Module: MiGA::Cli::Action::Download::Base

Included in:
Gtdb, Ncbi, Seqcode, Get
Defined in:
lib/miga/cli/action/download/base.rb

Overview

Helper module including download functions for the *_get actions

Instance Method Summary collapse

Instance Method Details

#cli_base_flags(opt) ⇒ Object 



10
11
12
13
14
15
16
17
18
19
20
 
# File 'lib/miga/cli/action/download/base.rb', line 10

def cli_base_flags(opt)
  opt.on(
    '--max-download INT', Integer,
    'Maximum number of datasets to download (by default: unlimited)'
  ) { |v| cli[:max_datasets] = v }
  opt.on(
    '-m', '--metadata STRING',
    'Metadata as key-value pairs separated by = and delimited by comma',
    'Values are saved as strings except for booleans (true / false) or nil'
  ) { |v| cli[:metadata] = v }
end

#cli_filters(opt) ⇒ Object 



22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
 
# File 'lib/miga/cli/action/download/base.rb', line 22

def cli_filters(opt)
  opt.on(
    '--exclude PATH',
    'A file with dataset names to exclude'
  ) { |v| cli[:exclude] = v }
  cli.opt_flag(opt, 'dry', 'Do not download or save the datasets')
  opt.on(
    '--ignore-until STRING',
    'Ignores all datasets until a name is found (useful for large reruns)'
  ) { |v| cli[:ignore_until] = v }
  opt.on(
    '--ignore-removed',
    'Ignores entries removed from NCBI (by default fails on removed entries)'
  ) { |v| cli[:ignore_removed] = v }
  cli.opt_flag(
    opt, 'get-metadata',
    'Only download and update metadata for existing datasets', :get_md
  )
  opt.on(
    '--updated-before DATE',
    'Only download metadata for datasets last updated before the given date',
    'Requires --get-metadata, supports date or date-time'
  ) { |v| cli[:updated_before] = DateTime.parse(v) }
end

#cli_save_actions(opt) ⇒ Object 



47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
 
# File 'lib/miga/cli/action/download/base.rb', line 47

def cli_save_actions(opt)
  cli.opt_flag(
    opt, 'only-metadata',
    'Create datasets without input data but retrieve all metadata',
    :only_md
  )
  opt.on(
    '--save-every INT', Integer,
    'Save project every this many downloaded datasets',
    'If zero, it saves the project only once upon completion',
    "By default: #{cli[:save_every]}"
  ) { |v| cli[:save_every] = v }
  opt.on(
    '-q', '--query',
    'Register the datasets as queries, not reference datasets'
  ) { |v| cli[:query] = v }
  opt.on(
    '-u', '--unlink',
    'Unlink all datasets in the project missing from the download list'
  ) { |v| cli[:unlink] = v }
  opt.on(
    '-R', '--remote-list PATH',
    'Path to an output file with the list of all datasets listed remotely'
  ) { |v| cli[:remote_list] = v }
  opt.on(
    '--ncbi-taxonomy-dump [path]',
    'Path to an NCBI Taxonomy dump directory to query instead of API calls',
    'If the path is not passed, the dump is automatically downloaded'
  ) { |v| cli[:ncbi_taxonomy_dump] = v || true }
end

#discard_excluded(ds) ⇒ Object 



135
136
137
138
139
140
141
142
143
144
 
# File 'lib/miga/cli/action/download/base.rb', line 135

def discard_excluded(ds)
  unless cli[:exclude].nil?
    cli.say "Discarding datasets in #{cli[:exclude]}"
    File.readlines(cli[:exclude])
        .select { |i| i !~ /^#/ }
        .map(&:chomp)
        .each { |i| ds.delete i }
  end
  ds
end

#download_entries(ds, p) ⇒ Object 



166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
 
# File 'lib/miga/cli/action/download/base.rb', line 166

def download_entries(ds, p)
  cli.say "Downloading #{ds.size} " + (ds.size == 1 ? 'entry' : 'entries')
  p.do_not_save = true if cli[:save_every] != 1
  ignore = !cli[:ignore_until].nil?
  downloaded = 0
  d = []
  ds.each do |name, body|
    d << name
    cli.puts name
    ignore = false if ignore && name == cli[:ignore_until]
    next if ignore || p.dataset(name).nil? == cli[:get_md]

    downloaded += 1
    unless cli[:dry]
      unless save_entry(name, body, p)
        downloaded -= 1
        d.pop
        next
      end
      p.save! if cli[:save_every] > 1 && (downloaded % cli[:save_every]).zero?
    end
  end
  p.do_not_save = false
  p.save! if cli[:save_every] != 1
  [d, downloaded]
end

#exclude_newer(ds) ⇒ Object 



146
147
148
149
150
151
152
153
154
 
# File 'lib/miga/cli/action/download/base.rb', line 146

def exclude_newer(ds)
  return ds unless cli[:updated_before]

  project = cli.load_project
  ds.select do |name|
    d = project.dataset(name)
    d && DateTime.parse(d.metadata[:updated]) < cli[:updated_before]
  end
end

#finalize_tasks(d, downloaded) ⇒ Object 



119
120
121
122
123
124
125
126
127
128
 
# File 'lib/miga/cli/action/download/base.rb', line 119

def finalize_tasks(d, downloaded)
  cli.say "Datasets listed: #{d.size}"
  act = cli[:dry] ? 'to download' : 'downloaded'
  cli.say "Datasets #{act}: #{downloaded}"
  unless cli[:remote_list].nil?
    File.open(cli[:remote_list], 'w') do |fh|
      d.each { |i| fh.puts i }
    end
  end
end

#generic_perform ⇒ Object 



78
79
80
81
82
83
84
85
 
# File 'lib/miga/cli/action/download/base.rb', line 78

def generic_perform
  p, ds = load_tasks
  d, downloaded = download_entries(ds, p)

  # Finalize
  finalize_tasks(d, downloaded)
  unlink_entries(p, p.dataset_names - d) if cli[:unlink]
end

#impose_limit(ds) ⇒ Object 



156
157
158
159
160
161
162
163
164
 
# File 'lib/miga/cli/action/download/base.rb', line 156

def impose_limit(ds)
  max = cli[:max_datasets].to_i
  if !max.zero? && max < ds.size
    cli.say "Subsampling list from #{ds.size} to #{max} datasets"
    sample = ds.keys.sample(max)
    ds.select! { |k, _| sample.include? k }
  end
  ds
end

#load_ncbi_taxonomy_dump ⇒ Object 



98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
 
# File 'lib/miga/cli/action/download/base.rb', line 98

def load_ncbi_taxonomy_dump
  return unless cli[:ncbi_taxonomy_dump]

  if cli[:ncbi_taxonomy_dump] == true
    cli.say 'Downloading and reading NCBI Taxonomy dump'
    Dir.mktmpdir do |dir|
      file = 'taxdump.tar.gz'
      path = File.join(dir, file)
      url  = 'https://ftp.ncbi.nih.gov/pub/taxonomy/%s' % file
      
      File.open(path, 'wb') { |fh| fh.print MiGA::MiGA.net_method(:get, url) }
      MiGA::MiGA.run_cmd('cd "%s" && tar -zxf "%s"' % [dir, file])
      MiGA::RemoteDataset.use_ncbi_taxonomy_dump(dir, cli)
    end
  else
    cli.say "Reading NCBI Taxonomy dump: #{cli[:ncbi_taxonomy_dump]}"
    MiGA::RemoteDataset.use_ncbi_taxonomy_dump(cli[:ncbi_taxonomy_dump], cli)
  end
end

#load_tasks ⇒ Object 



87
88
89
90
91
92
93
94
95
96
 
# File 'lib/miga/cli/action/download/base.rb', line 87

def load_tasks
  sanitize_cli
  p = cli.load_project
  load_ncbi_taxonomy_dump
  ds = remote_list
  ds = discard_excluded(ds)
  ds = exclude_newer(ds)
  ds = impose_limit(ds)
  [p, ds]
end

#save_entry(name, body, p) ⇒ Object

Saves the (generic remote) entry identified by name with body into the project p, and returns true on success and false otherwise



196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
 
# File 'lib/miga/cli/action/download/base.rb', line 196

def save_entry(name, body, p)
  cli.say "  Locating remote dataset: #{name}"
  body[:md][:metadata_only] = true if cli[:only_md]
  rd = MiGA::RemoteDataset.new(body[:ids], body[:db], body[:universe])
  if cli[:get_md]
    cli.say '  Updating dataset'
    rd.update_metadata(p.dataset(name), body[:md])
  else
    cli.say '  Creating dataset'
    rd.save_to(p, name, !cli[:query], body[:md])
    cli.add_metadata(p.add_dataset(name))
  end
  true
rescue MiGA::RemoteDataMissingError => e
  raise(e) unless cli[:ignore_removed]
  cli.say "    Removed dataset ignored: #{name}"
  false
end

#unlink_entries(p, unlink) ⇒ Object 



130
131
132
133
 
# File 'lib/miga/cli/action/download/base.rb', line 130

def unlink_entries(p, unlink)
  unlink.each { |i| p.unlink_dataset(i).remove! }
  cli.say "Datasets unlinked: #{unlink.size}"
end