sequenceserver 3.1.0 → 3.1.2
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- checksums.yaml +4 -4
- data/lib/sequenceserver/api_errors.rb +55 -1
- data/lib/sequenceserver/blast.rb +6 -0
- data/lib/sequenceserver/database.rb +13 -0
- data/lib/sequenceserver/routes.rb +35 -5
- data/lib/sequenceserver/sequence.rb +34 -7
- data/lib/sequenceserver/server.rb +1 -1
- data/lib/sequenceserver/version.rb +1 -1
- data/public/404.html +1 -1
- data/public/css/app.min.css +1 -1
- data/public/js/download_fasta.js +1 -0
- data/public/js/form.js +1 -0
- data/public/js/sidebar.js +9 -0
- data/public/js/tests/form.spec.js +28 -0
- data/public/js/tests/search_query.spec.js +11 -0
- data/public/sequenceserver-report.min.js +2 -2
- data/public/sequenceserver-search.min.js +1 -1
- data/views/layout.erb +1 -0
- data/views/search_layout.erb +1 -0
- metadata +23 -3
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 1579fdcd4e8dc694025ccde8534ab3a48d935cfef4830a8de2c446657449aaf8
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4
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+
data.tar.gz: 25561e738f1511d4ee40730eec04c943148749313d29ccf362098b15a1e922c5
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 965a7ab34577a0180d8ac1ac830c84737118e4c3fe2997cc61886424929066a95d3df3869c01ca46ffceb3a9ef3d39b96676e87841bf57c0c4903cd99700fde0
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7
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+
data.tar.gz: 3a5fa2dce619076a5e0b626981c2bb95ffc544ae8b920942b2979cabe4869120e549f494cbd15a02bf10e265bb303f8988264824839ea934f80797e280b8045a
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@@ -1,9 +1,10 @@
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1
1
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module SequenceServer
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2
2
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Error = Class.new(Sinatra::Error)
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3
3
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4
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+
ValidationError = Class.new(Error)
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4
5
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# DatabaseUnreachableError is raised when the serialised Job object is
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5
6
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# refering to a database that is not present in the current filesystem.
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6
|
-
class DatabaseUnreachableError <
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7
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+
class DatabaseUnreachableError < ValidationError
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7
8
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attr_reader :more_info
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8
9
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9
10
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def initialize(more_info)
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@@ -11,6 +12,10 @@ module SequenceServer
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11
12
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@more_info = more_info
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12
13
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end
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13
14
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15
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+
def http_status
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16
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+
422
|
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17
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+
end
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18
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+
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|
14
19
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def title
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15
20
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'Sequence database unreachable'
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16
21
|
end
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@@ -22,6 +27,55 @@ module SequenceServer
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22
27
|
end
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23
28
|
end
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24
29
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|
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30
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+
# InvalidSequenceIdError is raised when the FASTA sequence ID provided by the
|
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31
|
+
# frontend appears to be invalid. It is important to validate the sequence ID
|
|
32
|
+
# format for security reasons.
|
|
33
|
+
class InvalidSequenceIdError < ValidationError
|
|
34
|
+
attr_reader :more_info
|
|
35
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+
|
|
36
|
+
def initialize(more_info)
|
|
37
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+
super
|
|
38
|
+
@more_info = more_info
|
|
39
|
+
end
|
|
40
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+
|
|
41
|
+
def http_status
|
|
42
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+
422
|
|
43
|
+
end
|
|
44
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+
|
|
45
|
+
def title
|
|
46
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+
'Sequence ID invalid'
|
|
47
|
+
end
|
|
48
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+
|
|
49
|
+
def message
|
|
50
|
+
"The action you're trying to perform is not possible because \
|
|
51
|
+
one of the FASTA ids seems to be invalid."
|
|
52
|
+
end
|
|
53
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+
end
|
|
54
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+
|
|
55
|
+
# InvalidParameterError is a more generic error class that can be
|
|
56
|
+
# raised when the frontend sends a request with an invalid parameter
|
|
57
|
+
class InvalidParameterError < ValidationError
|
|
58
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+
attr_reader :more_info
|
|
59
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+
|
|
60
|
+
def initialize(more_info)
|
|
61
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+
super
|
|
62
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+
@more_info = more_info
|
|
63
|
+
end
|
|
64
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+
|
|
65
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+
def http_status
|
|
66
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+
422
|
|
67
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+
end
|
|
68
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+
|
|
69
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+
def title
|
|
70
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+
'Invalid parameter'
|
|
71
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+
end
|
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72
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+
|
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73
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+
def message
|
|
74
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+
"The action you're trying to perform is not possible because \
|
|
75
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+
one of the provided parameters is invalid."
|
|
76
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+
end
|
|
77
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+
end
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78
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+
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25
79
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# API errors have an http status, title, message, and additional information
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26
80
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# like stacktrace or information from program output.
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27
81
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APIError = Class.new(Error)
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data/lib/sequenceserver/blast.rb
CHANGED
|
@@ -37,8 +37,19 @@ module SequenceServer
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37
37
|
alias path name
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38
38
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|
|
39
39
|
def retrieve(accession, coords = nil)
|
|
40
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+
fail(
|
|
41
|
+
InvalidSequenceIdError,
|
|
42
|
+
"Invalid sequence id: #{accession}"
|
|
43
|
+
) unless accession =~ SequenceServer::BLAST::VALID_SEQUENCE_ID
|
|
44
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+
|
|
40
45
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cmd = "blastdbcmd -db #{name} -entry '#{accession}'"
|
|
46
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+
|
|
41
47
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if coords
|
|
48
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+
fail(
|
|
49
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+
InvalidParameterError,
|
|
50
|
+
"Invalid range coordinates: #{coords}"
|
|
51
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+
) unless coords =~ /[0-9]+-[0-9]*/
|
|
52
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+
|
|
42
53
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cmd << " -range #{coords}"
|
|
43
54
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end
|
|
44
55
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out, = sys(cmd, path: config[:bin])
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@@ -52,6 +63,8 @@ module SequenceServer
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52
63
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# Returns true if the database contains the given sequence id.
|
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53
64
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# Returns false otherwise.
|
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54
65
|
def include?(id)
|
|
66
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+
fail ArgumentError, "Invalid sequence id: #{id}" unless id =~ SequenceServer::BLAST::VALID_SEQUENCE_ID
|
|
67
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+
|
|
55
68
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cmd = "blastdbcmd -entry '#{id}' -db #{name}"
|
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56
69
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sys(cmd, path: config[:bin]) rescue false
|
|
57
70
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end
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|
@@ -9,6 +9,7 @@ require 'sequenceserver/blast/tasks'
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|
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9
9
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require 'sequenceserver/report'
|
|
10
10
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require 'sequenceserver/database'
|
|
11
11
|
require 'sequenceserver/sequence'
|
|
12
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+
require 'rack/csrf'
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|
12
13
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|
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13
14
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module SequenceServer
|
|
14
15
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# Controller.
|
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@@ -58,6 +59,14 @@ module SequenceServer
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58
59
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frame_options = SequenceServer.config[:frame_options]
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59
60
|
frame_options && { frame_options: frame_options }
|
|
60
61
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}
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|
62
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+
|
|
63
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+
use(
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|
64
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+
Rack::Session::Cookie,
|
|
65
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+
key: 'rack.session.sequenceserver',
|
|
66
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+
secret: ENV.fetch('SESSION_SECRET') { SecureRandom.alphanumeric(64) }
|
|
67
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+
)
|
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68
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+
|
|
69
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+
use Rack::Csrf, raise: true, skip: ['POST:/cloud_share']
|
|
61
70
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end
|
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62
71
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|
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63
72
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unless ENV['SEQUENCE_SERVER_COMPRESS_RESPONSES'] == 'false'
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|
@@ -147,15 +156,35 @@ module SequenceServer
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147
156
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# in identifiers) and retreival_databases (we don't allow whitespace in a
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148
157
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# database's name, so it's safe).
|
|
149
158
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get '/get_sequence/' do
|
|
150
|
-
sequence_ids = params[:sequence_ids].split(',')
|
|
151
|
-
database_ids = params[:database_ids].split(',')
|
|
159
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+
sequence_ids = params[:sequence_ids].to_s.split(',')
|
|
160
|
+
database_ids = params[:database_ids].to_s.split(',')
|
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161
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+
if sequence_ids.empty?
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162
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+
status 422
|
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163
|
+
return { error: 'No sequence ids provided' }.to_json
|
|
164
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+
end
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165
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+
|
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166
|
+
if database_ids.empty?
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167
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+
status 422
|
|
168
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+
return { error: 'No database ids provided' }.to_json
|
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169
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+
end
|
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152
170
|
sequences = Sequence::Retriever.new(sequence_ids, database_ids)
|
|
153
171
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sequences.to_json
|
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154
172
|
end
|
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155
173
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156
174
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post '/get_sequence' do
|
|
157
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-
sequence_ids = params['sequence_ids'].split(',')
|
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158
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-
database_ids = params['database_ids'].split(',')
|
|
175
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+
sequence_ids = params['sequence_ids'].to_s.split(',')
|
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176
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+
database_ids = params['database_ids'].to_s.split(',')
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177
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+
|
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178
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+
if sequence_ids.empty?
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179
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+
status 422
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180
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+
return 'No sequence ids provided'
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181
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+
end
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182
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+
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183
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+
if database_ids.empty?
|
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184
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+
status 422
|
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185
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+
return 'No database ids provided'
|
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186
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+
end
|
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187
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+
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159
188
|
sequences = Sequence::Retriever.new(sequence_ids, database_ids, true)
|
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160
189
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send_file(sequences.file.path,
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161
190
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type: sequences.mime,
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@@ -319,7 +348,8 @@ module SequenceServer
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319
348
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download_links: [
|
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320
349
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{ name: 'Standard Tabular Report', url: "download/#{jid}.std_tsv" },
|
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321
350
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{ name: 'Full Tabular Report', url: "/download/#{jid}.full_tsv" },
|
|
322
|
-
{ name: 'Results in XML', url: "/download/#{jid}.xml" }
|
|
351
|
+
{ name: 'Results in XML', url: "/download/#{jid}.xml" },
|
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352
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+
{ name: 'Pairwise', url: "/download/#{jid}.pairwise" },
|
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323
353
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]
|
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324
354
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}
|
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325
355
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end
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@@ -180,7 +180,7 @@ module SequenceServer
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180
180
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@database_ids = Array database_ids
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181
181
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@in_file = in_file
|
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182
182
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|
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183
|
-
validate && run
|
|
183
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+
validate && create_entry_batch_file && run
|
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184
184
|
end
|
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185
185
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|
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186
186
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attr_reader :sequence_ids, :database_ids, :in_file, :sequences
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@@ -197,10 +197,9 @@ module SequenceServer
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197
197
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def run
|
|
198
198
|
command = "blastdbcmd -outfmt '%g %i %a %t %s'" \
|
|
199
199
|
" -db '#{database_names.join(' ')}'" \
|
|
200
|
-
" -
|
|
200
|
+
" -entry_batch '#{@batch_file.path}'"
|
|
201
201
|
|
|
202
202
|
out, = sys(command, path: config[:bin])
|
|
203
|
-
|
|
204
203
|
@sequences = out.each_line.map do |line|
|
|
205
204
|
# Stop codons in amino acid sequence databases show up as invalid
|
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206
205
|
# UTF-8 characters in the output and cause the subsequent call to
|
|
@@ -208,6 +207,8 @@ module SequenceServer
|
|
|
208
207
|
line = line.encode('UTF-8', invalid: :replace, replace: 'X')
|
|
209
208
|
Sequence.new(*line.chomp.split(' '))
|
|
210
209
|
end
|
|
210
|
+
|
|
211
|
+
@batch_file.unlink
|
|
211
212
|
extend(IO) && write if in_file
|
|
212
213
|
end
|
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213
214
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|
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@@ -221,11 +222,37 @@ module SequenceServer
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221
222
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222
223
|
def validate
|
|
223
224
|
ids = Database.ids
|
|
224
|
-
|
|
225
|
-
|
|
225
|
+
unless database_ids.is_a?(Array) &&
|
|
226
|
+
!database_ids.empty? &&
|
|
227
|
+
(ids & database_ids).length == database_ids.length
|
|
228
|
+
|
|
229
|
+
fail(
|
|
230
|
+
DatabaseUnreachableError,
|
|
231
|
+
"Database id should be one of: #{ids.join("\n")}"
|
|
232
|
+
)
|
|
233
|
+
end
|
|
234
|
+
|
|
235
|
+
invalid_sequence_ids = sequence_ids.reject do |id|
|
|
236
|
+
id =~ SequenceServer::BLAST::VALID_SEQUENCE_ID
|
|
237
|
+
end
|
|
226
238
|
|
|
227
|
-
|
|
228
|
-
|
|
239
|
+
unless invalid_sequence_ids.empty?
|
|
240
|
+
fail(
|
|
241
|
+
InvalidSequenceIdError,
|
|
242
|
+
"Invalid sequence id(s): #{invalid_sequence_ids.join(', ')}"
|
|
243
|
+
)
|
|
244
|
+
end
|
|
245
|
+
|
|
246
|
+
true
|
|
247
|
+
end
|
|
248
|
+
|
|
249
|
+
##
|
|
250
|
+
# Create a temporary file containing sequence ids to fetch.
|
|
251
|
+
def create_entry_batch_file
|
|
252
|
+
@batch_file = Tempfile.new("#{Time.now}_batch").tap do |f|
|
|
253
|
+
f.write(sequence_ids.join("\n"))
|
|
254
|
+
f.flush
|
|
255
|
+
end
|
|
229
256
|
end
|
|
230
257
|
|
|
231
258
|
# rubocop:disable Metrics/MethodLength
|
data/public/404.html
CHANGED
|
@@ -14,7 +14,7 @@
|
|
|
14
14
|
|
|
15
15
|
<body class="bg-light text-dark text-center">
|
|
16
16
|
|
|
17
|
-
<img src="
|
|
17
|
+
<img src="/sequenceserver_logo.webp" alt="SequenceServer Logo" class="mt-5 mb-3" style="max-width: 200px;">
|
|
18
18
|
|
|
19
19
|
<div class="container" style="margin-top: 10%;">
|
|
20
20
|
<h1 class="display-4">404 Not Found</h1>
|
data/public/css/app.min.css
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
/*! tailwindcss v3.4.3 | MIT License | https://tailwindcss.com*/*,:after,:before{box-sizing:border-box;border:0 solid #e5e7eb}:after,:before{--tw-content:""}:host,html{line-height:1.5;-webkit-text-size-adjust:100%;-moz-tab-size:4;-o-tab-size:4;tab-size:4;font-family:ui-sans-serif,system-ui,sans-serif,Apple Color Emoji,Segoe UI Emoji,Segoe UI Symbol,Noto Color Emoji;font-feature-settings:normal;font-variation-settings:normal;-webkit-tap-highlight-color:transparent}body{margin:0;line-height:inherit}hr{height:0;color:inherit;border-top-width:1px}abbr:where([title]){-webkit-text-decoration:underline dotted;text-decoration:underline dotted}h1,h2,h3,h4,h5,h6{font-size:inherit;font-weight:inherit}a{color:inherit;text-decoration:inherit}b,strong{font-weight:bolder}code,kbd,pre,samp{font-family:ui-monospace,SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,monospace;font-feature-settings:normal;font-variation-settings:normal;font-size:1em}small{font-size:80%}sub,sup{font-size:75%;line-height:0;position:relative;vertical-align:initial}sub{bottom:-.25em}sup{top:-.5em}table{text-indent:0;border-color:inherit;border-collapse:collapse}button,input,optgroup,select,textarea{font-family:inherit;font-feature-settings:inherit;font-variation-settings:inherit;font-size:100%;font-weight:inherit;line-height:inherit;letter-spacing:inherit;color:inherit;margin:0;padding:0}button,select{text-transform:none}button,input:where([type=button]),input:where([type=reset]),input:where([type=submit]){-webkit-appearance:button;background-color:initial;background-image:none}:-moz-focusring{outline:auto}:-moz-ui-invalid{box-shadow:none}progress{vertical-align:initial}::-webkit-inner-spin-button,::-webkit-outer-spin-button{height:auto}[type=search]{-webkit-appearance:textfield;outline-offset:-2px}::-webkit-search-decoration{-webkit-appearance:none}::-webkit-file-upload-button{-webkit-appearance:button;font:inherit}summary{display:list-item}blockquote,dd,dl,figure,h1,h2,h3,h4,h5,h6,hr,p,pre{margin:0}fieldset{margin:0}fieldset,legend{padding:0}menu,ol,ul{list-style:none;margin:0;padding:0}dialog{padding:0}textarea{resize:vertical}input::-moz-placeholder,textarea::-moz-placeholder{opacity:1;color:#9ca3af}input::placeholder,textarea::placeholder{opacity:1;color:#9ca3af}[role=button],button{cursor:pointer}:disabled{cursor:default}audio,canvas,embed,iframe,img,object,svg,video{display:block;vertical-align:middle}img,video{max-width:100%;height:auto}[hidden]{display:none}*,::backdrop,:after,:before{--tw-border-spacing-x:0;--tw-border-spacing-y:0;--tw-translate-x:0;--tw-translate-y:0;--tw-rotate:0;--tw-skew-x:0;--tw-skew-y:0;--tw-scale-x:1;--tw-scale-y:1;--tw-pan-x: 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0;border-right-color:#000}.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-width:5px 0 5px 5px;border-left-color:#000}.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip.bottom-left .tooltip-arrow{top:0;right:5px;margin-top:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip.bottom-right .tooltip-arrow{top:0;left:5px;margin-top:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip-inner{max-width:200px;padding:3px 8px;color:#fff;text-align:center;background-color:#000;border-radius:4px}.tooltip-arrow{position:absolute;width:0;height:0;border-color:#0000;border-style:solid}.hover\:bg-blue-400:hover{--tw-bg-opacity:1;background-color:rgb(96 165 250/var(--tw-bg-opacity))}.hover\:bg-gray-200:hover{--tw-bg-opacity:1;background-color:rgb(229 231 235/var(--tw-bg-opacity))}.hover\:bg-gray-300:hover{--tw-bg-opacity:1;background-color:rgb(209 213 219/var(--tw-bg-opacity))}.hover\:bg-red-600:hover{--tw-bg-opacity:1;background-color:rgb(220 38 38/var(--tw-bg-opacity))}.hover\:bg-seqorange:hover{--tw-bg-opacity:1;background-color:rgb(199 79 19/var(--tw-bg-opacity))}.hover\:bg-sky-400:hover{--tw-bg-opacity:1;background-color:rgb(56 189 248/var(--tw-bg-opacity))}.hover\:bg-sky-500:hover{--tw-bg-opacity:1;background-color:rgb(14 165 233/var(--tw-bg-opacity))}.hover\:bg-yellow-100:hover{--tw-bg-opacity:1;background-color:rgb(254 249 195/var(--tw-bg-opacity))}.hover\:font-bold:hover{font-weight:700}.hover\:text-white:hover{--tw-text-opacity:1;color:rgb(255 255 255/var(--tw-text-opacity))}.focus\:outline-none:focus{outline:2px solid #0000;outline-offset:2px}.focus\:ring-1:focus{--tw-ring-offset-shadow:var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);--tw-ring-shadow:var(--tw-ring-inset) 0 0 0 calc(1px + var(--tw-ring-offset-width)) var(--tw-ring-color)}.focus\:ring-1:focus,.focus\:ring-2:focus{box-shadow:var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow,0 0 #0000)}.focus\:ring-2:focus{--tw-ring-offset-shadow:var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);--tw-ring-shadow:var(--tw-ring-inset) 0 0 0 calc(2px + var(--tw-ring-offset-width)) var(--tw-ring-color)}.focus\:ring-seqorange:focus{--tw-ring-opacity:1;--tw-ring-color:rgb(199 79 19/var(--tw-ring-opacity))}.focus\:ring-offset-2:focus{--tw-ring-offset-width:2px}.group:hover .group-hover\:visible{visibility:visible}@media (min-width:640px){.sm\:my-8{margin-top:2rem;margin-bottom:2rem}.sm\:ml-3{margin-left:.75rem}.sm\:mt-0{margin-top:0}.sm\:block{display:block}.sm\:inline-block{display:inline-block}.sm\:flex{display:flex}.sm\:h-screen{height:100vh}.sm\:w-auto{width:auto}.sm\:w-full{width:100%}.sm\:max-w-screen-md{max-width:768px}.sm\:grid-cols-3{grid-template-columns:repeat(3,minmax(0,1fr))}.sm\:flex-row-reverse{flex-direction:row-reverse}.sm\:items-center{align-items:center}.sm\:p-0{padding:0}.sm\:p-6{padding:1.5rem}.sm\:px-6{padding-left:1.5rem;padding-right:1.5rem}.sm\:pb-4{padding-bottom:1rem}.sm\:align-middle{vertical-align:middle}.sm\:text-sm{font-size:.875rem;line-height:1.25rem}}@media (min-width:768px){.md\:my-2{margin-top:.5rem;margin-bottom:.5rem}.md\:flex{display:flex}.md\:w-auto{width:auto}.md\:grid-cols-2{grid-template-columns:repeat(2,minmax(0,1fr))}.md\:grid-cols-3{grid-template-columns:repeat(3,minmax(0,1fr))}.md\:space-x-4>:not([hidden])~:not([hidden]){--tw-space-x-reverse:0;margin-right:calc(1rem*var(--tw-space-x-reverse));margin-left:calc(1rem*(1 - var(--tw-space-x-reverse)))}.md\:divide-x>:not([hidden])~:not([hidden]){--tw-divide-x-reverse:0;border-right-width:calc(1px*var(--tw-divide-x-reverse));border-left-width:calc(1px*(1 - var(--tw-divide-x-reverse)))}.md\:divide-y-0>:not([hidden])~:not([hidden]){--tw-divide-y-reverse:0;border-top-width:calc(0px*(1 - var(--tw-divide-y-reverse)));border-bottom-width:calc(0px*var(--tw-divide-y-reverse))}.md\:pl-2{padding-left:.5rem}.md\:pt-0{padding-top:0}}@media (min-width:1024px){.lg\:px-8{padding-left:2rem;padding-right:2rem}}
|
data/public/js/download_fasta.js
CHANGED
|
@@ -7,6 +7,7 @@ export default function downloadFASTA(sequence_ids, database_ids) {
|
|
|
7
7
|
var form = $('<form/>').attr('method', 'post').attr('action', 'get_sequence');
|
|
8
8
|
addField('sequence_ids', sequence_ids);
|
|
9
9
|
addField('database_ids', database_ids);
|
|
10
|
+
addField('_csrf', document.querySelector('meta[name="_csrf"]').content);
|
|
10
11
|
form.appendTo('body').submit().remove();
|
|
11
12
|
|
|
12
13
|
function addField(name, val) {
|
data/public/js/form.js
CHANGED
|
@@ -203,6 +203,7 @@ export class Form extends Component {
|
|
|
203
203
|
</div>
|
|
204
204
|
|
|
205
205
|
<form id="blast" ref={this.formRef} onSubmit={this.handleFormSubmission}>
|
|
206
|
+
<input type="hidden" name="_csrf" value={document.querySelector('meta[name="_csrf"]').content} />
|
|
206
207
|
<div className="px-4">
|
|
207
208
|
<SearchQueryWidget ref="query" onSequenceTypeChanged={this.handleSequenceTypeChanged} onSequenceChanged={this.handleSequenceChanged}/>
|
|
208
209
|
|
data/public/js/sidebar.js
CHANGED
|
@@ -350,6 +350,15 @@ export default class extends Component {
|
|
|
350
350
|
</a>
|
|
351
351
|
</li>
|
|
352
352
|
}
|
|
353
|
+
{
|
|
354
|
+
!this.props.data.imported_xml && <li>
|
|
355
|
+
<a className="btn-link download" data-toggle="tooltip"
|
|
356
|
+
title="Results in pairwise format."
|
|
357
|
+
href={'download/' + this.props.data.search_id + '.pairwise'}>
|
|
358
|
+
Full Pairwise report
|
|
359
|
+
</a>
|
|
360
|
+
</li>
|
|
361
|
+
}
|
|
353
362
|
<DownloadLinks imported_xml={this.props.data.imported_xml} search_id={this.props.data.search_id} />
|
|
354
363
|
</ul>
|
|
355
364
|
</div>
|
|
@@ -13,6 +13,20 @@ export const setMockJSONResult = (result) => {
|
|
|
13
13
|
};
|
|
14
14
|
|
|
15
15
|
describe('ADVANCED PARAMETERS', () => {
|
|
16
|
+
let csrfMetaTag;
|
|
17
|
+
|
|
18
|
+
beforeEach(() => {
|
|
19
|
+
csrfMetaTag = document.createElement('meta');
|
|
20
|
+
csrfMetaTag.setAttribute('name', '_csrf');
|
|
21
|
+
csrfMetaTag.setAttribute('content', 'test-token');
|
|
22
|
+
document.head.appendChild(csrfMetaTag);
|
|
23
|
+
});
|
|
24
|
+
|
|
25
|
+
afterEach(() => {
|
|
26
|
+
// Remove the CSRF meta tag after each test to clean up
|
|
27
|
+
document.head.removeChild(csrfMetaTag);
|
|
28
|
+
});
|
|
29
|
+
|
|
16
30
|
const getInputElement = () => screen.getByRole('textbox', { name: '' });
|
|
17
31
|
test('should not render the link to advanced parameters modal if blast algorithm is unknown', () => {
|
|
18
32
|
setMockJSONResult(data);
|
|
@@ -37,6 +51,20 @@ describe('ADVANCED PARAMETERS', () => {
|
|
|
37
51
|
});
|
|
38
52
|
|
|
39
53
|
describe('query stats', () => {
|
|
54
|
+
let csrfMetaTag;
|
|
55
|
+
|
|
56
|
+
beforeEach(() => {
|
|
57
|
+
csrfMetaTag = document.createElement('meta');
|
|
58
|
+
csrfMetaTag.setAttribute('name', '_csrf');
|
|
59
|
+
csrfMetaTag.setAttribute('content', 'test-token');
|
|
60
|
+
document.head.appendChild(csrfMetaTag);
|
|
61
|
+
});
|
|
62
|
+
|
|
63
|
+
afterEach(() => {
|
|
64
|
+
// Remove the CSRF meta tag after each test to clean up
|
|
65
|
+
document.head.removeChild(csrfMetaTag);
|
|
66
|
+
});
|
|
67
|
+
|
|
40
68
|
const getInputElement = () => screen.getByRole('textbox', { name: '' });
|
|
41
69
|
|
|
42
70
|
test('should render the query stats modal when clicked', () => {
|
|
@@ -10,12 +10,23 @@ let container;
|
|
|
10
10
|
let inputEl;
|
|
11
11
|
|
|
12
12
|
describe('SEARCH COMPONENT', () => {
|
|
13
|
+
let csrfMetaTag;
|
|
14
|
+
|
|
13
15
|
beforeEach(() => {
|
|
16
|
+
csrfMetaTag = document.createElement('meta');
|
|
17
|
+
csrfMetaTag.setAttribute('name', '_csrf');
|
|
18
|
+
csrfMetaTag.setAttribute('content', 'test-token');
|
|
19
|
+
document.head.appendChild(csrfMetaTag);
|
|
14
20
|
container = render(<Form onSequenceTypeChanged={() => { }
|
|
15
21
|
} />).container;
|
|
16
22
|
inputEl = screen.getByRole('textbox', { name: '' });
|
|
17
23
|
});
|
|
18
24
|
|
|
25
|
+
afterEach(() => {
|
|
26
|
+
// Remove the CSRF meta tag after each test to clean up
|
|
27
|
+
document.head.removeChild(csrfMetaTag);
|
|
28
|
+
});
|
|
29
|
+
|
|
19
30
|
test('should render the search component textarea', () => {
|
|
20
31
|
expect(inputEl).toBeInTheDocument();
|
|
21
32
|
});
|
|
@@ -60,7 +60,7 @@ eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpac
|
|
|
60
60
|
/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
|
|
61
61
|
|
|
62
62
|
"use strict";
|
|
63
|
-
eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */ \"default\": () => (/* binding */ downloadFASTA)\n/* harmony export */ });\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\n/**\n * Dynamically create form and submit.\n *\n * Author: Filip Ter\n */\nfunction downloadFASTA(sequence_ids, database_ids) {\n var form = $('<form/>').attr('method', 'post').attr('action', 'get_sequence');\n addField('sequence_ids', sequence_ids);\n addField('database_ids', database_ids);\n form.appendTo('body').submit().remove();\n function addField(name, val) {\n form.append($('<input>').attr('type', 'hidden').attr('name', name).val(val));\n }\n}\n\n//# sourceURL=webpack://SequenceServer/./public/js/download_fasta.js?");
|
|
63
|
+
eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */ \"default\": () => (/* binding */ downloadFASTA)\n/* harmony export */ });\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\n/**\n * Dynamically create form and submit.\n *\n * Author: Filip Ter\n */\nfunction downloadFASTA(sequence_ids, database_ids) {\n var form = $('<form/>').attr('method', 'post').attr('action', 'get_sequence');\n addField('sequence_ids', sequence_ids);\n addField('database_ids', database_ids);\n addField('_csrf', document.querySelector('meta[name=\"_csrf\"]').content);\n form.appendTo('body').submit().remove();\n function addField(name, val) {\n form.append($('<input>').attr('type', 'hidden').attr('name', name).val(val));\n }\n}\n\n//# sourceURL=webpack://SequenceServer/./public/js/download_fasta.js?");
|
|
64
64
|
|
|
65
65
|
/***/ }),
|
|
66
66
|
|
|
@@ -302,7 +302,7 @@ eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpac
|
|
|
302
302
|
/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
|
|
303
303
|
|
|
304
304
|
"use strict";
|
|
305
|
-
eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */ \"default\": () => (/* binding */ _default)\n/* harmony export */ });\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_0__);\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var _download_fasta__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! ./download_fasta */ \"./public/js/download_fasta.js\");\n/* harmony import */ var _mailto__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./mailto */ \"./public/js/mailto.js\");\n/* harmony import */ var _cloud_share_modal__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./cloud_share_modal */ \"./public/js/cloud_share_modal.js\");\n/* harmony import */ var download_links__WEBPACK_IMPORTED_MODULE_5__ = __webpack_require__(/*! download_links */ \"./public/js/null_plugins/download_links.js\");\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\nfunction _callSuper(_this, derived, args) {\n function isNativeReflectConstruct() {\n if (typeof Reflect === \"undefined\" || !Reflect.construct) return false;\n if (Reflect.construct.sham) return false;\n if (typeof Proxy === \"function\") return true;\n try {\n return !Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {}));\n } catch (e) {\n return false;\n }\n }\n derived = _getPrototypeOf(derived);\n return _possibleConstructorReturn(_this, isNativeReflectConstruct() ? Reflect.construct(derived, args || [], _getPrototypeOf(_this).constructor) : derived.apply(_this, args));\n}\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\n\n\n\n\n\n/**\n * checks whether code is being run by jest\n */\n// eslint-disable-next-line no-undef\n\nvar isTestMode = function isTestMode() {\n return ({}).JEST_WORKER_ID !== undefined || \"development\" === 'test';\n};\n/**\n * Renders links for downloading hit information in different formats.\n * Renders links for navigating to each query.\n */\nvar _default = /*#__PURE__*/function (_Component) {\n function _default(props) {\n var _this2;\n _classCallCheck(this, _default);\n _this2 = _callSuper(this, _default, [props]);\n _this2.downloadFastaOfAll = _this2.downloadFastaOfAll.bind(_this2);\n _this2.downloadFastaOfSelected = _this2.downloadFastaOfSelected.bind(_this2);\n _this2.topPanelJSX = _this2.topPanelJSX.bind(_this2);\n _this2.summaryString = _this2.summaryString.bind(_this2);\n _this2.indexJSX = _this2.indexJSX.bind(_this2);\n _this2.downloadsPanelJSX = _this2.downloadsPanelJSX.bind(_this2);\n _this2.handleQueryIndexChange = _this2.handleQueryIndexChange.bind(_this2);\n _this2.isElementInViewPort = _this2.isElementInViewPort.bind(_this2);\n _this2.setVisibleQueryIndex = _this2.setVisibleQueryIndex.bind(_this2);\n _this2.debounceScrolling = _this2.debounceScrolling.bind(_this2);\n _this2.scrollListener = _this2.scrollListener.bind(_this2);\n _this2.copyURL = _this2.copyURL.bind(_this2);\n _this2.shareCloudInit = _this2.shareCloudInit.bind(_this2);\n _this2.sharingPanelJSX = _this2.sharingPanelJSX.bind(_this2);\n _this2.timeout = null;\n _this2.queryElems = [];\n _this2.state = {\n queryIndex: 1\n };\n return _this2;\n }\n _inherits(_default, _Component);\n return _createClass(_default, [{\n key: \"componentDidMount\",\n value: function componentDidMount() {\n /**\n * Fixes tooltips in the sidebar, allows tooltip display on click\n */\n $(function () {\n $('.sidebar [data-toggle=\"tooltip\"]').tooltip({\n placement: 'right'\n });\n $('#copyURL').tooltip({\n title: 'Copied!',\n trigger: 'click',\n placement: 'right',\n delay: 0\n });\n });\n\n //keep track of the current queryIndex so it doesn't get lost on page reload\n var urlMatch = window.location.href.match(/#Query_(\\d+)/);\n if (urlMatch && urlMatch.length > 1) {\n var queryNumber = +urlMatch[1];\n var index = this.props.data.queries.findIndex(function (query) {\n return query.number === queryNumber;\n });\n this.setState({\n queryIndex: index + 1\n });\n }\n window.addEventListener('scroll', this.scrollListener);\n $('a[href^=\"#Query_\"]').on('click', this.animateAnchorElements);\n }\n }, {\n key: \"componentWillUnmount\",\n value: function componentWillUnmount() {\n window.removeEventListener('scroll', this.scrollListener);\n }\n }, {\n key: \"componentDidUpdate\",\n value: function componentDidUpdate(prevProps) {\n if (this.props.allQueriesLoaded && !prevProps.allQueriesLoaded) {\n /**\n * storing all query elements in this variable once they all become available so we don't have to fetch them all over again\n */\n this.queryElems = Array.from(document.querySelectorAll('.resultn'));\n }\n }\n\n /**\n * to avoid unnecessary computations, we debounce the scroll listener so it only fires after user has stopped scrolling for some milliseconds\n */\n }, {\n key: \"scrollListener\",\n value: function scrollListener() {\n this.debounceScrolling(this.setVisibleQueryIndex, 500);\n }\n }, {\n key: \"debounceScrolling\",\n value: function debounceScrolling(callback, timer) {\n if (this.timeout) {\n clearTimeout(this.timeout);\n }\n this.timeout = setTimeout(callback, timer);\n }\n\n /**\n * This method makes the page aware of what query is visible so that clicking previous / next button at any point\n * navigates to the proper query\n */\n }, {\n key: \"setVisibleQueryIndex\",\n value: function setVisibleQueryIndex() {\n var queryElems = this.queryElems.length ? this.queryElems : Array.from(document.querySelectorAll('.resultn'));\n var hits = Array.from(document.querySelectorAll('.hit[id^=Query_]'));\n // get the first visible element and marks it as the current query\n var topmostEl = queryElems.find(this.isElementInViewPort) || hits.find(this.isElementInViewPort);\n if (topmostEl) {\n var queryIndex = Number(topmostEl.id.match(/Query_(\\d+)/)[1]);\n var hash = \"#Query_\".concat(queryIndex);\n // if we can guarantee that the browser can handle change in url hash without the page jumping,\n // then we update the url hash after scroll. else, hash is only updated on click of next or prev button\n if (window.history.pushState) {\n window.history.pushState(null, null, hash);\n }\n this.setState({\n queryIndex: queryIndex\n });\n }\n }\n }, {\n key: \"animateAnchorElements\",\n value: function animateAnchorElements(e) {\n // allow normal behavior in test mode to prevent warnings or errors from jquery\n if (isTestMode()) return;\n e.preventDefault();\n $('html, body').animate({\n scrollTop: $(this.hash).offset().top\n }, 300);\n if (window.history.pushState) {\n window.history.pushState(null, null, this.hash);\n } else {\n window.location.hash = this.hash;\n }\n }\n }, {\n key: \"isElementInViewPort\",\n value: function isElementInViewPort(elem) {\n var _elem$getBoundingClie = elem.getBoundingClientRect(),\n top = _elem$getBoundingClie.top,\n left = _elem$getBoundingClie.left,\n right = _elem$getBoundingClie.right,\n bottom = _elem$getBoundingClie.bottom;\n return top >= 0 && left >= 0 && bottom <= (window.innerHeight || document.documentElement.clientHeight) && right <= (window.innerWidth || document.documentElement.clientWidth);\n }\n /**\n * Clear sessionStorage - useful to initiate a new search in the same tab.\n * Passing sessionStorage.clear directly as onclick callback didn't work\n * (on macOS Chrome).\n */\n }, {\n key: \"clearSession\",\n value: function clearSession() {\n sessionStorage.clear();\n }\n /**\n *\n * handle next and previous query button clicks\n */\n }, {\n key: \"handleQueryIndexChange\",\n value: function handleQueryIndexChange(nextQuery) {\n if (nextQuery < 1 || nextQuery > this.props.data.queries.length) return;\n var anchorEl = document.createElement('a');\n //indexing at [nextQuery - 1] because array is 0-indexed\n anchorEl.setAttribute('href', '#Query_' + this.props.data.queries[nextQuery - 1].number);\n anchorEl.setAttribute('hidden', true);\n document.body.appendChild(anchorEl);\n // add smooth scrolling animation with jquery\n $(anchorEl).on('click', this.animateAnchorElements);\n anchorEl.click();\n document.body.removeChild(anchorEl);\n this.setState({\n queryIndex: nextQuery\n });\n }\n /**\n * Event-handler for downloading fasta of all hits.\n */\n }, {\n key: \"downloadFastaOfAll\",\n value: function downloadFastaOfAll() {\n var sequence_ids = [];\n this.props.data.queries.forEach(function (query) {\n return query.hits.forEach(function (hit) {\n return sequence_ids.push(hit.id);\n });\n });\n var database_ids = this.props.data.querydb.map(function (querydb) {\n return querydb.id;\n });\n (0,_download_fasta__WEBPACK_IMPORTED_MODULE_2__[\"default\"])(sequence_ids, database_ids);\n return false;\n }\n\n /**\n * Handles downloading fasta of selected hits.\n */\n }, {\n key: \"downloadFastaOfSelected\",\n value: function downloadFastaOfSelected() {\n var sequence_ids = $('.hit-links :checkbox:checked').map(function () {\n return this.value;\n }).get();\n if (sequence_ids.length === 0) {\n return false;\n }\n var database_ids = underscore__WEBPACK_IMPORTED_MODULE_1__[\"default\"].map(this.props.data.querydb, underscore__WEBPACK_IMPORTED_MODULE_1__[\"default\"].iteratee('id'));\n (0,_download_fasta__WEBPACK_IMPORTED_MODULE_2__[\"default\"])(sequence_ids, database_ids);\n return false;\n }\n\n /**\n * Handles copying the URL into the user's clipboard. Modified from: https://stackoverflow.com/a/49618964/18117380\n * Hides the 'Copied!' tooltip after 3 seconds\n */\n }, {\n key: \"copyURL\",\n value: function copyURL() {\n var element = document.createElement('input');\n var url = window.location.href;\n document.body.appendChild(element);\n element.value = url;\n element.select();\n document.execCommand('copy');\n document.body.removeChild(element);\n setTimeout(function () {\n $('#copyURL')._tooltip('hide');\n }, 3000);\n }\n }, {\n key: \"shareCloudInit\",\n value: function shareCloudInit() {\n this.refs.cloudShareModal.show();\n }\n }, {\n key: \"topPanelJSX\",\n value: function topPanelJSX() {\n var path = location.pathname.split('/');\n // Get job id.\n var job_id = path.pop();\n // Deriving rootURL this way is required for subURI deployments\n // - we cannot just send to '/'.\n var rootURL = path.join('/');\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"sidebar-top-panel\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"div\", {\n className: \"section-header-sidebar\",\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"h4\", {\n children: this.summaryString()\n })\n }), this.props.data.queries.length > 12 && this.queryIndexButtons(), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n href: \"\".concat(rootURL, \"/?job_id=\").concat(job_id),\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-pencil\"\n }), \" Edit search\"]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"span\", {\n className: \"line\",\n children: \"|\"\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n href: \"\".concat(rootURL, \"/\"),\n onClick: this.clearSession,\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-file-o\"\n }), \" New search\"]\n })]\n }), this.props.shouldShowIndex && this.indexJSX()]\n });\n }\n }, {\n key: \"summaryString\",\n value: function summaryString() {\n var program = this.props.data.program;\n var numqueries = this.props.data.queries.length;\n var numquerydb = this.props.data.querydb.length;\n return program.toUpperCase() + ': ' + numqueries + ' ' + (numqueries > 1 ? 'queries' : 'query') + ', ' + numquerydb + ' ' + (numquerydb > 1 ? 'databases' : 'database');\n }\n }, {\n key: \"queryIndexButtons\",\n value: function queryIndexButtons() {\n var _this3 = this;\n var buttonStyle = {\n outline: 'none',\n border: 'none',\n background: 'none'\n };\n var buttonClasses = 'btn-link nowrap-ellipsis hover-bold';\n var handlePreviousBtnClick = function handlePreviousBtnClick() {\n return _this3.handleQueryIndexChange(_this3.state.queryIndex - 1);\n };\n var handleNextBtnClick = function handleNextBtnClick() {\n return _this3.handleQueryIndexChange(_this3.state.queryIndex + 1);\n };\n\n // eslint-disable-next-line no-unused-vars\n var NavButton = function NavButton(_ref) {\n var text = _ref.text,\n onClick = _ref.onClick;\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"button\", {\n className: buttonClasses,\n onClick: onClick,\n style: buttonStyle,\n children: text\n });\n };\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n style: {\n display: 'flex',\n width: '100%',\n margin: '7px 0'\n },\n children: [this.state.queryIndex > 1 && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(NavButton, {\n text: \"Previous Query\",\n onClick: handlePreviousBtnClick\n }), this.state.queryIndex > 1 && this.state.queryIndex < this.props.data.queries.length && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"span\", {\n className: \"line\",\n children: \"|\"\n }), this.state.queryIndex < this.props.data.queries.length && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(NavButton, {\n onClick: handleNextBtnClick,\n text: \"Next Query\"\n })]\n });\n }\n }, {\n key: \"indexJSX\",\n value: function indexJSX() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"ul\", {\n className: \"nav hover-reset active-bold\",\n children: [\" \", underscore__WEBPACK_IMPORTED_MODULE_1__[\"default\"].map(this.props.data.queries, function (query) {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link nowrap-ellipsis hover-bold\",\n title: 'Query= ' + query.id + ' ' + query.title,\n href: '#Query_' + query.number,\n children: 'Query= ' + query.id\n })\n }, 'Side_bar_' + query.id);\n })]\n });\n }\n }, {\n key: \"downloadsPanelJSX\",\n value: function downloadsPanelJSX() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"downloads\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"div\", {\n className: \"section-header-sidebar\",\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"h4\", {\n children: \"Download FASTA, XML, TSV\"\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"ul\", {\n className: \"nav\",\n children: [!(this.props.data.imported_xml || this.props.data.non_parse_seqids) && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n href: \"#\",\n className: \"btn-link download-fasta-of-all \".concat(!this.props.atLeastOneHit && 'disabled'),\n onClick: this.downloadFastaOfAll,\n children: \"FASTA of all hits\"\n })\n }), !(this.props.data.imported_xml || this.props.data.non_parse_seqids) && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n href: \"#\",\n className: \"btn-link download-fasta-of-selected disabled\",\n onClick: this.downloadFastaOfSelected,\n children: [\"FASTA of \", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"span\", {\n className: \"text-bold\"\n }), \" selected hit(s)\"]\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n href: \"#\",\n className: \"btn-link download-alignment-of-all \".concat(!this.props.atLeastOneHit && 'disabled'),\n children: \"Alignment of all hits\"\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n href: \"#\",\n className: \"btn-link download-alignment-of-selected disabled\",\n children: [\"Alignment of \", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"span\", {\n className: \"text-bold\"\n }), \" selected hit(s)\"]\n })\n }), !this.props.data.imported_xml && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link download\",\n \"data-toggle\": \"tooltip\",\n title: \"15 columns: query and subject ID; scientific name, alignment length, mismatches, gaps, identity, start and end coordinates, e value, bitscore, query coverage per subject and per HSP.\",\n href: 'download/' + this.props.data.search_id + '.std_tsv',\n children: \"Standard tabular report\"\n })\n }), !this.props.data.imported_xml && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link download\",\n \"data-toggle\": \"tooltip\",\n title: \"44 columns: query and subject ID, GI, accessions, and length; alignment details; taxonomy details of subject sequence(s) and query coverage per subject and per HSP.\",\n href: 'download/' + this.props.data.search_id + '.full_tsv',\n children: \"Full tabular report\"\n })\n }), !this.props.data.imported_xml && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link download\",\n \"data-toggle\": \"tooltip\",\n title: \"Results in XML format.\",\n href: 'download/' + this.props.data.search_id + '.xml',\n children: \"Full XML report\"\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(download_links__WEBPACK_IMPORTED_MODULE_5__[\"default\"], {\n imported_xml: this.props.data.imported_xml,\n search_id: this.props.data.search_id\n })]\n })]\n });\n }\n }, {\n key: \"sharingPanelJSX\",\n value: function sharingPanelJSX() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"sharing-panel\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"div\", {\n className: \"section-header-sidebar\",\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"h4\", {\n children: \"Share results\"\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"ul\", {\n className: \"nav\",\n children: [!this.props.cloudSharingEnabled && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n id: \"copyURL\",\n className: \"btn-link copy-URL cursor-pointer\",\n \"data-toggle\": \"tooltip\",\n onClick: this.copyURL,\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-copy\"\n }), \" Copy URL to clipboard\"]\n })\n }), !this.props.cloudSharingEnabled && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n id: \"sendEmail\",\n className: \"btn-link email-URL cursor-pointer\",\n \"data-toggle\": \"tooltip\",\n title: \"Send by email\",\n href: (0,_mailto__WEBPACK_IMPORTED_MODULE_3__[\"default\"])(this.props.data.querydb, this.props.data.program, this.props.data.queries.length, window.location.href),\n target: \"_blank\",\n rel: \"noopener noreferrer\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-envelope\"\n }), \" Send by email\"]\n })\n }), this.props.cloudSharingEnabled && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"button\", {\n className: \"btn-link cloud-Post cursor-pointer\",\n \"data-toggle\": \"tooltip\",\n title: \"Upload results to SequenceServer Cloud where it will become accessable to everyone who has a link.\",\n onClick: this.shareCloudInit,\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-cloud\"\n }), \" Share to cloud\"]\n })\n })]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(_cloud_share_modal__WEBPACK_IMPORTED_MODULE_4__[\"default\"], {\n ref: \"cloudShareModal\",\n querydb: this.props.data.querydb,\n program: this.props.data.program,\n queryLength: this.props.data.queries.length\n })]\n });\n }\n }, {\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"sidebar\",\n children: [this.topPanelJSX(), this.downloadsPanelJSX(), this.sharingPanelJSX(), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"div\", {\n className: \"referral-panel\",\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"section-header-sidebar\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"h4\", {\n children: \"Recommend SequenceServer\"\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"p\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n href: \"https://sequenceserver.com/referral-program\",\n target: \"_blank\",\n children: \"Earn up to $100 per signup\"\n })\n })]\n })\n })]\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\n\n//# sourceURL=webpack://SequenceServer/./public/js/sidebar.js?");
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eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */ \"default\": () => (/* binding */ _default)\n/* harmony export */ });\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_0__);\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var _download_fasta__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! ./download_fasta */ \"./public/js/download_fasta.js\");\n/* harmony import */ var _mailto__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./mailto */ \"./public/js/mailto.js\");\n/* harmony import */ var _cloud_share_modal__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./cloud_share_modal */ \"./public/js/cloud_share_modal.js\");\n/* harmony import */ var download_links__WEBPACK_IMPORTED_MODULE_5__ = __webpack_require__(/*! download_links */ \"./public/js/null_plugins/download_links.js\");\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\nfunction _callSuper(_this, derived, args) {\n function isNativeReflectConstruct() {\n if (typeof Reflect === \"undefined\" || !Reflect.construct) return false;\n if (Reflect.construct.sham) return false;\n if (typeof Proxy === \"function\") return true;\n try {\n return !Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {}));\n } catch (e) {\n return false;\n }\n }\n derived = _getPrototypeOf(derived);\n return _possibleConstructorReturn(_this, isNativeReflectConstruct() ? Reflect.construct(derived, args || [], _getPrototypeOf(_this).constructor) : derived.apply(_this, args));\n}\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\n\n\n\n\n\n/**\n * checks whether code is being run by jest\n */\n// eslint-disable-next-line no-undef\n\nvar isTestMode = function isTestMode() {\n return ({}).JEST_WORKER_ID !== undefined || \"development\" === 'test';\n};\n/**\n * Renders links for downloading hit information in different formats.\n * Renders links for navigating to each query.\n */\nvar _default = /*#__PURE__*/function (_Component) {\n function _default(props) {\n var _this2;\n _classCallCheck(this, _default);\n _this2 = _callSuper(this, _default, [props]);\n _this2.downloadFastaOfAll = _this2.downloadFastaOfAll.bind(_this2);\n _this2.downloadFastaOfSelected = _this2.downloadFastaOfSelected.bind(_this2);\n _this2.topPanelJSX = _this2.topPanelJSX.bind(_this2);\n _this2.summaryString = _this2.summaryString.bind(_this2);\n _this2.indexJSX = _this2.indexJSX.bind(_this2);\n _this2.downloadsPanelJSX = _this2.downloadsPanelJSX.bind(_this2);\n _this2.handleQueryIndexChange = _this2.handleQueryIndexChange.bind(_this2);\n _this2.isElementInViewPort = _this2.isElementInViewPort.bind(_this2);\n _this2.setVisibleQueryIndex = _this2.setVisibleQueryIndex.bind(_this2);\n _this2.debounceScrolling = _this2.debounceScrolling.bind(_this2);\n _this2.scrollListener = _this2.scrollListener.bind(_this2);\n _this2.copyURL = _this2.copyURL.bind(_this2);\n _this2.shareCloudInit = _this2.shareCloudInit.bind(_this2);\n _this2.sharingPanelJSX = _this2.sharingPanelJSX.bind(_this2);\n _this2.timeout = null;\n _this2.queryElems = [];\n _this2.state = {\n queryIndex: 1\n };\n return _this2;\n }\n _inherits(_default, _Component);\n return _createClass(_default, [{\n key: \"componentDidMount\",\n value: function componentDidMount() {\n /**\n * Fixes tooltips in the sidebar, allows tooltip display on click\n */\n $(function () {\n $('.sidebar [data-toggle=\"tooltip\"]').tooltip({\n placement: 'right'\n });\n $('#copyURL').tooltip({\n title: 'Copied!',\n trigger: 'click',\n placement: 'right',\n delay: 0\n });\n });\n\n //keep track of the current queryIndex so it doesn't get lost on page reload\n var urlMatch = window.location.href.match(/#Query_(\\d+)/);\n if (urlMatch && urlMatch.length > 1) {\n var queryNumber = +urlMatch[1];\n var index = this.props.data.queries.findIndex(function (query) {\n return query.number === queryNumber;\n });\n this.setState({\n queryIndex: index + 1\n });\n }\n window.addEventListener('scroll', this.scrollListener);\n $('a[href^=\"#Query_\"]').on('click', this.animateAnchorElements);\n }\n }, {\n key: \"componentWillUnmount\",\n value: function componentWillUnmount() {\n window.removeEventListener('scroll', this.scrollListener);\n }\n }, {\n key: \"componentDidUpdate\",\n value: function componentDidUpdate(prevProps) {\n if (this.props.allQueriesLoaded && !prevProps.allQueriesLoaded) {\n /**\n * storing all query elements in this variable once they all become available so we don't have to fetch them all over again\n */\n this.queryElems = Array.from(document.querySelectorAll('.resultn'));\n }\n }\n\n /**\n * to avoid unnecessary computations, we debounce the scroll listener so it only fires after user has stopped scrolling for some milliseconds\n */\n }, {\n key: \"scrollListener\",\n value: function scrollListener() {\n this.debounceScrolling(this.setVisibleQueryIndex, 500);\n }\n }, {\n key: \"debounceScrolling\",\n value: function debounceScrolling(callback, timer) {\n if (this.timeout) {\n clearTimeout(this.timeout);\n }\n this.timeout = setTimeout(callback, timer);\n }\n\n /**\n * This method makes the page aware of what query is visible so that clicking previous / next button at any point\n * navigates to the proper query\n */\n }, {\n key: \"setVisibleQueryIndex\",\n value: function setVisibleQueryIndex() {\n var queryElems = this.queryElems.length ? this.queryElems : Array.from(document.querySelectorAll('.resultn'));\n var hits = Array.from(document.querySelectorAll('.hit[id^=Query_]'));\n // get the first visible element and marks it as the current query\n var topmostEl = queryElems.find(this.isElementInViewPort) || hits.find(this.isElementInViewPort);\n if (topmostEl) {\n var queryIndex = Number(topmostEl.id.match(/Query_(\\d+)/)[1]);\n var hash = \"#Query_\".concat(queryIndex);\n // if we can guarantee that the browser can handle change in url hash without the page jumping,\n // then we update the url hash after scroll. else, hash is only updated on click of next or prev button\n if (window.history.pushState) {\n window.history.pushState(null, null, hash);\n }\n this.setState({\n queryIndex: queryIndex\n });\n }\n }\n }, {\n key: \"animateAnchorElements\",\n value: function animateAnchorElements(e) {\n // allow normal behavior in test mode to prevent warnings or errors from jquery\n if (isTestMode()) return;\n e.preventDefault();\n $('html, body').animate({\n scrollTop: $(this.hash).offset().top\n }, 300);\n if (window.history.pushState) {\n window.history.pushState(null, null, this.hash);\n } else {\n window.location.hash = this.hash;\n }\n }\n }, {\n key: \"isElementInViewPort\",\n value: function isElementInViewPort(elem) {\n var _elem$getBoundingClie = elem.getBoundingClientRect(),\n top = _elem$getBoundingClie.top,\n left = _elem$getBoundingClie.left,\n right = _elem$getBoundingClie.right,\n bottom = _elem$getBoundingClie.bottom;\n return top >= 0 && left >= 0 && bottom <= (window.innerHeight || document.documentElement.clientHeight) && right <= (window.innerWidth || document.documentElement.clientWidth);\n }\n /**\n * Clear sessionStorage - useful to initiate a new search in the same tab.\n * Passing sessionStorage.clear directly as onclick callback didn't work\n * (on macOS Chrome).\n */\n }, {\n key: \"clearSession\",\n value: function clearSession() {\n sessionStorage.clear();\n }\n /**\n *\n * handle next and previous query button clicks\n */\n }, {\n key: \"handleQueryIndexChange\",\n value: function handleQueryIndexChange(nextQuery) {\n if (nextQuery < 1 || nextQuery > this.props.data.queries.length) return;\n var anchorEl = document.createElement('a');\n //indexing at [nextQuery - 1] because array is 0-indexed\n anchorEl.setAttribute('href', '#Query_' + this.props.data.queries[nextQuery - 1].number);\n anchorEl.setAttribute('hidden', true);\n document.body.appendChild(anchorEl);\n // add smooth scrolling animation with jquery\n $(anchorEl).on('click', this.animateAnchorElements);\n anchorEl.click();\n document.body.removeChild(anchorEl);\n this.setState({\n queryIndex: nextQuery\n });\n }\n /**\n * Event-handler for downloading fasta of all hits.\n */\n }, {\n key: \"downloadFastaOfAll\",\n value: function downloadFastaOfAll() {\n var sequence_ids = [];\n this.props.data.queries.forEach(function (query) {\n return query.hits.forEach(function (hit) {\n return sequence_ids.push(hit.id);\n });\n });\n var database_ids = this.props.data.querydb.map(function (querydb) {\n return querydb.id;\n });\n (0,_download_fasta__WEBPACK_IMPORTED_MODULE_2__[\"default\"])(sequence_ids, database_ids);\n return false;\n }\n\n /**\n * Handles downloading fasta of selected hits.\n */\n }, {\n key: \"downloadFastaOfSelected\",\n value: function downloadFastaOfSelected() {\n var sequence_ids = $('.hit-links :checkbox:checked').map(function () {\n return this.value;\n }).get();\n if (sequence_ids.length === 0) {\n return false;\n }\n var database_ids = underscore__WEBPACK_IMPORTED_MODULE_1__[\"default\"].map(this.props.data.querydb, underscore__WEBPACK_IMPORTED_MODULE_1__[\"default\"].iteratee('id'));\n (0,_download_fasta__WEBPACK_IMPORTED_MODULE_2__[\"default\"])(sequence_ids, database_ids);\n return false;\n }\n\n /**\n * Handles copying the URL into the user's clipboard. Modified from: https://stackoverflow.com/a/49618964/18117380\n * Hides the 'Copied!' tooltip after 3 seconds\n */\n }, {\n key: \"copyURL\",\n value: function copyURL() {\n var element = document.createElement('input');\n var url = window.location.href;\n document.body.appendChild(element);\n element.value = url;\n element.select();\n document.execCommand('copy');\n document.body.removeChild(element);\n setTimeout(function () {\n $('#copyURL')._tooltip('hide');\n }, 3000);\n }\n }, {\n key: \"shareCloudInit\",\n value: function shareCloudInit() {\n this.refs.cloudShareModal.show();\n }\n }, {\n key: \"topPanelJSX\",\n value: function topPanelJSX() {\n var path = location.pathname.split('/');\n // Get job id.\n var job_id = path.pop();\n // Deriving rootURL this way is required for subURI deployments\n // - we cannot just send to '/'.\n var rootURL = path.join('/');\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"sidebar-top-panel\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"div\", {\n className: \"section-header-sidebar\",\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"h4\", {\n children: this.summaryString()\n })\n }), this.props.data.queries.length > 12 && this.queryIndexButtons(), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n href: \"\".concat(rootURL, \"/?job_id=\").concat(job_id),\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-pencil\"\n }), \" Edit search\"]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"span\", {\n className: \"line\",\n children: \"|\"\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n href: \"\".concat(rootURL, \"/\"),\n onClick: this.clearSession,\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-file-o\"\n }), \" New search\"]\n })]\n }), this.props.shouldShowIndex && this.indexJSX()]\n });\n }\n }, {\n key: \"summaryString\",\n value: function summaryString() {\n var program = this.props.data.program;\n var numqueries = this.props.data.queries.length;\n var numquerydb = this.props.data.querydb.length;\n return program.toUpperCase() + ': ' + numqueries + ' ' + (numqueries > 1 ? 'queries' : 'query') + ', ' + numquerydb + ' ' + (numquerydb > 1 ? 'databases' : 'database');\n }\n }, {\n key: \"queryIndexButtons\",\n value: function queryIndexButtons() {\n var _this3 = this;\n var buttonStyle = {\n outline: 'none',\n border: 'none',\n background: 'none'\n };\n var buttonClasses = 'btn-link nowrap-ellipsis hover-bold';\n var handlePreviousBtnClick = function handlePreviousBtnClick() {\n return _this3.handleQueryIndexChange(_this3.state.queryIndex - 1);\n };\n var handleNextBtnClick = function handleNextBtnClick() {\n return _this3.handleQueryIndexChange(_this3.state.queryIndex + 1);\n };\n\n // eslint-disable-next-line no-unused-vars\n var NavButton = function NavButton(_ref) {\n var text = _ref.text,\n onClick = _ref.onClick;\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"button\", {\n className: buttonClasses,\n onClick: onClick,\n style: buttonStyle,\n children: text\n });\n };\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n style: {\n display: 'flex',\n width: '100%',\n margin: '7px 0'\n },\n children: [this.state.queryIndex > 1 && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(NavButton, {\n text: \"Previous Query\",\n onClick: handlePreviousBtnClick\n }), this.state.queryIndex > 1 && this.state.queryIndex < this.props.data.queries.length && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"span\", {\n className: \"line\",\n children: \"|\"\n }), this.state.queryIndex < this.props.data.queries.length && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(NavButton, {\n onClick: handleNextBtnClick,\n text: \"Next Query\"\n })]\n });\n }\n }, {\n key: \"indexJSX\",\n value: function indexJSX() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"ul\", {\n className: \"nav hover-reset active-bold\",\n children: [\" \", underscore__WEBPACK_IMPORTED_MODULE_1__[\"default\"].map(this.props.data.queries, function (query) {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link nowrap-ellipsis hover-bold\",\n title: 'Query= ' + query.id + ' ' + query.title,\n href: '#Query_' + query.number,\n children: 'Query= ' + query.id\n })\n }, 'Side_bar_' + query.id);\n })]\n });\n }\n }, {\n key: \"downloadsPanelJSX\",\n value: function downloadsPanelJSX() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"downloads\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"div\", {\n className: \"section-header-sidebar\",\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"h4\", {\n children: \"Download FASTA, XML, TSV\"\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"ul\", {\n className: \"nav\",\n children: [!(this.props.data.imported_xml || this.props.data.non_parse_seqids) && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n href: \"#\",\n className: \"btn-link download-fasta-of-all \".concat(!this.props.atLeastOneHit && 'disabled'),\n onClick: this.downloadFastaOfAll,\n children: \"FASTA of all hits\"\n })\n }), !(this.props.data.imported_xml || this.props.data.non_parse_seqids) && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n href: \"#\",\n className: \"btn-link download-fasta-of-selected disabled\",\n onClick: this.downloadFastaOfSelected,\n children: [\"FASTA of \", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"span\", {\n className: \"text-bold\"\n }), \" selected hit(s)\"]\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n href: \"#\",\n className: \"btn-link download-alignment-of-all \".concat(!this.props.atLeastOneHit && 'disabled'),\n children: \"Alignment of all hits\"\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n href: \"#\",\n className: \"btn-link download-alignment-of-selected disabled\",\n children: [\"Alignment of \", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"span\", {\n className: \"text-bold\"\n }), \" selected hit(s)\"]\n })\n }), !this.props.data.imported_xml && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link download\",\n \"data-toggle\": \"tooltip\",\n title: \"15 columns: query and subject ID; scientific name, alignment length, mismatches, gaps, identity, start and end coordinates, e value, bitscore, query coverage per subject and per HSP.\",\n href: 'download/' + this.props.data.search_id + '.std_tsv',\n children: \"Standard tabular report\"\n })\n }), !this.props.data.imported_xml && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link download\",\n \"data-toggle\": \"tooltip\",\n title: \"44 columns: query and subject ID, GI, accessions, and length; alignment details; taxonomy details of subject sequence(s) and query coverage per subject and per HSP.\",\n href: 'download/' + this.props.data.search_id + '.full_tsv',\n children: \"Full tabular report\"\n })\n }), !this.props.data.imported_xml && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link download\",\n \"data-toggle\": \"tooltip\",\n title: \"Results in XML format.\",\n href: 'download/' + this.props.data.search_id + '.xml',\n children: \"Full XML report\"\n })\n }), !this.props.data.imported_xml && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n className: \"btn-link download\",\n \"data-toggle\": \"tooltip\",\n title: \"Results in pairwise format.\",\n href: 'download/' + this.props.data.search_id + '.pairwise',\n children: \"Full Pairwise report\"\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(download_links__WEBPACK_IMPORTED_MODULE_5__[\"default\"], {\n imported_xml: this.props.data.imported_xml,\n search_id: this.props.data.search_id\n })]\n })]\n });\n }\n }, {\n key: \"sharingPanelJSX\",\n value: function sharingPanelJSX() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"sharing-panel\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"div\", {\n className: \"section-header-sidebar\",\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"h4\", {\n children: \"Share results\"\n })\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"ul\", {\n className: \"nav\",\n children: [!this.props.cloudSharingEnabled && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n id: \"copyURL\",\n className: \"btn-link copy-URL cursor-pointer\",\n \"data-toggle\": \"tooltip\",\n onClick: this.copyURL,\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-copy\"\n }), \" Copy URL to clipboard\"]\n })\n }), !this.props.cloudSharingEnabled && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"a\", {\n id: \"sendEmail\",\n className: \"btn-link email-URL cursor-pointer\",\n \"data-toggle\": \"tooltip\",\n title: \"Send by email\",\n href: (0,_mailto__WEBPACK_IMPORTED_MODULE_3__[\"default\"])(this.props.data.querydb, this.props.data.program, this.props.data.queries.length, window.location.href),\n target: \"_blank\",\n rel: \"noopener noreferrer\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-envelope\"\n }), \" Send by email\"]\n })\n }), this.props.cloudSharingEnabled && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"li\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"button\", {\n className: \"btn-link cloud-Post cursor-pointer\",\n \"data-toggle\": \"tooltip\",\n title: \"Upload results to SequenceServer Cloud where it will become accessable to everyone who has a link.\",\n onClick: this.shareCloudInit,\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"i\", {\n className: \"fa fa-cloud\"\n }), \" Share to cloud\"]\n })\n })]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(_cloud_share_modal__WEBPACK_IMPORTED_MODULE_4__[\"default\"], {\n ref: \"cloudShareModal\",\n querydb: this.props.data.querydb,\n program: this.props.data.program,\n queryLength: this.props.data.queries.length\n })]\n });\n }\n }, {\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"sidebar\",\n children: [this.topPanelJSX(), this.downloadsPanelJSX(), this.sharingPanelJSX(), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"div\", {\n className: \"referral-panel\",\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsxs)(\"div\", {\n className: \"section-header-sidebar\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"h4\", {\n children: \"Recommend SequenceServer\"\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"p\", {\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_6__.jsx)(\"a\", {\n href: \"https://sequenceserver.com/referral-program\",\n target: \"_blank\",\n children: \"Earn up to $100 per signup\"\n })\n })]\n })\n })]\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\n\n//# sourceURL=webpack://SequenceServer/./public/js/sidebar.js?");
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eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */ Form: () => (/* binding */ Form)\n/* harmony export */ });\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_0__);\n/* harmony import */ var _search_button__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! ./search_button */ \"./public/js/search_button.js\");\n/* harmony import */ var _query__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! ./query */ \"./public/js/query.js\");\n/* harmony import */ var _databases_tree__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./databases_tree */ \"./public/js/databases_tree.js\");\n/* harmony import */ var _databases__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./databases */ \"./public/js/databases.js\");\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_5__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var options__WEBPACK_IMPORTED_MODULE_6__ = __webpack_require__(/*! options */ \"./public/js/null_plugins/options.js\");\n/* harmony import */ var query_stats__WEBPACK_IMPORTED_MODULE_7__ = __webpack_require__(/*! query_stats */ \"./public/js/null_plugins/query_stats.js\");\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\nfunction _callSuper(_this, derived, args) {\n function isNativeReflectConstruct() {\n if (typeof Reflect === \"undefined\" || !Reflect.construct) return false;\n if (Reflect.construct.sham) return false;\n if (typeof Proxy === \"function\") return true;\n try {\n return !Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {}));\n } catch (e) {\n return false;\n }\n }\n derived = _getPrototypeOf(derived);\n return _possibleConstructorReturn(_this, isNativeReflectConstruct() ? Reflect.construct(derived, args || [], _getPrototypeOf(_this).constructor) : derived.apply(_this, args));\n}\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\n\n\n\n\n\n\n\n\n/**\n * Search form.\n *\n * Top level component that initialises and holds all other components, and\n * facilitates communication between them.\n */\n\nvar Form = /*#__PURE__*/function (_Component) {\n function Form(props) {\n var _this2;\n _classCallCheck(this, Form);\n _this2 = _callSuper(this, Form, [props]);\n _this2.state = {\n databases: [],\n preSelectedDbs: [],\n currentlySelectedDbs: [],\n preDefinedOpts: {},\n tree: {},\n residuesInQuerySequence: 0,\n blastMethod: ''\n };\n _this2.useTreeWidget = _this2.useTreeWidget.bind(_this2);\n _this2.determineBlastMethods = _this2.determineBlastMethods.bind(_this2);\n _this2.handleSequenceTypeChanged = _this2.handleSequenceTypeChanged.bind(_this2);\n _this2.handleSequenceChanged = _this2.handleSequenceChanged.bind(_this2);\n _this2.handleDatabaseTypeChanged = _this2.handleDatabaseTypeChanged.bind(_this2);\n _this2.handleDatabaseSelectionChanged = _this2.handleDatabaseSelectionChanged.bind(_this2);\n _this2.handleAlgoChanged = _this2.handleAlgoChanged.bind(_this2);\n _this2.handleFormSubmission = _this2.handleFormSubmission.bind(_this2);\n _this2.formRef = /*#__PURE__*/(0,react__WEBPACK_IMPORTED_MODULE_0__.createRef)();\n _this2.setButtonState = _this2.setButtonState.bind(_this2);\n return _this2;\n }\n _inherits(Form, _Component);\n return _createClass(Form, [{\n key: \"componentDidMount\",\n value: function componentDidMount() {\n /**\n * Fetch data to initialise the search interface from the server. These\n * include list of databases to search against, advanced options to\n * apply when an algorithm is selected, and a query sequence that\n * the user may want to search in the databases.\n */\n var search = location.search.split(/\\?|&/).filter(Boolean);\n var job_id = sessionStorage.getItem('job_id');\n if (job_id) {\n search.unshift(\"job_id=\".concat(job_id));\n }\n $.getJSON(\"searchdata.json?\".concat(search.join('&')), function (data) {\n /* Update form state (i.e., list of databases and predefined\n * advanced options.\n */\n this.setState({\n tree: data['tree'],\n databases: data['database'],\n preSelectedDbs: data['preSelectedDbs'],\n preDefinedOpts: data['options'],\n blastTaskMap: data['blastTaskMap']\n });\n\n /* Pre-populate the form with server sent query sequences\n * (if any).\n */\n if (data['query']) {\n this.refs.query.value(data['query']);\n }\n setTimeout(function () {\n $('.jstree_div').click();\n }, 1000);\n }.bind(this));\n\n /* Enable submitting form on Cmd+Enter */\n $(document).on('keydown', function (e) {\n var $button = $('#method');\n if (!$button.is(':disabled') && e.ctrlKey && e.key === 'Enter') {\n $button.trigger('click');\n }\n });\n\n // show overlay to create visual feedback on button click\n $('#method').on('click', function () {\n $('#overlay').css('display', 'block');\n });\n }\n }, {\n key: \"useTreeWidget\",\n value: function useTreeWidget() {\n return !underscore__WEBPACK_IMPORTED_MODULE_5__[\"default\"].isEmpty(this.state.tree);\n }\n }, {\n key: \"handleFormSubmission\",\n value: function handleFormSubmission(evt) {\n evt.preventDefault();\n var form = this.formRef.current;\n var formData = new FormData(form);\n formData.append('method', this.refs.button.state.methods[0]);\n fetch(window.location.href, {\n method: 'POST',\n body: formData\n }).then(function (res) {\n //remove overlay when form is submitted\n $('#overlay').css('display', 'none');\n // redirect\n if (res.redirected && res.url) {\n // setTimeout is needed here as a workaround because safari doesnt allow async calling of window.open\n // so setTimeout makes the method get called on the main thread.\n setTimeout(function () {\n window.open(res.url, $('#toggleNewTab').is(':checked') ? '_blank' : '_self');\n }, 0);\n }\n });\n }\n }, {\n key: \"determineBlastMethods\",\n value: function determineBlastMethods() {\n var database_type = this.databaseType;\n var sequence_type = this.sequenceType;\n if (this.refs.query.isEmpty()) {\n return [];\n }\n\n //database type is always known\n switch (database_type) {\n case 'protein':\n switch (sequence_type) {\n case undefined:\n return ['blastp', 'blastx'];\n case 'protein':\n return ['blastp'];\n case 'nucleotide':\n return ['blastx'];\n }\n break;\n case 'nucleotide':\n switch (sequence_type) {\n case undefined:\n return ['tblastn', 'blastn', 'tblastx'];\n case 'protein':\n return ['tblastn'];\n case 'nucleotide':\n return ['blastn', 'tblastx'];\n }\n break;\n }\n return [];\n }\n }, {\n key: \"handleSequenceChanged\",\n value: function handleSequenceChanged(residuesInQuerySequence) {\n if (residuesInQuerySequence !== this.state.residuesInQuerySequence) this.setState({\n residuesInQuerySequence: residuesInQuerySequence\n });\n }\n }, {\n key: \"handleSequenceTypeChanged\",\n value: function handleSequenceTypeChanged(type) {\n this.sequenceType = type;\n this.setButtonState();\n }\n }, {\n key: \"handleDatabaseTypeChanged\",\n value: function handleDatabaseTypeChanged(type) {\n this.databaseType = type;\n this.setButtonState();\n }\n }, {\n key: \"setButtonState\",\n value: function setButtonState() {\n this.refs.button.setState({\n hasQuery: !this.refs.query.isEmpty(),\n hasDatabases: !!this.databaseType,\n methods: this.determineBlastMethods()\n });\n }\n }, {\n key: \"handleDatabaseSelectionChanged\",\n value: function handleDatabaseSelectionChanged(selectedDbs) {\n if (!underscore__WEBPACK_IMPORTED_MODULE_5__[\"default\"].isEqual(selectedDbs, this.state.currentlySelectedDbs)) this.setState({\n currentlySelectedDbs: selectedDbs\n });\n }\n }, {\n key: \"handleAlgoChanged\",\n value: function handleAlgoChanged(algo) {\n if (algo in this.state.preDefinedOpts) {\n this.setState({\n blastMethod: algo\n });\n } else {\n this.setState({\n blastMethod: ''\n });\n }\n }\n }, {\n key: \"residuesInSelectedDbs\",\n value: function residuesInSelectedDbs() {\n return this.state.currentlySelectedDbs.reduce(function (sum, db) {\n return sum + parseInt(db.ncharacters, 10);\n }, 0);\n }\n }, {\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"div\", {\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n id: \"overlay\",\n style: {\n position: 'absolute',\n top: 0,\n left: 0,\n width: '100vw',\n height: '100vw',\n background: 'rgba(0, 0, 0, 0.2)',\n display: 'none',\n zIndex: 99\n }\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"div\", {\n className: \"fixed top-0 left-0 w-full max-h-8 px-8\",\n \"data-notifications\": true,\n id: \"notifications\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(FastqNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(NucleotideNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(ProteinNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(MixedNotification, {})]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"form\", {\n id: \"blast\",\n ref: this.formRef,\n onSubmit: this.handleFormSubmission,\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"div\", {\n className: \"px-4\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(_query__WEBPACK_IMPORTED_MODULE_2__.SearchQueryWidget, {\n ref: \"query\",\n onSequenceTypeChanged: this.handleSequenceTypeChanged,\n onSequenceChanged: this.handleSequenceChanged\n }), this.useTreeWidget() ? /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(_databases_tree__WEBPACK_IMPORTED_MODULE_3__[\"default\"], {\n ref: \"databases\",\n databases: this.state.databases,\n tree: this.state.tree,\n preSelectedDbs: this.state.preSelectedDbs,\n onDatabaseTypeChanged: this.handleDatabaseTypeChanged,\n onDatabaseSelectionChanged: this.handleDatabaseSelectionChanged\n }) : /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(_databases__WEBPACK_IMPORTED_MODULE_4__.Databases, {\n ref: \"databases\",\n databases: this.state.databases,\n preSelectedDbs: this.state.preSelectedDbs,\n onDatabaseTypeChanged: this.handleDatabaseTypeChanged,\n onDatabaseSelectionChanged: this.handleDatabaseSelectionChanged\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(options__WEBPACK_IMPORTED_MODULE_6__.Options, {\n blastMethod: this.state.blastMethod,\n predefinedOptions: this.state.preDefinedOpts[this.state.blastMethod] || {},\n blastTasks: (this.state.blastTaskMap || {})[this.state.blastMethod]\n })]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"py-6\"\n }), \" \", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"div\", {\n className: \"pb-4 pt-2 px-4 sticky bottom-0 md:flex flex-row md:space-x-4 items-center justify-end bg-gradient-to-t to-gray-100/90 from-white/90\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(query_stats__WEBPACK_IMPORTED_MODULE_7__[\"default\"], {\n residuesInQuerySequence: this.state.residuesInQuerySequence,\n numberOfDatabasesSelected: this.state.currentlySelectedDbs.length,\n residuesInSelectedDbs: this.residuesInSelectedDbs(),\n currentBlastMethod: this.state.blastMethod\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"label\", {\n className: \"block my-4 md:my-2\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"input\", {\n type: \"checkbox\",\n id: \"toggleNewTab\"\n }), \" Open results in new tab\"]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(_search_button__WEBPACK_IMPORTED_MODULE_1__.SearchButton, {\n ref: \"button\",\n onAlgoChanged: this.handleAlgoChanged\n })]\n })]\n })]\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\nvar ProteinNotification = /*#__PURE__*/function (_Component2) {\n function ProteinNotification() {\n _classCallCheck(this, ProteinNotification);\n return _callSuper(this, ProteinNotification, arguments);\n }\n _inherits(ProteinNotification, _Component2);\n return _createClass(ProteinNotification, [{\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n \"data-role\": \"notification\",\n id: \"protein-sequence-notification\",\n style: {\n display: 'none'\n },\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2\",\n children: \"Detected: amino-acid sequence(s).\"\n })\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\nvar NucleotideNotification = /*#__PURE__*/function (_Component3) {\n function NucleotideNotification() {\n _classCallCheck(this, NucleotideNotification);\n return _callSuper(this, NucleotideNotification, arguments);\n }\n _inherits(NucleotideNotification, _Component3);\n return _createClass(NucleotideNotification, [{\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n \"data-role\": \"notification\",\n id: \"nucleotide-sequence-notification\",\n style: {\n display: 'none'\n },\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2\",\n children: \"Detected: nucleotide sequence(s).\"\n })\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\nvar FastqNotification = /*#__PURE__*/function (_Component4) {\n function FastqNotification() {\n _classCallCheck(this, FastqNotification);\n return _callSuper(this, FastqNotification, arguments);\n }\n _inherits(FastqNotification, _Component4);\n return _createClass(FastqNotification, [{\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n \"data-role\": \"notification\",\n id: \"fastq-sequence-notification\",\n style: {\n display: 'none'\n },\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2\",\n children: \"Detected FASTQ and automatically converted to FASTA.\"\n })\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\nvar MixedNotification = /*#__PURE__*/function (_Component5) {\n function MixedNotification() {\n _classCallCheck(this, MixedNotification);\n return _callSuper(this, MixedNotification, arguments);\n }\n _inherits(MixedNotification, _Component5);\n return _createClass(MixedNotification, [{\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n \"data-role\": \"notification\",\n id: \"mixed-sequence-notification\",\n style: {\n display: 'none'\n },\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"alert-danger col-md-10 col-md-offset-1\",\n children: \"Error: mixed nucleotide and amino-acid sequences detected.\"\n })\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\n//# sourceURL=webpack://SequenceServer/./public/js/form.js?");
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eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */ Form: () => (/* binding */ Form)\n/* harmony export */ });\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_0__);\n/* harmony import */ var _search_button__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! ./search_button */ \"./public/js/search_button.js\");\n/* harmony import */ var _query__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! ./query */ \"./public/js/query.js\");\n/* harmony import */ var _databases_tree__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./databases_tree */ \"./public/js/databases_tree.js\");\n/* harmony import */ var _databases__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./databases */ \"./public/js/databases.js\");\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_5__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var options__WEBPACK_IMPORTED_MODULE_6__ = __webpack_require__(/*! options */ \"./public/js/null_plugins/options.js\");\n/* harmony import */ var query_stats__WEBPACK_IMPORTED_MODULE_7__ = __webpack_require__(/*! query_stats */ \"./public/js/null_plugins/query_stats.js\");\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\nfunction _callSuper(_this, derived, args) {\n function isNativeReflectConstruct() {\n if (typeof Reflect === \"undefined\" || !Reflect.construct) return false;\n if (Reflect.construct.sham) return false;\n if (typeof Proxy === \"function\") return true;\n try {\n return !Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {}));\n } catch (e) {\n return false;\n }\n }\n derived = _getPrototypeOf(derived);\n return _possibleConstructorReturn(_this, isNativeReflectConstruct() ? Reflect.construct(derived, args || [], _getPrototypeOf(_this).constructor) : derived.apply(_this, args));\n}\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\n\n\n\n\n\n\n\n\n/**\n * Search form.\n *\n * Top level component that initialises and holds all other components, and\n * facilitates communication between them.\n */\n\nvar Form = /*#__PURE__*/function (_Component) {\n function Form(props) {\n var _this2;\n _classCallCheck(this, Form);\n _this2 = _callSuper(this, Form, [props]);\n _this2.state = {\n databases: [],\n preSelectedDbs: [],\n currentlySelectedDbs: [],\n preDefinedOpts: {},\n tree: {},\n residuesInQuerySequence: 0,\n blastMethod: ''\n };\n _this2.useTreeWidget = _this2.useTreeWidget.bind(_this2);\n _this2.determineBlastMethods = _this2.determineBlastMethods.bind(_this2);\n _this2.handleSequenceTypeChanged = _this2.handleSequenceTypeChanged.bind(_this2);\n _this2.handleSequenceChanged = _this2.handleSequenceChanged.bind(_this2);\n _this2.handleDatabaseTypeChanged = _this2.handleDatabaseTypeChanged.bind(_this2);\n _this2.handleDatabaseSelectionChanged = _this2.handleDatabaseSelectionChanged.bind(_this2);\n _this2.handleAlgoChanged = _this2.handleAlgoChanged.bind(_this2);\n _this2.handleFormSubmission = _this2.handleFormSubmission.bind(_this2);\n _this2.formRef = /*#__PURE__*/(0,react__WEBPACK_IMPORTED_MODULE_0__.createRef)();\n _this2.setButtonState = _this2.setButtonState.bind(_this2);\n return _this2;\n }\n _inherits(Form, _Component);\n return _createClass(Form, [{\n key: \"componentDidMount\",\n value: function componentDidMount() {\n /**\n * Fetch data to initialise the search interface from the server. These\n * include list of databases to search against, advanced options to\n * apply when an algorithm is selected, and a query sequence that\n * the user may want to search in the databases.\n */\n var search = location.search.split(/\\?|&/).filter(Boolean);\n var job_id = sessionStorage.getItem('job_id');\n if (job_id) {\n search.unshift(\"job_id=\".concat(job_id));\n }\n $.getJSON(\"searchdata.json?\".concat(search.join('&')), function (data) {\n /* Update form state (i.e., list of databases and predefined\n * advanced options.\n */\n this.setState({\n tree: data['tree'],\n databases: data['database'],\n preSelectedDbs: data['preSelectedDbs'],\n preDefinedOpts: data['options'],\n blastTaskMap: data['blastTaskMap']\n });\n\n /* Pre-populate the form with server sent query sequences\n * (if any).\n */\n if (data['query']) {\n this.refs.query.value(data['query']);\n }\n setTimeout(function () {\n $('.jstree_div').click();\n }, 1000);\n }.bind(this));\n\n /* Enable submitting form on Cmd+Enter */\n $(document).on('keydown', function (e) {\n var $button = $('#method');\n if (!$button.is(':disabled') && e.ctrlKey && e.key === 'Enter') {\n $button.trigger('click');\n }\n });\n\n // show overlay to create visual feedback on button click\n $('#method').on('click', function () {\n $('#overlay').css('display', 'block');\n });\n }\n }, {\n key: \"useTreeWidget\",\n value: function useTreeWidget() {\n return !underscore__WEBPACK_IMPORTED_MODULE_5__[\"default\"].isEmpty(this.state.tree);\n }\n }, {\n key: \"handleFormSubmission\",\n value: function handleFormSubmission(evt) {\n evt.preventDefault();\n var form = this.formRef.current;\n var formData = new FormData(form);\n formData.append('method', this.refs.button.state.methods[0]);\n fetch(window.location.href, {\n method: 'POST',\n body: formData\n }).then(function (res) {\n //remove overlay when form is submitted\n $('#overlay').css('display', 'none');\n // redirect\n if (res.redirected && res.url) {\n // setTimeout is needed here as a workaround because safari doesnt allow async calling of window.open\n // so setTimeout makes the method get called on the main thread.\n setTimeout(function () {\n window.open(res.url, $('#toggleNewTab').is(':checked') ? '_blank' : '_self');\n }, 0);\n }\n });\n }\n }, {\n key: \"determineBlastMethods\",\n value: function determineBlastMethods() {\n var database_type = this.databaseType;\n var sequence_type = this.sequenceType;\n if (this.refs.query.isEmpty()) {\n return [];\n }\n\n //database type is always known\n switch (database_type) {\n case 'protein':\n switch (sequence_type) {\n case undefined:\n return ['blastp', 'blastx'];\n case 'protein':\n return ['blastp'];\n case 'nucleotide':\n return ['blastx'];\n }\n break;\n case 'nucleotide':\n switch (sequence_type) {\n case undefined:\n return ['tblastn', 'blastn', 'tblastx'];\n case 'protein':\n return ['tblastn'];\n case 'nucleotide':\n return ['blastn', 'tblastx'];\n }\n break;\n }\n return [];\n }\n }, {\n key: \"handleSequenceChanged\",\n value: function handleSequenceChanged(residuesInQuerySequence) {\n if (residuesInQuerySequence !== this.state.residuesInQuerySequence) this.setState({\n residuesInQuerySequence: residuesInQuerySequence\n });\n }\n }, {\n key: \"handleSequenceTypeChanged\",\n value: function handleSequenceTypeChanged(type) {\n this.sequenceType = type;\n this.setButtonState();\n }\n }, {\n key: \"handleDatabaseTypeChanged\",\n value: function handleDatabaseTypeChanged(type) {\n this.databaseType = type;\n this.setButtonState();\n }\n }, {\n key: \"setButtonState\",\n value: function setButtonState() {\n this.refs.button.setState({\n hasQuery: !this.refs.query.isEmpty(),\n hasDatabases: !!this.databaseType,\n methods: this.determineBlastMethods()\n });\n }\n }, {\n key: \"handleDatabaseSelectionChanged\",\n value: function handleDatabaseSelectionChanged(selectedDbs) {\n if (!underscore__WEBPACK_IMPORTED_MODULE_5__[\"default\"].isEqual(selectedDbs, this.state.currentlySelectedDbs)) this.setState({\n currentlySelectedDbs: selectedDbs\n });\n }\n }, {\n key: \"handleAlgoChanged\",\n value: function handleAlgoChanged(algo) {\n if (algo in this.state.preDefinedOpts) {\n this.setState({\n blastMethod: algo\n });\n } else {\n this.setState({\n blastMethod: ''\n });\n }\n }\n }, {\n key: \"residuesInSelectedDbs\",\n value: function residuesInSelectedDbs() {\n return this.state.currentlySelectedDbs.reduce(function (sum, db) {\n return sum + parseInt(db.ncharacters, 10);\n }, 0);\n }\n }, {\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"div\", {\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n id: \"overlay\",\n style: {\n position: 'absolute',\n top: 0,\n left: 0,\n width: '100vw',\n height: '100vw',\n background: 'rgba(0, 0, 0, 0.2)',\n display: 'none',\n zIndex: 99\n }\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"div\", {\n className: \"fixed top-0 left-0 w-full max-h-8 px-8\",\n \"data-notifications\": true,\n id: \"notifications\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(FastqNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(NucleotideNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(ProteinNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(MixedNotification, {})]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"form\", {\n id: \"blast\",\n ref: this.formRef,\n onSubmit: this.handleFormSubmission,\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"input\", {\n type: \"hidden\",\n name: \"_csrf\",\n value: document.querySelector('meta[name=\"_csrf\"]').content\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"div\", {\n className: \"px-4\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(_query__WEBPACK_IMPORTED_MODULE_2__.SearchQueryWidget, {\n ref: \"query\",\n onSequenceTypeChanged: this.handleSequenceTypeChanged,\n onSequenceChanged: this.handleSequenceChanged\n }), this.useTreeWidget() ? /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(_databases_tree__WEBPACK_IMPORTED_MODULE_3__[\"default\"], {\n ref: \"databases\",\n databases: this.state.databases,\n tree: this.state.tree,\n preSelectedDbs: this.state.preSelectedDbs,\n onDatabaseTypeChanged: this.handleDatabaseTypeChanged,\n onDatabaseSelectionChanged: this.handleDatabaseSelectionChanged\n }) : /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(_databases__WEBPACK_IMPORTED_MODULE_4__.Databases, {\n ref: \"databases\",\n databases: this.state.databases,\n preSelectedDbs: this.state.preSelectedDbs,\n onDatabaseTypeChanged: this.handleDatabaseTypeChanged,\n onDatabaseSelectionChanged: this.handleDatabaseSelectionChanged\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(options__WEBPACK_IMPORTED_MODULE_6__.Options, {\n blastMethod: this.state.blastMethod,\n predefinedOptions: this.state.preDefinedOpts[this.state.blastMethod] || {},\n blastTasks: (this.state.blastTaskMap || {})[this.state.blastMethod]\n })]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"py-6\"\n }), \" \", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"div\", {\n className: \"pb-4 pt-2 px-4 sticky bottom-0 md:flex flex-row md:space-x-4 items-center justify-end bg-gradient-to-t to-gray-100/90 from-white/90\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(query_stats__WEBPACK_IMPORTED_MODULE_7__[\"default\"], {\n residuesInQuerySequence: this.state.residuesInQuerySequence,\n numberOfDatabasesSelected: this.state.currentlySelectedDbs.length,\n residuesInSelectedDbs: this.residuesInSelectedDbs(),\n currentBlastMethod: this.state.blastMethod\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsxs)(\"label\", {\n className: \"block my-4 md:my-2\",\n children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"input\", {\n type: \"checkbox\",\n id: \"toggleNewTab\"\n }), \" Open results in new tab\"]\n }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(_search_button__WEBPACK_IMPORTED_MODULE_1__.SearchButton, {\n ref: \"button\",\n onAlgoChanged: this.handleAlgoChanged\n })]\n })]\n })]\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\nvar ProteinNotification = /*#__PURE__*/function (_Component2) {\n function ProteinNotification() {\n _classCallCheck(this, ProteinNotification);\n return _callSuper(this, ProteinNotification, arguments);\n }\n _inherits(ProteinNotification, _Component2);\n return _createClass(ProteinNotification, [{\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n \"data-role\": \"notification\",\n id: \"protein-sequence-notification\",\n style: {\n display: 'none'\n },\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2\",\n children: \"Detected: amino-acid sequence(s).\"\n })\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\nvar NucleotideNotification = /*#__PURE__*/function (_Component3) {\n function NucleotideNotification() {\n _classCallCheck(this, NucleotideNotification);\n return _callSuper(this, NucleotideNotification, arguments);\n }\n _inherits(NucleotideNotification, _Component3);\n return _createClass(NucleotideNotification, [{\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n \"data-role\": \"notification\",\n id: \"nucleotide-sequence-notification\",\n style: {\n display: 'none'\n },\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2\",\n children: \"Detected: nucleotide sequence(s).\"\n })\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\nvar FastqNotification = /*#__PURE__*/function (_Component4) {\n function FastqNotification() {\n _classCallCheck(this, FastqNotification);\n return _callSuper(this, FastqNotification, arguments);\n }\n _inherits(FastqNotification, _Component4);\n return _createClass(FastqNotification, [{\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n \"data-role\": \"notification\",\n id: \"fastq-sequence-notification\",\n style: {\n display: 'none'\n },\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2\",\n children: \"Detected FASTQ and automatically converted to FASTA.\"\n })\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\nvar MixedNotification = /*#__PURE__*/function (_Component5) {\n function MixedNotification() {\n _classCallCheck(this, MixedNotification);\n return _callSuper(this, MixedNotification, arguments);\n }\n _inherits(MixedNotification, _Component5);\n return _createClass(MixedNotification, [{\n key: \"render\",\n value: function render() {\n return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n \"data-role\": \"notification\",\n id: \"mixed-sequence-notification\",\n style: {\n display: 'none'\n },\n children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_8__.jsx)(\"div\", {\n className: \"alert-danger col-md-10 col-md-offset-1\",\n children: \"Error: mixed nucleotide and amino-acid sequences detected.\"\n })\n });\n }\n }]);\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\n//# sourceURL=webpack://SequenceServer/./public/js/form.js?");
|
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86
86
|
|
|
87
87
|
/***/ }),
|
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88
88
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|
data/views/layout.erb
CHANGED
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@@ -9,6 +9,7 @@
|
|
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9
9
|
<meta name="author" content="Pragmatic Genomics Ltd">
|
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10
10
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<meta name="description" content="Custom BLAST server provided by SequenceServer (https://sequenceserver.com)"/>
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11
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12
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+
<%= Rack::Csrf.metatag(env) %>
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12
13
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<!-- CSS -->
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13
14
|
<% if settings.production? || settings.test? %>
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14
15
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<link rel="stylesheet" media="screen,print" type="text/css" href="css/sequenceserver.min.css?ver=<%= SequenceServer::VERSION %>"/>
|
data/views/search_layout.erb
CHANGED
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@@ -6,6 +6,7 @@
|
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6
6
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<meta name="author" content="Pragmatic Genomics Limited"/>
|
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7
7
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<meta charset="UTF-8">
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8
8
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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9
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+
<%= Rack::Csrf.metatag(env) %>
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9
10
|
<link rel="stylesheet" media="screen,print" type="text/css" href="css/app.min.css"/>
|
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10
11
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.5.2/css/all.min.css" integrity="sha512-SnH5WK+bZxgPHs44uWIX+LLJAJ9/2PkPKZ5QiAj6Ta86w+fsb2TkcmfRyVX3pBnMFcV7oQPJkl9QevSCWr3W6A==" crossorigin="anonymous" referrerpolicy="no-referrer" />
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11
12
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</head>
|
metadata
CHANGED
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@@ -1,7 +1,7 @@
|
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1
1
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--- !ruby/object:Gem::Specification
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2
2
|
name: sequenceserver
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3
3
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version: !ruby/object:Gem::Version
|
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4
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-
version: 3.1.
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4
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+
version: 3.1.2
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5
5
|
platform: ruby
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6
6
|
authors:
|
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7
7
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- Queen Mary University of London
|
|
@@ -9,7 +9,7 @@ authors:
|
|
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9
9
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autorequire:
|
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10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date: 2024-
|
|
12
|
+
date: 2024-07-04 00:00:00.000000000 Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: json_pure
|
|
@@ -51,6 +51,26 @@ dependencies:
|
|
|
51
51
|
- - ">="
|
|
52
52
|
- !ruby/object:Gem::Version
|
|
53
53
|
version: 2.1.1
|
|
54
|
+
- !ruby/object:Gem::Dependency
|
|
55
|
+
name: rack_csrf
|
|
56
|
+
requirement: !ruby/object:Gem::Requirement
|
|
57
|
+
requirements:
|
|
58
|
+
- - "~>"
|
|
59
|
+
- !ruby/object:Gem::Version
|
|
60
|
+
version: '2.7'
|
|
61
|
+
- - ">="
|
|
62
|
+
- !ruby/object:Gem::Version
|
|
63
|
+
version: 2.7.0
|
|
64
|
+
type: :runtime
|
|
65
|
+
prerelease: false
|
|
66
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
67
|
+
requirements:
|
|
68
|
+
- - "~>"
|
|
69
|
+
- !ruby/object:Gem::Version
|
|
70
|
+
version: '2.7'
|
|
71
|
+
- - ">="
|
|
72
|
+
- !ruby/object:Gem::Version
|
|
73
|
+
version: 2.7.0
|
|
54
74
|
- !ruby/object:Gem::Dependency
|
|
55
75
|
name: rackup
|
|
56
76
|
requirement: !ruby/object:Gem::Requirement
|
|
@@ -3539,7 +3559,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
3539
3559
|
- !ruby/object:Gem::Version
|
|
3540
3560
|
version: '0'
|
|
3541
3561
|
requirements: []
|
|
3542
|
-
rubygems_version: 3.5.
|
|
3562
|
+
rubygems_version: 3.5.14
|
|
3543
3563
|
signing_key:
|
|
3544
3564
|
specification_version: 4
|
|
3545
3565
|
summary: BLAST search made easy!
|