miga-base 0.2.3.0 → 0.2.3.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/miga/project_result.rb +3 -3
- data/lib/miga/remote_dataset.rb +12 -6
- data/lib/miga/version.rb +1 -1
- metadata +1 -1
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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SHA1:
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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: 8204affac00281361567c3a597321dd3ab5a5145
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4
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data.tar.gz: 62fbd4daf6698b317e9f76b89b352b7bf33d3b54
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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: f1d1b5e052e91e176529a6cec60736f2c21bca0591ba4b184485e59f6d906204ae34c1dba0464f1d5b1d01ed691e599cf15f63b3e1760f89c222187030a2a830
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7
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data.tar.gz: 1611ac19a30c23bb7fd79c7acc2d1b0559b03ae3d179dd8881c10d0a828ba447f4546e1ce18b9907a277260656bcb85120054e739395922a505e93f9a84efe70
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data/lib/miga/project_result.rb
CHANGED
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@@ -11,7 +11,7 @@ module MiGA::ProjectResult
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11
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# Internal alias for all add_result_*_distances.
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12
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def add_result_distances(base)
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return nil unless result_files_exist?(base, %w[.Rdata .log .txt])
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14
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-
r = Result.new(base + ".json")
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14
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+
r = MiGA::Result.new(base + ".json")
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r.add_file(:rdata, "miga-project.Rdata")
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r.add_file(:matrix, "miga-project.txt")
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r.add_file(:log, "miga-project.log")
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@@ -41,7 +41,7 @@ module MiGA::ProjectResult
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end
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def add_result_iter_clades(base)
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-
r = Result.new(base + ".json")
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44
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r = MiGA::Result.new(base + ".json")
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r.add_file(:report, "miga-project.pdf")
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r.add_file(:class_table, "miga-project.class.tsv")
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r.add_file(:class_tree, "miga-project.class.nwk")
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@@ -52,7 +52,7 @@ module MiGA::ProjectResult
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def add_result_ogs(base)
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return nil unless result_files_exist?(base, %w[.ogs .stats])
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-
r = Result.new(base + ".json")
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+
r = MiGA::Result.new(base + ".json")
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r.add_file(:ogs, "miga-project.ogs")
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r.add_file(:stats, "miga-project.stats")
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r.add_file(:rbm, "miga-project.rbm")
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data/lib/miga/remote_dataset.rb
CHANGED
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@@ -63,16 +63,22 @@ class MiGA::RemoteDataset < MiGA::MiGA
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@@UNIVERSE[universe][:dbs][db][:map_to]
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url = sprintf @@UNIVERSE[universe][:url],
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db, ids.join(","), format, map_to
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response = RestClient::Request.execute(:
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raise "Unable to reach #{universe} client, error code "+
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response = RestClient::Request.execute(method: :get, url:url, timeout:600)
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raise "Unable to reach #{universe} client, error code " +
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"#{response.code}." unless response.code == 200
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doc = response.to_s
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when :net
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url = sprintf @@UNIVERSE[universe][:url],
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db, ids.join(","), format, map_to
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url = sprintf @@UNIVERSE[universe][:url],db,ids.join(","),format,map_to
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doc = ""
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-
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@timeout_try = 0
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begin
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open(url) { |f| doc = f.read }
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rescue Net::ReadTimeout
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@timeout_try += 1
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if @timeout_try > 3 ; raise Net::ReadTimeout
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else ; retry
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end
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81
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end
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end
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unless file.nil?
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ofh = File.open(file, "w")
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data/lib/miga/version.rb
CHANGED
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@@ -10,7 +10,7 @@ module MiGA
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# - Float representing the major.minor version.
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# - Integer representing gem releases of the current version.
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# - Integer representing minor changes that require new version number.
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-
VERSION = [0.2, 3,
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VERSION = [0.2, 3, 1]
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##
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# Nickname for the current major.minor version.
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