Merge branch 'master' of github.com:RobertRosca/JAXTAM.jl

RobertRosca · Aug 8, 2018 · 7842103 · 7842103
2 parents 01b001d + c6fb3ad
commit 7842103
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Showing 4 changed files with 132 additions and 21 deletions.
diff --git a/src/JAXTAM.jl b/src/JAXTAM.jl
@@ -13,6 +13,7 @@ using Compat
 using FITSIO
 using Feather
 using StatsBase
+using Mustache
 using DSP
 using Plots
 gr()
@@ -32,5 +33,6 @@ include("science/lcurve.jl")
 include("science/fspec.jl")
 include("science/plots.jl")
 include("web/webgen.jl")
+include("web/subgen.jl")
 
 end
diff --git a/src/science/read_events.jl b/src/science/read_events.jl
@@ -9,14 +9,20 @@ struct InstrumentData <: JAXTAMData
     header::DataFrame
 end
 
-function _read_fits_hdu(fits_file, hdu_id)
-    fits_cols_events = Array{String,1}
-
-    try
-        fits_cols_events = FITSIO.colnames(fits_file[hdu_id])
-    catch UndefVarError
-        @warn "FITSIO colnames function not found, try trunning `Pkg.checkout(\"FITSIO\")`"
-        throw(UndefVarError("colnames not defined"))
+function _read_fits_hdu(fits_file, hdu_id; cols="auto")
+    if cols == "auto"
+        fits_cols_events = Array{String,1}
+
+        try
+            fits_cols_events = FITSIO.colnames(fits_file[hdu_id])
+        catch UndefVarError
+            @warn "FITSIO colnames function not found, try trunning `Pkg.checkout(\"FITSIO\")`"
+            throw(UndefVarError("colnames not defined"))
+        end
+
+        println(fits_cols_events)
+    else
+        fits_cols_events = cols
     end
 
     fits_hdu_data = DataFrame()
@@ -28,25 +34,25 @@ function _read_fits_hdu(fits_file, hdu_id)
             if ndims(fits_col_data) == 1
                 fits_hdu_data[Symbol(col)] = fits_col_data
             end
-        catch
-            @warn "$col not supported by FITSIO, skipped"
+        catch error
+            @warn "$col not supported by FITSIO, skipped - $error"
         end
     end
 
     return fits_hdu_data
 end
 
 function _read_fits_event(fits_path)
-    print("\n"); @info "Loading $fits_path"
+    @info "Loading $fits_path"
     fits_file   = FITS(fits_path)
 
-    fits_header = read_header(fits_file[1])
+    fits_header = read_header(fits_file["EVENTS"])
 
     instrument_name = fits_header["INSTRUME"]
     fits_telescope  = fits_header["TELESCOP"]
     fits_telescope  = Symbol(lowercase(fits_telescope))
 
-    fits_events_df = _read_fits_hdu(fits_file, "EVENTS")
+    fits_events_df = _read_fits_hdu(fits_file, "EVENTS"; cols=String["TIME", "PI"])
 
     fits_gtis_df = _read_fits_hdu(fits_file, "GTI")
 
@@ -122,7 +128,7 @@ function _save_cl_feather(feather_dir, instrument_name, fits_events_df, fits_gti
     Feather.write(joinpath(feather_dir, "$instrument_name\_meta.feather"), fits_meta_df)
 end
 
-function read_cl(mission_name::Symbol, obs_row::DataFrames.DataFrame)
+function read_cl(mission_name::Symbol, obs_row::DataFrames.DataFrame; overwrite=false)
     obsid       = obs_row[:obsid][1]
     JAXTAM_path = abspath(string(obs_row[:obs_path][1], "/JAXTAM/"))
 
@@ -138,7 +144,7 @@ function read_cl(mission_name::Symbol, obs_row::DataFrames.DataFrame)
     JAXTAM_e_files = count(contains.(JAXTAM_content, "events"))
     JAXTAM_g_files = count(contains.(JAXTAM_content, "gtis"))
 
-    if JAXTAM_e_files > 0 && JAXTAM_g_files > 0 && JAXTAM_e_files == JAXTAM_g_files
+    if JAXTAM_e_files > 0 && JAXTAM_g_files > 0 && JAXTAM_e_files == JAXTAM_g_files && !overwrite
         mission_data = Dict{Symbol,InstrumentData}()
 
         #instruments = unique(replace.(JAXTAM_content, r"(_gtis|_events|_meta|_calib|.feather)", ""))
@@ -177,14 +183,14 @@ function read_cl(mission_name::Symbol, obs_row::DataFrames.DataFrame)
     return mission_data
 end
 
-function read_cl(mission_name::Symbol, append_df::DataFrames.DataFrame, obsid::String)
+function read_cl(mission_name::Symbol, append_df::DataFrames.DataFrame, obsid::String; overwrite=false)
     obs_row = master_query(append_df, :obsid, obsid)
 
-    return read_cl(mission_name, obs_row)
+    return read_cl(mission_name, obs_row; overwrite=overwrite)
 end
 
-function read_cl(mission_name::Symbol, obsid::String)
+function read_cl(mission_name::Symbol, obsid::String; overwrite=false)
     append_df = master_a(mission_name)
 
-    return read_cl(mission_name, append_df, obsid)
+    return read_cl(mission_name, append_df, obsid; overwrite=overwrite)
 end
diff --git a/src/web/subgen.jl b/src/web/subgen.jl
@@ -0,0 +1,98 @@
+function _webgen_format_table(row::DataFrames.DataFrame)
+    col_num = size(row, 2)
+
+    table_th_full = ""
+    table_td_full = ""
+
+    for i = 1:col_num
+        table_th = """
+        <th>$(names(row)[i])</th>
+        """
+
+        table_th_full = string(table_th_full, table_th)
+
+        table_td = """
+        <td>$(row[1, i])</td>
+        """
+
+        table_td_full = string(table_td_full, table_td)
+    end
+
+    table_html = """
+    <table id=\"example\" class=\"table table-striped table-bordered\" style=\"width:100%\">
+    <thead>
+    <tr>
+    $table_th_full</tr>
+    </thead>
+    <tbody>
+    <tr>
+    $table_td_full</tr>
+    </tbody>
+    </table>
+    """
+
+    return table_html
+end
+
+_webgen_sub_body_intro = mt"""
+<body>
+<div class=\"container\">
+<h1>Observation {{obsid}} - {{name}}</h1>
+<hr>
+<h2>Abstract</h2>
+<h4>{{title}} - {{subject_category}}</h4>
+<p>{{abstract}}</p>
+<hr>
+<h4>Status</h4>
+<table id=\"example\" class=\"table table-striped table-bordered\" style=\"width:100%\">
+<thead>
+<tr>
+<th>public_date</th>
+<th>publicity</th>
+<th>time</th>
+<th>downloaded</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>{{public_date}}</td>
+<td>{{publicity}}</td>
+<td>{{time}}</td>
+<td>{{downloaded}}</td>
+</tr>
+</tbody>
+</table>
+<h4>Source Details</h4>
+"""
+
+function _webgen_sub(row::DataFrames.DataFrame)
+    table_status = _webgen_format_table(row[[:public_date, :publicity, :time, :downloaded]])
+    table_source = _webgen_format_table(row[[:name, :ra, :dec, :lii, :bii, :obs_type]])
+    table_obsdet = _webgen_format_table(row[[:time, :end_time, :exposure, :remarks]])
+    table_misc   = _webgen_format_table(row[[:processing_status, :processing_date, :processing_version, :num_processed, :caldb_version, :remarks]])
+
+    header = _webgen_head(title="$(row[1, :obsid]) - $(row[1, :name])")
+
+    result_html = """
+    $header
+    <body>
+    <div class=\"container\">
+    <h1>Observation {{obsid}} - {{name}}</h1>
+    <hr>
+    <h2>Abstract</h2>
+    <h4>{{title}} - {{subject_category}}</h4>
+    <p>{{abstract}}</p>
+    <hr>
+    <h4>Status</h4>
+    $table_status
+    <h4>Source Details</h4>
+    $table_source
+    <h4>Observation Details</h4>
+    $table_obsdet
+    <h4>Misc</h4>
+    $table_misc
+    </body>
+    """
+
+    return result_html
+end
diff --git a/src/web/webgen.jl b/src/web/webgen.jl
@@ -98,7 +98,12 @@ function _webgen_mastertable(mission_name::Symbol)
 end
 
 function webgen_mission(mission_name::Symbol)
-    web_html = string(_webgen_home(mission_name), _webgen_mastertable(mission_name))
+    web_dir = config(:web)
+
+    web_home_dir  = joinpath(web_dir, "index.html")
+    web_home_html = string(_webgen_home(mission_name), _webgen_mastertable(mission_name))
+
+    write(web_home_dir, web_home_html)
 
-    return web_html
+    return web_home_dir
 end