute, University of Illinois at Urbana-Champaign. doi:10.13012/J8H41PB9"
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],
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"notes": "Development of BETYdb is supported by the National Science Foundation (ABI #1062547, ABI #1458021), the Department of Energy (ARPA-E awards #DE-AR0000594 and DE-AR0000598), and the Energy Biosciences Institute.",
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"resource_type": {
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"title": "Software",
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"type": "software"
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{
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"name": "Carl Crott"
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},
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{
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"affiliation": "University of Arizona",
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"name": "David LeBauer"
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},
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{
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"name": "Patrick Mulrooney"
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},
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{
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"affiliation": "National Center for Supercomputing Applications",
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"name": "Rob Kooper"
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},
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{
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"name": "Jeremy Kemball"
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},
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{
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"name": "Jimmy Chen"
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},
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{
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"name": "Andrew Shirk"
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},
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{
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"name": "Zhengqi Yang"
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},
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{
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"affiliation": "National Center for Supercomputing Applications",
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"name": "Max Burnette"
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},
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{
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"name": "Haotian Jiang"
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},
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{
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"name": "Yilin Dong"
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},
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{
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"name": "Uday Saraf"
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},
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{
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"affiliation": "Boston University",
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"name": "Michael Dietze"
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},
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{
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"name": "Chris Black"
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}
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],
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"language": "eng",
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"license": {
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"id": "NCSA"
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},
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"references": [
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"LeBauer, D., Kooper, R., Mulrooney, P., Rohde, S., Wang, D., Long, S. P., & Dietze, M. C. (2018). BETYdb: a yield, trait, and ecosystem service database applied to second\u2010generation bioenergy feedstock production. GCB Bioenergy, 10(1), 61-71",
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"LeBauer, David, Michael Dietze, Rob Kooper, Steven Long, Patrick Mulrooney, Gareth Scott Rohde, Dan Wang (2010). Biofuel Ecophysiological Traits and Yields Database (BETYdb), Energy Biosciences Institute, University of Illinois at Urbana-Champaign. doi:10.13012/J8H41PB9"
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],
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"notes": "Development of BETYdb is supported by the National Science Foundation (ABI #1062547, ABI #1458021), the Department of Energy (ARPA-E awards #DE-AR0000594 and DE-AR0000598), and the Energy Biosciences Institute.",
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"resource_type": {
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"title": "Software",
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"type": "software"
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}
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}

‎CHANGELOG.md‎

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For more information about this file see also [Keep a Changelog](http://keepachangelog.com/) .
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## [5.1.0] - 2019-01-14
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### Fixes
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- #611 : could not close alerts
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- #585 : Pressing "Show" on the Covariates Edit page attempts an update
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- #621 : A fix for a critical vulnerability reported by Danny Rosseau at Carve Systems (www.carvesystems.com).
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- #596 : Crop Model Maps links are broken
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- #605 : Allow for keyless API access (using guestuser access)
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- #618 : Can not download results of search as csv
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## [5.0.5] - 2018-10-23
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‎app/assets/javascripts/application.js‎

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// defines showHide
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//= require min
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// enables close button in "alert" divs:
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//= require script
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//= require lazy/simple_search
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//= require lazy/application

‎app/controllers/covariates_controller.rb‎

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def show
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@covariate = Covariate.find(params[:id])
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if @covariate.trait.nil?
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flash[:error] = 'This covariate is not associated with a trait! Consider removing it.'
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end
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respond_to do |format|
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format.html # show.html.erb
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format.xml { render :xml => @covariate }

‎app/controllers/search_controller.rb‎

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end
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str = header + @results.to_comma
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send_data str, type: Mime::CSV,
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send_data str, type: :csv,
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disposition: "attachment; filename=search_results.csv"
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end
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format.json { render :json => @results }

‎app/models/bulk_upload_data_set.rb‎

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t.site_id = row['site_id']
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# Modify each Trait class instance so that date strings are
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# interpreted as being in the time zone of the trait site
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# (or UTC, if the trait site time_zone column is null)
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# interpreted as being in the time zone of the trait site (or UTC, if
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# the trait site time_zone column is null). Note that in the Bulk
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# Upload Wizard, the validation step will prevent reaching this code
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# if a site without time zone is in the data file. But nothing
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# prevents a site without time zone from being specified
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# interactively.
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class <<t
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def date=(value)
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date = Time.use_zone(Site.find(site_id).time_zone || 'UTC') do
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# dates are assumed always to be accurate to the day:
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csv_row_as_hash["dateloc"] = 5
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# bulk upload doesn't handles "date only" dates and dates with time to the
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# second; determine which:
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# bulk upload handles "date only" dates and dates with time to the
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# second and no other cases; determine which:
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if csv_row_as_hash["date"].length == 19
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csv_row_as_hash["timeloc"] = 1
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elsif csv_row_as_hash["date"].length == 10

‎app/models/db_file.rb‎

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self[:created_user_id] = user_id
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self[:updated_user_id] = user_id
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if upload # Uploaded file
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# check to see it is a valid filename
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if upload.original_filename.match(/^[a-zA-Z0-9._\-]+$/).nil?
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raise("Invalid filename \"#{upload.original_filename}\"; filenames can only contain letters, numbers, periods, underscores, and dashes.")
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end
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self[:file_name] = upload.original_filename
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self[:md5] = Digest::MD5.file(upload.path).hexdigest
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‎app/services/api_authentication_system.rb‎

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# coding: utf-8
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module ApiAuthenticationSystem
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include AuthenticatedSystem
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# Override default access_denied action.
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def access_denied
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@errors = "authentication failed"
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if @errors
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@errors = "authentication failed: " + @errors
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else
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@errors = "authentication failed"
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end
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render status: 401
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end
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end
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end
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# Override "login_from_api_key" so that if no key is given or the given key is
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# invalid, the user is logged in as the guest user.
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def login_from_api_key
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key = params[:key]
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if key.nil?
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u = User.find_by_login('guestuser')
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if u.nil?
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@errors = "For key-less access to the API, you must set up the guest user account."
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end
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else
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u = User.find_by_apikey(key)
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if u.nil?
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@errors = "Invalid API key. To access the API as a guest user, omit the “key” parameter."
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end
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end
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return u
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end
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end

‎app/views/covariates/edit.html.erb‎

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<%= f.label :statname %><br />
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<%= f.select :statname, $statname_list %>
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</p>
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<p>
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<%= f.submit 'Update' %>
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</p>
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<div class="form-actions">
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<div class="button-group">
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<%= link_to( covariates_path ) do %>
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<button class="button"><i class="icon-arrow-left"></i> All Records</button>
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<button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
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<% end %>
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<%= link_to( @covariate ) do %>
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<button class="button">Show</button>
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<button class="button" type="button">Show</button>
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<% end %>
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</div>
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<div class="button-group pull-right">

‎app/views/covariates/show.html.erb‎

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<dd><%= @covariate.stat %></dd>
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<dt>Statname:</dt>
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<dd><%= @covariate.statname %></dd>
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<% if @covariate.trait %>
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<dt>Associated Trait:</dt>
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<dd>
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<%= link_to_if @covariate.trait, @covariate.trait, @covariate.trait %>
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<dd><%= link_to_if @covariate.trait.specie, @covariate.trait.specie, @covariate.trait.specie %></dd>
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<dt>Citation:</dt>
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<dd><%= link_to_if @covariate.trait.citation, @covariate.trait.citation, @covariate.trait.citation %></dd>
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<% end %>
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</dl>
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