[ARVADOS] updated: 2606f4df5861ff34ca9e42389a1509e77c102c5a
git at public.curoverse.com
git at public.curoverse.com
Fri Mar 20 14:32:26 EDT 2015
Summary of changes:
apps/workbench/app/helpers/collections_helper.rb | 3 +-
apps/workbench/config/application.default.yml | 6 +--
apps/workbench/config/initializers/mime_types.rb | 34 ++++-----------
apps/workbench/test/unit/collection_test.rb | 1 +
sdk/cli/bin/arv-run-pipeline-instance | 53 ++++--------------------
sdk/cli/bin/crunch-job | 30 ++++++++++----
services/api/test/fixtures/collections.yml | 8 ++--
7 files changed, 46 insertions(+), 89 deletions(-)
via 2606f4df5861ff34ca9e42389a1509e77c102c5a (commit)
via 03e8ba641e0161f15d96351e2432805977fd9d57 (commit)
via 4925686f6aa7214568ebd60be3acaa49dbf9dd1a (commit)
via a578a055456693d66ccf4d65a09822380d2cc7a8 (commit)
via 1ed0df4d4b2221a06e37effce42ab5b2e23b29c8 (commit)
via a239e2db534cc36aa8c3e08077383d84bf6ba8e8 (commit)
via 3365d47ab4f504a1e849852691313cddd89d0f15 (commit)
from a9c8f2dd15af7843ac4d86e5820ab0771cc5fd78 (commit)
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commit 2606f4df5861ff34ca9e42389a1509e77c102c5a
Author: Radhika Chippada <radhika at curoverse.com>
Date: Fri Mar 20 14:30:35 2015 -0400
5375: improved mime_types initializer. enhance collections_helper to use mime_type sub_type instead of relying on suffix.
update config param name, value, and comment. add .seq, which is another supported extension of fasta to test.
diff --git a/apps/workbench/app/helpers/collections_helper.rb b/apps/workbench/app/helpers/collections_helper.rb
index 0564ec9..25f2cb5 100644
--- a/apps/workbench/app/helpers/collections_helper.rb
+++ b/apps/workbench/app/helpers/collections_helper.rb
@@ -59,13 +59,12 @@ module CollectionsHelper
#
def preview_allowed_for file_name
file_type = MIME::Types.type_for(file_name).first
-
if file_type.nil?
false
elsif (file_type.raw_media_type == "text") || (file_type.raw_media_type == "image")
true
elsif (file_type.raw_media_type == "application") &&
- (Rails.configuration.filename_suffixes_with_view_icon.include? ((file_name.split('.')[-1]).downcase))
+ (Rails.configuration.application_mimetypes_with_view_icon.include? (file_type.sub_type))
true
else
false
diff --git a/apps/workbench/config/application.default.yml b/apps/workbench/config/application.default.yml
index c613453..d87ca9b 100644
--- a/apps/workbench/config/application.default.yml
+++ b/apps/workbench/config/application.default.yml
@@ -188,11 +188,11 @@ common:
# generic issue email from
email_from: arvados at example.com
- # Filename suffixes of applications for which the
- # view icon would be shown in collection show page.
+ # Mimetypes of applications for which the view icon
+ # would be shown in collection show page.
# It is sufficient to list only applications here.
# No need to list text and image types.
- filename_suffixes_with_view_icon: [fa, fasta, go, json, pdf, py, r, sam, sh, xml, xsl]
+ application_mimetypes_with_view_icon: [fasta, go, json, pdf, python, r, sam, sh, xml, xsl]
# the maximum number of bytes to load in the log viewer
log_viewer_max_bytes: 1000000
diff --git a/apps/workbench/config/initializers/mime_types.rb b/apps/workbench/config/initializers/mime_types.rb
index 848b3dc..6dd0eae 100644
--- a/apps/workbench/config/initializers/mime_types.rb
+++ b/apps/workbench/config/initializers/mime_types.rb
@@ -8,29 +8,13 @@
require 'mime/types'
include MIME
-
-# register and add new MIME types to MIME::Types gem
-if (MIME::Types.type_for('file.fa').first.nil?)
- Mime::Type.register "application/fa", :fa
- MIME::Types.add(MIME::Type.new(["application/fa", %(fa)]))
-end
-
-if (MIME::Types.type_for('file.fasta').first.nil?)
- Mime::Type.register "application/fasta", :fasta
- MIME::Types.add(MIME::Type.new(["application/fasta", %(fasta)]))
-end
-
-if (MIME::Types.type_for('file.go').first.nil?)
- Mime::Type.register "application/go", :go
- MIME::Types.add(MIME::Type.new(["application/go", %(go)]))
-end
-
-if (MIME::Types.type_for('file.r').first.nil?)
- Mime::Type.register "application/r", :r
- MIME::Types.add(MIME::Type.new(["application/r", %(r)]))
-end
-
-if (MIME::Types.type_for('file.sam').first.nil?)
- Mime::Type.register "application/sam", :sam
- MIME::Types.add(MIME::Type.new(["application/sam", %(sam)]))
+[
+ %w(fasta fa fas fsa seq),
+ %w(go),
+ %w(r),
+ %w(sam),
+].each do |suffixes|
+ if (MIME::Types.type_for(suffixes[0]).first.nil?)
+ MIME::Types.add(MIME::Type.new(["application/#{suffixes[0]}", suffixes]))
+ end
end
diff --git a/apps/workbench/test/unit/collection_test.rb b/apps/workbench/test/unit/collection_test.rb
index 4185909..e7afa69 100644
--- a/apps/workbench/test/unit/collection_test.rb
+++ b/apps/workbench/test/unit/collection_test.rb
@@ -78,6 +78,7 @@ class CollectionTest < ActiveSupport::TestCase
["filename.csv", true],
["filename.fa", true],
["filename.fasta", true],
+ ["filename.seq", true], # another fasta extension
["filename.go", true],
["filename.htm", true],
["filename.html", true],
diff --git a/services/api/test/fixtures/collections.yml b/services/api/test/fixtures/collections.yml
index d3e6beb..4be154a 100644
--- a/services/api/test/fixtures/collections.yml
+++ b/services/api/test/fixtures/collections.yml
@@ -522,26 +522,26 @@ multi_level_to_combine:
# collection with several file types to test view icon enabled state in collection show page
collection_with_several_supported_file_types:
uuid: zzzzz-4zz18-supportedtypes1
- portable_data_hash: 7a6ef4c162a5c6413070a8bd0bffc818+150
+ portable_data_hash: f7bb16c306b97974afd310749a9848d6+0
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
created_at: 2014-02-03T17:22:54Z
modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
modified_at: 2014-02-03T17:22:54Z
updated_at: 2014-02-03T17:22:54Z
- manifest_text: ". 85877ca2d7e05498dd3d109baf2df106+95 0:0:file.csv 0:0:file.fa 0:0:file.fasta 0:0:file.gif 0:0:file.json 0:0:file.md 0:0:file.pdf 0:0:file.py 0:0:file.R 0:0:file.sam 0:0:file.sh 0:0:file.tiff 0:0:file.tsv 0:0:file.txt 0:0:file.vcf 0:0:file.xml 0:0:file.xsl 0:0:file.yml\n"
+ manifest_text: ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:file.csv 0:0:file.fa 0:0:file.fasta 0:0:file.gif 0:0:file.json 0:0:file.md 0:0:file.pdf 0:0:file.py 0:0:file.R 0:0:file.sam 0:0:file.sh 0:0:file.tiff 0:0:file.tsv 0:0:file.txt 0:0:file.vcf 0:0:file.xml 0:0:file.xsl 0:0:file.yml\n"
name: collection_with_several_supported_file_types
collection_with_several_unsupported_file_types:
uuid: zzzzz-4zz18-supportedtypes2
- portable_data_hash: 7a6ef4c162a5c6413070a8bd0bffc818+150
+ portable_data_hash: 97620c05fbb3041a19471bc1e06f3f78+0
owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
created_at: 2014-02-03T17:22:54Z
modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
modified_at: 2014-02-03T17:22:54Z
updated_at: 2014-02-03T17:22:54Z
- manifest_text: ". 85877ca2d7e05498dd3d109baf2df106+95 0:0:file 0:0:file.bam\n"
+ manifest_text: ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:file 0:0:file.bam\n"
name: collection_with_several_unsupported_file_types
# Test Helper trims the rest of the file
commit 03e8ba641e0161f15d96351e2432805977fd9d57
Merge: a9c8f2d 4925686
Author: Radhika Chippada <radhika at curoverse.com>
Date: Fri Mar 20 11:30:59 2015 -0400
Merge branch 'master' into 5375-preview-collection-text-files
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