rbbt-util 5.19.32 → 5.19.34
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- checksums.yaml +4 -4
- data/etc/app.d/entities.rb +0 -8
- data/etc/app.d/requires.rb +7 -0
- data/lib/rbbt/association/item.rb +13 -4
- data/lib/rbbt/tsv/manipulate.rb +1 -1
- data/lib/rbbt/tsv/serializers.rb +2 -1
- data/share/config.ru +3 -0
- data/share/rbbt_commands/workflow/knowledge_base +3 -1
- data/share/rbbt_commands/workflow/server +4 -2
- metadata +3 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
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2
2
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SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 891d8471ba86780e53a5363adac579490a665f05
|
4
|
+
data.tar.gz: f80a9947a157c9aaa5b8de42f2119004afe391b1
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 330ec02481ecae70a0748a0d33f6478576b185a8db7aac15624a2df5473f4762263c320c244f30e80977e377c1daaf82943cb387930e34ee10807107d8a4fbbd
|
7
|
+
data.tar.gz: e49d24357ed693a1cedfe88ae3b9c43d92f28080de7cacf627bc6c5aa2bd3d0c072c07c74a30b9a10f7e7c7f6a46b88771f1e3e40d3967cbe5ce2a25f3c7938a
|
data/etc/app.d/entities.rb
CHANGED
@@ -1,11 +1,3 @@
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|
1
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-
|
2
|
-
#{{{ Require files
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3
|
-
Rbbt.etc.requires.read.split("\n").each do |file|
|
4
|
-
next if file.empty?
|
5
|
-
Log.debug("requiring #{ file }")
|
6
|
-
require file
|
7
|
-
end if Rbbt.etc.requires.exists?
|
8
|
-
|
9
1
|
Entity.entity_list_cache = Rbbt.var.sinatra.find.entity_lists
|
10
2
|
Entity.entity_map_cache = Rbbt.var.sinatra.find.entity_maps
|
11
3
|
Entity.entity_property_cache = Rbbt.var.sinatra.find.entity_properties
|
@@ -108,8 +108,17 @@ module AssociationItem
|
|
108
108
|
fields = [self.source_type, self.target_type].concat info_fields
|
109
109
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type = [self.source_type, self.target_type] * "~"
|
110
110
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tsv = TSV.setup({}, :key_field => type, :fields => fields, :type => :list, :namespace => self.namespace)
|
111
|
-
|
112
|
-
|
111
|
+
index = index(database)
|
112
|
+
index.with_unnamed do
|
113
|
+
index.chunked_values_at(self).each_with_index do |v,i|
|
114
|
+
p = self[i]
|
115
|
+
source, _sep, target = p.partition("~")
|
116
|
+
if info_fields.empty?
|
117
|
+
tsv[p] = [source, target]
|
118
|
+
else
|
119
|
+
tsv[p] = [source, target].concat v
|
120
|
+
end
|
121
|
+
end
|
113
122
|
end
|
114
123
|
tsv.entity_options = {:organism => namespace}
|
115
124
|
knowledge_base.entity_options.each do |type,options|
|
@@ -119,8 +128,8 @@ module AssociationItem
|
|
119
128
|
end
|
120
129
|
|
121
130
|
property :filter => :array do |*args,&block|
|
122
|
-
keys = tsv.select(*args,&block).keys
|
123
|
-
keys = self.annotate
|
131
|
+
keys = tsv.with_unnamed do tsv.select(*args,&block).keys end
|
132
|
+
keys = self.annotate keys
|
124
133
|
keys
|
125
134
|
end
|
126
135
|
|
data/lib/rbbt/tsv/manipulate.rb
CHANGED
data/lib/rbbt/tsv/serializers.rb
CHANGED
data/share/config.ru
CHANGED
@@ -43,6 +43,9 @@ load_file Rbbt.etc['app.d/resources.rb'].find
|
|
43
43
|
#{{{ KNOWLEDGEBASE
|
44
44
|
load_file Rbbt.etc['app.d/knowledge_bases.rb'].find
|
45
45
|
|
46
|
+
#{{{ REQUIRES
|
47
|
+
load_file Rbbt.etc['app.d/requires.rb'].find
|
48
|
+
|
46
49
|
#{{{ ENTITIES
|
47
50
|
load_file Rbbt.etc['app.d/entities.rb'].find
|
48
51
|
|
@@ -10,7 +10,7 @@ Access workflow knowledge_base
|
|
10
10
|
|
11
11
|
$ rbbt workflow knowledge_base <workflow> [<database>] [<action>] [<options>]
|
12
12
|
|
13
|
-
Access workflow knowledge base
|
13
|
+
Access workflow knowledge base. Allowed actions are: list_databases, summary, and subset
|
14
14
|
|
15
15
|
-h--help Show this help:
|
16
16
|
-s--source_entities* Source entities
|
@@ -78,4 +78,6 @@ when :subset
|
|
78
78
|
end
|
79
79
|
end
|
80
80
|
end
|
81
|
+
else
|
82
|
+
raise ParameterException, "Action not understood: #{ action }"
|
81
83
|
end
|
@@ -14,8 +14,6 @@ require 'rbbt/rest/knowledge_base'
|
|
14
14
|
require 'rbbt/rest/helpers'
|
15
15
|
require 'rbbt/rest/web_tool'
|
16
16
|
|
17
|
-
#options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*:-w--workflows*"
|
18
|
-
|
19
17
|
options = SOPT.setup <<EOF
|
20
18
|
Start an rbbt app
|
21
19
|
|
@@ -69,6 +67,10 @@ app.use Rack::Deflater
|
|
69
67
|
|
70
68
|
load Rbbt.etc['app.d/resources.rb'].find
|
71
69
|
|
70
|
+
load Rbbt.etc['app.d/requires.rb'].find
|
71
|
+
|
72
|
+
load Rbbt.etc['app.d/entities.rb'].find
|
73
|
+
|
72
74
|
app.class_eval do
|
73
75
|
eval Rbbt.etc['app.d/finder.rb'].read
|
74
76
|
end
|
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: 5.19.34
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2016-04-
|
11
|
+
date: 2016-04-20 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -163,6 +163,7 @@ files:
|
|
163
163
|
- etc/app.d/grid_system.rb
|
164
164
|
- etc/app.d/init.rb
|
165
165
|
- etc/app.d/knowledge_bases.rb
|
166
|
+
- etc/app.d/requires.rb
|
166
167
|
- etc/app.d/resources.rb
|
167
168
|
- etc/app.d/workflows.rb
|
168
169
|
- lib/rbbt-util.rb
|