rbbt-util 5.27.2 → 5.27.3
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- checksums.yaml +4 -4
- data/lib/rbbt/persist/tsv.rb +5 -5
- data/lib/rbbt/persist/tsv/adapter.rb +39 -13
- data/lib/rbbt/persist/tsv/tokyocabinet.rb +3 -1
- data/lib/rbbt/tsv/accessor.rb +1 -1
- data/lib/rbbt/tsv/change_id.rb +3 -1
- data/lib/rbbt/workflow.rb +1 -1
- data/share/install/software/lib/install_helpers +7 -3
- data/share/rbbt_commands/migrate_job +3 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: ee7d7e81ee4a7981fd286ef0c5d8435aa482d0598068e7d1d19d526dd17a1e9d
|
4
|
+
data.tar.gz: 070db371b5d3ab7e11e52795b648e65dd5f296863cd516ce830b82e3a20e8471
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 6a7d93d19efeac98230ba8d9ba131a2e670b4ff3421606bdef8b0ec5c004e1e0aee2110dc18c64ca59066b4c3c3feb463ed86cc3295010fdb94fcd6f467e6ea0
|
7
|
+
data.tar.gz: 0a53f17d0bced1858aaaede6b55e30caed1347d87a120ed580a6e7bc8031ac4aba8ede384473ec92327b64d5922093e2fe1e0fa0990baca18b88873364ace8b6
|
data/lib/rbbt/persist/tsv.rb
CHANGED
@@ -148,13 +148,13 @@ module Persist
|
|
148
148
|
|
149
149
|
data.write_and_read do
|
150
150
|
yield data
|
151
|
-
end
|
152
151
|
|
153
|
-
|
154
|
-
|
155
|
-
|
152
|
+
FileUtils.mv data.persistence_path, path if File.exist? data.persistence_path and not File.exist? path
|
153
|
+
tsv = CONNECTIONS[path] = CONNECTIONS.delete tmp_path
|
154
|
+
tsv.persistence_path = path
|
156
155
|
|
157
|
-
|
156
|
+
tsv.fix_io if tsv.respond_to? :fix_io
|
157
|
+
end
|
158
158
|
|
159
159
|
data
|
160
160
|
rescue Exception
|
@@ -22,12 +22,6 @@ module Persist
|
|
22
22
|
@closed
|
23
23
|
end
|
24
24
|
|
25
|
-
def close
|
26
|
-
@closed = true
|
27
|
-
super
|
28
|
-
self
|
29
|
-
end
|
30
|
-
|
31
25
|
def write?
|
32
26
|
@writable
|
33
27
|
end
|
@@ -47,8 +41,10 @@ module Persist
|
|
47
41
|
def close(*args)
|
48
42
|
begin
|
49
43
|
super(*args)
|
44
|
+
@closed = true
|
50
45
|
rescue NoMethodError
|
51
46
|
end
|
47
|
+
self
|
52
48
|
end
|
53
49
|
|
54
50
|
def read(*args)
|
@@ -87,6 +83,16 @@ module Persist
|
|
87
83
|
end
|
88
84
|
end
|
89
85
|
|
86
|
+
def lock_and_close
|
87
|
+
lock do
|
88
|
+
begin
|
89
|
+
yield
|
90
|
+
ensure
|
91
|
+
close
|
92
|
+
end
|
93
|
+
end
|
94
|
+
end
|
95
|
+
|
90
96
|
def write_and_read
|
91
97
|
if write?
|
92
98
|
begin
|
@@ -97,7 +103,7 @@ module Persist
|
|
97
103
|
end
|
98
104
|
|
99
105
|
lock do
|
100
|
-
write
|
106
|
+
write(true) if closed? || !write?
|
101
107
|
begin
|
102
108
|
yield
|
103
109
|
ensure
|
@@ -111,12 +117,12 @@ module Persist
|
|
111
117
|
begin
|
112
118
|
return yield
|
113
119
|
ensure
|
114
|
-
close
|
120
|
+
close unless @locked
|
115
121
|
end
|
116
122
|
end
|
117
123
|
|
118
124
|
lock do
|
119
|
-
write
|
125
|
+
write(true) if closed? || ! write?
|
120
126
|
res = begin
|
121
127
|
yield
|
122
128
|
rescue Exception
|
@@ -130,11 +136,12 @@ module Persist
|
|
130
136
|
end
|
131
137
|
|
132
138
|
def read_and_close
|
133
|
-
if
|
139
|
+
#return yield if @locked
|
140
|
+
if read? || write?
|
134
141
|
begin
|
135
142
|
return yield
|
136
143
|
ensure
|
137
|
-
close
|
144
|
+
close unless @locked
|
138
145
|
end
|
139
146
|
end
|
140
147
|
|
@@ -161,8 +168,27 @@ module Persist
|
|
161
168
|
end
|
162
169
|
|
163
170
|
def include?(*args)
|
164
|
-
|
165
|
-
|
171
|
+
self.read_and_close do
|
172
|
+
super(*args) #- TSV::ENTRY_KEYS.to_a
|
173
|
+
end
|
174
|
+
end
|
175
|
+
|
176
|
+
def [](*args)
|
177
|
+
self.read_and_close do
|
178
|
+
super(*args) #- TSV::ENTRY_KEYS.to_a
|
179
|
+
end
|
180
|
+
end
|
181
|
+
|
182
|
+
def []=(*args)
|
183
|
+
self.write_and_close do
|
184
|
+
super(*args) #- TSV::ENTRY_KEYS.to_a
|
185
|
+
end
|
186
|
+
end
|
187
|
+
|
188
|
+
def keys(*args)
|
189
|
+
self.read_and_close do
|
190
|
+
super(*args) #- TSV::ENTRY_KEYS.to_a
|
191
|
+
end
|
166
192
|
end
|
167
193
|
end
|
168
194
|
end
|
data/lib/rbbt/tsv/accessor.rb
CHANGED
@@ -243,7 +243,7 @@ module TSV
|
|
243
243
|
end
|
244
244
|
|
245
245
|
def []=(key, value, clean = false)
|
246
|
-
return super(key, value) if clean
|
246
|
+
return super(key, value) if clean || value.nil? || TSV::CleanSerializer == self.serializer_module
|
247
247
|
super(key, @serializer_module.dump(value))
|
248
248
|
end
|
249
249
|
|
data/lib/rbbt/tsv/change_id.rb
CHANGED
@@ -10,7 +10,8 @@ module TSV
|
|
10
10
|
|
11
11
|
identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace
|
12
12
|
|
13
|
-
|
13
|
+
|
14
|
+
if ! tsv.fields.include?(format)
|
14
15
|
new = {}
|
15
16
|
tsv.each do |k,v|
|
16
17
|
if v === String or v === Array
|
@@ -32,6 +33,7 @@ module TSV
|
|
32
33
|
tsv = tsv.attach identifiers, :fields => [format], :persist_input => true
|
33
34
|
end
|
34
35
|
|
36
|
+
|
35
37
|
tsv = tsv.reorder(format, tsv.fields[0..-2])
|
36
38
|
|
37
39
|
tsv = tsv.to_flat if orig_type == :flat
|
data/lib/rbbt/workflow.rb
CHANGED
@@ -71,7 +71,7 @@ get_pkg(){
|
|
71
71
|
local url="$2"
|
72
72
|
|
73
73
|
if [ ! -f "$OPT_SRC_DIR/$name.pkg" ]; then
|
74
|
-
|
74
|
+
wget "$url" -O "$OPT_SRC_DIR/$name.pkg" || wget "$url" -O "$OPT_SRC_DIR/$name.pkg" --no-check-certificate || (rm -f "$OPT_SRC_DIR/$name.pkg"; echo "Error downloading"; exit -1)
|
75
75
|
fi
|
76
76
|
}
|
77
77
|
|
@@ -85,7 +85,7 @@ uncompress_pkg(){
|
|
85
85
|
mkdir -p "$OPT_BUILD_DIR"
|
86
86
|
cd "$OPT_BUILD_DIR"
|
87
87
|
|
88
|
-
(tar xvfz $pkg || tar xvfJ $pkg || tar xvfj $pkg || unzip $pkg || echo "Error decompressing") 2> /dev/null
|
88
|
+
(tar xvfz $pkg || tar xvfJ $pkg || tar xvfj $pkg || unzip $pkg || (echo "Error decompressing" & cd & rmdir "$OPT_BUILD_DIR" & exit -1 ) ) 2> /dev/null
|
89
89
|
|
90
90
|
cd "$old_pwd"
|
91
91
|
}
|
@@ -207,6 +207,8 @@ prepare_make(){
|
|
207
207
|
|
208
208
|
[ -d src -a ! -e CMakeLists.txt -a ! -e Makefile -a ! -e configure ] && cd src
|
209
209
|
|
210
|
+
[ -f bootstrap ] && (./bootstrap || exit -1)
|
211
|
+
|
210
212
|
if [ -f config/m4 ]; then
|
211
213
|
libtoolize --force
|
212
214
|
aclocal
|
@@ -275,6 +277,8 @@ build_make(){
|
|
275
277
|
setup "$name"
|
276
278
|
clean_build
|
277
279
|
fi
|
280
|
+
|
281
|
+
cd "$old_pwd"
|
278
282
|
}
|
279
283
|
|
280
284
|
buid_cmake(){
|
@@ -489,7 +493,7 @@ install_jar(){
|
|
489
493
|
local url="$2"
|
490
494
|
|
491
495
|
[ -d "$OPT_DIR/$name/" ] || mkdir -p "$OPT_DIR/$name/"
|
492
|
-
wget "$url" -O "$OPT_DIR/$name/$name.jar" --no-check-certificate
|
496
|
+
wget "$url" -O "$OPT_DIR/jars/$name.jar" || wget "$url" -O "$OPT_DIR/jars/$name.jar" --no-check-certificate || (rm "$OPT_DIR/jars/$name.jar"; exit -1)
|
493
497
|
link "$OPT_DIR/$name/$name.jar" "$OPT_JAR_DIR/$name.jar"
|
494
498
|
}
|
495
499
|
|
@@ -3,7 +3,7 @@
|
|
3
3
|
require 'rbbt-util'
|
4
4
|
require 'rbbt/util/simpleopt'
|
5
5
|
require 'rbbt/workflow'
|
6
|
-
require 'rbbt/workflow/
|
6
|
+
require 'rbbt/workflow/remote_workflow'
|
7
7
|
|
8
8
|
$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
|
9
9
|
|
@@ -34,4 +34,6 @@ end
|
|
34
34
|
|
35
35
|
path, search_path, _sep, *other = ARGV
|
36
36
|
|
37
|
+
search_path = 'user' if search_path.nil?
|
38
|
+
|
37
39
|
Step.migrate(path, search_path, options)
|
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: 5.27.
|
4
|
+
version: 5.27.3
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2020-
|
11
|
+
date: 2020-05-05 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|