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Code Issues Packages Projects Releases Wiki Activity

include pictures in zip again (#449)

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* include pictures in zip again

* 🐶
This commit is contained in:
Bastian Greshake Tzovaras
2017-12-10 23:23:45 -08:00
committed by Philipp Bayer
parent c3fed5ee99
commit 2dd67a7657
2 changed files with 10 additions and 8 deletions
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13
app/workers/zipfulldata.rb
View File

@@ -25,7 +25,7 @@ class Zipfulldata
@time_str = time.strftime("%Y%m%d%H%M")
@csv_options = { col_sep: ';' }
@dump_file_name = "opensnp_datadump.#{time_str}"
@zip_public_path = "/data/zip/#{dump_file_name}.zip"
@zip_public_path = "public/data/zip/#{dump_file_name}.zip"
@zip_fs_path = "/tmp/#{dump_file_name}.zip"
@tmp_dir = "#{Rails.root}/tmp/#{dump_file_name}"
@link_path = Rails.root.join('public/data/zip/opensnp_datadump.current.zip')
@@ -48,15 +48,14 @@ class Zipfulldata
Zip::File.open(zip_fs_path, Zip::File::CREATE) do |zipfile|
create_user_csv(genotypes, zipfile)
create_fitbit_csv(zipfile)
# list_of_pics = create_picture_phenotype_csv(zipfile)
# create_picture_zip(list_of_pics, zipfile)
list_of_pics = create_picture_phenotype_csv(zipfile)
create_picture_zip(list_of_pics, zipfile)
create_readme(zipfile)
zip_genotype_files(genotypes, zipfile)
end
FileUtils.chmod(0o644, @zip_fs_path)
# move from local storage to network storage
FileUtils.mv(@zip_fs_path, Rails.root.join("public/data/zip/#{dump_file_name}.zip"))
logger.info('created zip-file')
FileUtils.ln_sf(
@@ -182,7 +181,7 @@ class Zipfulldata
picture_phenotypes.each do |pp|
# copy the picture with name to +user_id+_+pic_phenotype_id+.png
logger.info("Looking for this picture #{pp.id}")
# logger.info("Looking for this picture #{pp.id}")
picture = pp.user_picture_phenotypes.where(user_id: u.id).first
# does this user have this pic?
if picture.present? && picture.phenotype_picture.present?
@@ -263,8 +262,8 @@ TXT
def delete_old_zips
forbidden_files = [link_path,
Rails.root.join('data', 'annotation.zip'),
Rails.root.join('public', 'data', 'zip', "#{dump_file_name}.zip")]
Rails.root.join('data', 'annotation.zip').to_s,
Rails.root.join('public', 'data', 'zip', "#{dump_file_name}.zip").to_s]
Dir[Rails.root.join('public/data/zip/*.zip')].each do |f|
if (not forbidden_files.include? f) and (File.ftype(f) == "file")
File.delete(f)

5
spec/workers/zipfulldata_spec.rb.tmp → spec/workers/zipfulldata_spec.rb
View File

@@ -18,6 +18,7 @@ describe Zipfulldata do
tmp_dir = job.instance_variable_get(:@tmp_dir) + '_test_' +
Digest::SHA1.hexdigest("#{Time.now.to_i}#{rand}")
job.instance_variable_set(:@tmp_dir, tmp_dir)
FileUtils.touch job.zip_fs_path.to_s
Dir.mkdir(tmp_dir)
genotype
end
@@ -25,6 +26,8 @@ describe Zipfulldata do
after do
link = Rails.root.join("public/data/zip/opensnp_datadump.current.zip")
FileUtils.rm(link) if File.exist?(link)
FileUtils.rm(job.zip_fs_path) if File.exist?(job.zip_fs_path)
FileUtils.rm(job.zip_public_path) if File.exist?(job.zip_public_path)
end
it "creates user CSVs" do
@@ -125,7 +128,7 @@ Thanks for using openSNP!
expect(job).to receive(:create_readme).with(zipfile)
expect(job).to receive(:zip_genotype_files).with([genotype], zipfile)
expect(FileUtils).to receive(:chmod).
with(0644, "#{Rails.root}/public/data/zip/#{job.dump_file_name}.zip")
with(0o644, "/tmp/#{job.dump_file_name}.zip")
expect(FileUtils).to receive(:ln_sf).with(
Rails.root.join("public/data/zip/#{job.dump_file_name}.zip"),
Rails.root.join("public/data/zip/opensnp_datadump.current.zip"))