Bump loofah from 2.1.1 to 2.3.0 in /web

bioinformatics/QpcrAnalysis/amp_analysis.jl

@@ -78,7 +78,7 @@ function set_ct_fluos!(
         map(1:i.num_channels) do channel_i
             const fits =
                 map(1:i.num_wells) do well_i
-                    const fluos = o.rbbs_3ary[:, well_i, channel_i]
+                    const fluos = o.rbbs_ary3[:, well_i, channel_i]
                     amp_fit_model(
                         Val{SFCModel},
                         AmpCqFluoModelResults,
@@ -127,7 +127,7 @@ function get_fit_results(
             const ipopt_file = string(join([prefix, ci, wi], '_')) * ".txt"
             push!(solver.options, (:output_file, ipopt_file))
         end
-        const fluos = o.rbbs_3ary[:, wi, ci]
+        const fluos = o.rbbs_ary3[:, wi, ci]
         amp_fit_model(
             Val{i.amp_model},
             i.amp_model_results,

bioinformatics/QpcrAnalysis/amp_fit_model.jl

@@ -55,15 +55,15 @@ function amp_fit_model(
     ## set output
     if isa(R, AmpShortModelResults)
         return AmpShortModelResults(
-            fluos, ## rbbs_3ary,
+            fluos, ## rbbs_ary3,
             blsub_fluos,
             NaN, ## dr1_pred
             NaN, ## dr2_pred
             NaN, ## cq
             d0())
     else
         return AmpLongModelResults(
-            fluos, ## rbbs_3ary,
+            fluos, ## rbbs_ary3,
             bl_fit,
             [string(amp_model)], ## bl_notes
             blsub_fluos,
@@ -355,7 +355,7 @@ function amp_fit_model(
     if R == AmpShortModelResults
         const cq_raw = calc_cq_raw(dr1_pred, dr2_pred)
         return AmpShortModelResults(
-            # fluos, ## rbbs_3ary,
+            # fluos, ## rbbs_ary3,
             blsub_fluos,
             dr1_pred[raw_cycs_index],
             dr2_pred[raw_cycs_index],
@@ -385,7 +385,7 @@ function amp_fit_model(
                     func_pred_eff(cyc_vals_4cq[key])
             end)
     return AmpLongModelResults(
-        fluos, ## rbbs_3ary
+        fluos, ## rbbs_ary3
         bl_fit,
         bl_notes,
         blsub_fluos,

bioinformatics/QpcrAnalysis/amp_models/defines/AmpModelResults.jl

@@ -17,9 +17,9 @@ import Ipopt: IpoptSolver #, NLoptSolver
     Field definitions >>
 ===============================================================================#
 
-## issue: rename `rbbs_3ary` as `calibrated` once juliaapi_new has been updated
+## issue: rename `rbbs_ary3` as `calibrated` once juliaapi_new has been updated
 const AMPLONGMODELRESULTS_FIELD_DEFS = [
-    Field(:rbbs_3ary,        Vector{Float_T}),
+    Field(:rbbs_ary3,        Vector{Float_T}),
     Field(:bl_fit,           Union{AmpModelFit,Symbol}),
     Field(:bl_notes,         Vector{String}),
     Field(:blsub_fluos,      Vector{Float_T}),
@@ -41,7 +41,7 @@ const AMPLONGMODELRESULTS_FIELD_DEFS = [
 
 
 const AMPSHORTMODELRESULTS_FIELDNAMES = [
-    # rbbs_3ary,
+    # rbbs_ary3,
     :blsub_fluos,
     :dr1_pred,
     :dr2_pred,

bioinformatics/QpcrAnalysis/amp_models/defines/AmpOutput.jl

@@ -26,7 +26,7 @@ const AMPLONGOUTPUT_FIELD_DEFS = [
     Field(:norm_data,                    SArray{S,<: Real} where {S}), ## wva_data
     Field(:k_deconv,                     DeconvolutionMatrices), ## k4dcv
     Field(:deconvoluted_data,            Array{<: Real,3}), ## dcvd_ary3
-    Field(:rbbs_3ary,                    Array{Float_T,3}), ## calibrated_data
+    Field(:rbbs_ary3,                    Array{Float_T,3}), ## calibrated_data
     # cq_method,                           Symbol
     ## for ct method
     Field(:ct_fluos,                     SVector{C,Float_T} where {C}),
@@ -64,7 +64,7 @@ const AMPLONGOUTPUT_FIELD_DEFS = [
 
 
 const AMPSHORTOUTPUT_FIELDNAMES = [
-    :rbbs_3ary,
+    :rbbs_ary3,
     :blsub_fluos,
     :dr1_pred,
     :dr2_pred,

bioinformatics/QpcrAnalysis/amplification.jl

@@ -90,7 +90,7 @@ function act(
         amp_output = AmpOutputOption(out_format),
         kw_bl...,
         kwargs...,)
-    const result = try
+    const result =
         ## issues:
         ## 1.
         ## the new code currently assumes only 1 step/ramp
@@ -135,9 +135,6 @@ function act(
                 key => getfield(first_sr_out, key)
             end...,
             :valid => true])
-    catch err
-        return fail(logger, err; bt = true) |> out(out_format)
-    end ## try
     return result |> out(out_format)
 end ## act(::Type{Val{amplification}})
 

bioinformatics/QpcrAnalysis/dispatch.jl

@@ -23,6 +23,7 @@ function dispatch(
 )
     debug(logger, "at dispatch() with action \"$action_key\"")
     debug(logger, "request body: " * request_body)
+	success = false
     const result = try
         ## NB. DefaultDict and DefaultOrderedDict constructors sometimes don't work
         ## on OrderedDict (https://github.com/JuliaLang/DataStructures.jl/issues/205)
@@ -74,23 +75,17 @@ function dispatch(
         end ## if !production_env
         #
         ## return value
+		success = true
         json_response
     catch err
-        fail(logger, err; bt = true)
+		JSON.json(fail(logger, err; bt = true) |> out(pre_json_output))
     end ## try
-    #
-    const success = !isa(result, Exception)
-    const response_body =
-        if success
-            string(result)
-        else
-            JSON.json(Dict(
-                :valid => false,
-                :error => sprint(showerror, result)))
-        end ## if
+
+    const response_body = string(result)
+
     debug(logger, "returning from dispatch()")
     debug(logger, "success: $success")
-    debug(logger, "response body: " * response_body)
+
     return (success, response_body)
 end ## dispatch()
 

bioinformatics/QpcrAnalysis/melting_curve.jl

@@ -59,11 +59,9 @@ function act(
     #
     ## pass data and parameter values to mc_analysis()
     ## which will perform the analysis for the entire dataset
-    const response = try
+    const response =
         mc_analysis(interface)
-    catch err
-        return fail(logger, err; bt = true) |> out(out_format)
-    end ## try
+
     return response |> out(out_format)
 end ## act(::Type{Val{meltcurve}})
 

bioinformatics/QpcrAnalysis/standard_curve.jl

@@ -35,7 +35,7 @@ function act(
         try
             parse_raw_data(Val{standard_curve}, req)
         catch()
-            fail(logger, ArgumentError(
+            throw(ArgumentError(
                 "cannot parse raw data for standard curve analysis"))
         end ## try
     #

bioinformatics/juliaserver.jl

@@ -40,8 +40,7 @@ function get_response(req ::HTTP.Request)
                 const success, response_body =
                     QpcrAnalysis.dispatch(action, request_body; kwargs...)
                 debug(logger, "at get_response() receiving results from QpcrAnalysis.dispatch()")
-                ## code =
-                (success) ? 200 : 500
+                code = (success) ? 200 : 500
             else ## length(nodes) < 3
                 404
             end

web/Gemfile.lock

@@ -61,7 +61,7 @@ GEM
       execjs
     coffee-script-source (1.12.2)
     concurrent-ruby (1.0.5)
-    crass (1.0.3)
+    crass (1.0.4)
     diff-lcs (1.3)
     ejs (1.1.1)
     erubis (2.7.0)
@@ -86,21 +86,21 @@ GEM
       thor (>= 0.14, < 2.0)
     json (1.8.6)
     kgio (2.11.1)
-    loofah (2.1.1)
+    loofah (2.3.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     mail (2.7.0)
       mini_mime (>= 0.1.1)
     migration_comments (0.4.1)
       activerecord (>= 4.2.0)
     mini_mime (1.0.0)
-    mini_portile2 (2.3.0)
+    mini_portile2 (2.4.0)
     minitest (5.11.1)
     multi_json (1.13.1)
     multi_xml (0.6.0)
     mysql2 (0.4.10)
-    nokogiri (1.8.1)
-      mini_portile2 (~> 2.3.0)
+    nokogiri (1.10.4)
+      mini_portile2 (~> 2.4.0)
     public_suffix (3.0.1)
     rabl (0.13.1)
       activesupport (>= 2.3.14)