rbbt-util 5.19.28 → 5.19.29
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- checksums.yaml +4 -4
- data/lib/rbbt/tsv/attach/util.rb +1 -1
- data/lib/rbbt/tsv/change_id.rb +3 -1
- data/lib/rbbt/tsv/stream.rb +6 -1
- data/lib/rbbt/tsv/util.rb +1 -1
- data/lib/rbbt/util/log.rb +2 -2
- data/lib/rbbt/util/misc/pipes.rb +4 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: dcf03395fb6992f9b928709c4c1a5b62bc8409f8
|
4
|
+
data.tar.gz: 3d06adac3fe7750350c7185c93f61afae8f0b09e
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 06501f7fca063beaff2358c021a46d14a93630d9ab3fd0b68c1df4e4f98e5c810916168401d2dd79d8e3b835b50a5907ac4cf41bae2bce7e18b28f7e9ef1245b
|
7
|
+
data.tar.gz: 91ee3cf063dc7b645b28c3005ee911d5a51d5f1eaf6d78b10a1fd19ebbf64e73d7a95e8793328883febfa67bfee7ee1a6ae77b41c57272432d2e0e98187a9a68
|
data/lib/rbbt/tsv/attach/util.rb
CHANGED
@@ -29,7 +29,7 @@ module TSV
|
|
29
29
|
end
|
30
30
|
end
|
31
31
|
|
32
|
-
new_values.collect!{|v| [v]} if type == :double and not other.type == :double
|
32
|
+
new_values.collect!{|v| [v]} if type == :double and not (other.type == :double or other.type == :flat)
|
33
33
|
new_values.collect!{|v| v.nil? ? nil : (other.type == :single ? v : v.first)} if not type == :double and other.type == :double
|
34
34
|
|
35
35
|
new_values.flatten if type == :flat
|
data/lib/rbbt/tsv/change_id.rb
CHANGED
@@ -51,8 +51,10 @@ module TSV
|
|
51
51
|
options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers, :compact => true
|
52
52
|
|
53
53
|
identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
|
54
|
+
identifiers = tsv.identifier_files.first if identifiers.nil?
|
55
|
+
identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace and Organism.identifiers(tsv.namespace).exists?
|
54
56
|
|
55
|
-
fields = identifiers.all_fields.include?(field)? [field] : nil
|
57
|
+
fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil
|
56
58
|
index = identifiers.index :target => format, :fields => fields, :persist => persist_input
|
57
59
|
|
58
60
|
orig_type = tsv.type
|
data/lib/rbbt/tsv/stream.rb
CHANGED
@@ -18,7 +18,7 @@ module TSV
|
|
18
18
|
|
19
19
|
def self.paste_streams(streams, options = {})
|
20
20
|
options = Misc.add_defaults options, :sep => "\t", :sort => true
|
21
|
-
sort, sep, preamble, header, same_fields, fix_flat = Misc.process_options options, :sort, :sep, :preamble, :header, :same_fields, :fix_flat
|
21
|
+
sort, sep, preamble, header, same_fields, fix_flat, all_match = Misc.process_options options, :sort, :sep, :preamble, :header, :same_fields, :fix_flat, :all_match
|
22
22
|
|
23
23
|
out = Misc.open_pipe do |sin|
|
24
24
|
|
@@ -127,6 +127,9 @@ module TSV
|
|
127
127
|
min = keys.compact.sort.first
|
128
128
|
break if min.nil?
|
129
129
|
str = []
|
130
|
+
|
131
|
+
skip = all_match && keys.uniq != [min]
|
132
|
+
|
130
133
|
keys.each_with_index do |key,i|
|
131
134
|
case key
|
132
135
|
when min
|
@@ -161,6 +164,8 @@ module TSV
|
|
161
164
|
end
|
162
165
|
end
|
163
166
|
|
167
|
+
next if skip
|
168
|
+
|
164
169
|
if same_fields
|
165
170
|
|
166
171
|
values = nil
|
data/lib/rbbt/tsv/util.rb
CHANGED
data/lib/rbbt/util/log.rb
CHANGED
@@ -247,8 +247,8 @@ module Log
|
|
247
247
|
|
248
248
|
def self.tsv(tsv)
|
249
249
|
STDERR.puts Log.color :magenta, "TSV log: " << Log.last_caller(caller)
|
250
|
-
puts Log.color(:blue, "=> "<< Misc.fingerprint(tsv), true)
|
251
|
-
puts Log.color(:cyan, "=> " << tsv.summary)
|
250
|
+
STDERR.puts Log.color(:blue, "=> "<< Misc.fingerprint(tsv), true)
|
251
|
+
STDERR.puts Log.color(:cyan, "=> " << tsv.summary)
|
252
252
|
end
|
253
253
|
|
254
254
|
def self.stack(stack)
|
data/lib/rbbt/util/misc/pipes.rb
CHANGED
@@ -365,6 +365,10 @@ module Misc
|
|
365
365
|
current_parts[i] = current_parts[i] << "|" << part
|
366
366
|
end
|
367
367
|
end
|
368
|
+
|
369
|
+
(parts.length..current_parts.length-1).to_a.each do |pos|
|
370
|
+
current_parts[pos] = current_parts[pos] << "|" << ""
|
371
|
+
end
|
368
372
|
when current_key != key
|
369
373
|
sin.puts [current_key, current_parts].flatten * sep
|
370
374
|
current_key = key
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.19.
|
4
|
+
version: 5.19.29
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2016-03-
|
11
|
+
date: 2016-03-30 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|