From 4ef82b2e13e6f3797a20e87121d9241ea768979f Mon Sep 17 00:00:00 2001
From: "taha@mkem" <taha@chepec.se>
Date: Wed, 21 May 2014 14:13:52 +0200
Subject: [PATCH] chertex.sh now handles sample-matrix jobs only to produce
 HTML (Shiny) output.

Previously a pdf file was always created as well, but from now on,
sample-matrix will be exclusively used in the Shiny app.
---
 chertex.sh          | 64 ++++++++++++++++++++++++---------------------
 chrome-with-tabs.sh |  6 +++--
 sendfromgmail.py    | 27 +++++++++----------
 3 files changed, 51 insertions(+), 46 deletions(-)
 mode change 100644 => 100755 sendfromgmail.py

diff --git a/chertex.sh b/chertex.sh
index 56aa16f..3ae34bc 100755
--- a/chertex.sh
+++ b/chertex.sh
@@ -10,11 +10,11 @@
 ####################################################
 
 clear
-echo "---------------------------------------------------------------"
-echo "cheRTeX -- a script for processing R-Sweave-LaTeX-TikZ projects"
-echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
-echo "MMX -- taha.ahmed@mkem.uu.se -- CHEPEC doctoral degree project"
-echo "---------------------------------------------------------------"
+echo "-----------------------------------------------------------------------"
+echo "cheRTeX -- a script for processing R--Sweave/knitr--LaTeX/TikZ projects"
+echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
+echo "MMXIV -- taha.ahmed@kemi.uu.se -- CHEPEC doctoral degree project"
+echo "-----------------------------------------------------------------------"
 
 ## If the file .latexmkrc exists in the current directory,
 ## set the flag ltxmkrc=TRUE
@@ -27,16 +27,18 @@ else
    echo "--- This job did not request LaTeXMK RC file"
 fi
 
-
+# define some commands
 Rfiletype="R"
 TeXfiletype="tex"
 tikzfiles="*.tikz"
 Rnwfiles="*.Rnw"
 auxfiles="*.aux *.bbl *.bcf *.blg *.fdb* *.figlist *.fls *.lof *.log *.lot *.lox *.makefile *.map *.out *.run* *.tdo *.toc *.dep *.dpth"
 
+
+# depending on number of args and their content, do different things...
 if [ $# -eq 1 ]; then
 	# Check if the argument contains a filetype
-	# Assumes a complete filename was passed
+	# (assumes a complete filename was passed)
 	jobfilename=$1
 	jobfiletype=${jobfilename#*.} # File extension
 	jobname=${jobfilename%.*} # Filename without extension part
@@ -44,14 +46,14 @@ if [ $# -eq 1 ]; then
 	echo "<cheRTeX> Detected filename: " $jobname
 	echo "<cheRTeX> Detected extension:" $jobfiletype
 
-	# Verifying that the file extension is *.Rnw
+	# Verify that the file extension is "[Rr][Nn][Ww]"
 	if [[ $jobfiletype == "Rnw" || $jobfiletype == "rnw" || $jobfiletype == "RNW" ]]; then
-		# File extension is *.Rnw
+		# File extension is indeed "[Rr][Nn][Ww]"
 		echo "<cheRTeX> Detected *.Rnw extension"
 		jobfiletype="Rnw"
 	else
-		# File extension is not *.Rnw
-		echo "<cheRTeX> File extension should be *.Rnw"
+		# File extension is NOT "[Rr][Nn][Ww]"
+		echo "<cheRTeX> This script only handles *.Rnw files"
 		echo "<cheRTeX> Terminating..."
 		exit 1
 	fi
@@ -59,8 +61,27 @@ if [ $# -eq 1 ]; then
 	# Introducing a short delay to enable on-screen reading of previous echo
 	/home/taha/chepec/chetex/common/bash/simpledelay.sh 2
 	echo "Delay completed"
-
-   ## Handle knitr or pgfSweave jobs separately
+	
+	
+	#### Special treatment for sample-matrix.Rnw
+   # If $jobname is sample-matrix, run only knitr and markdown, then exit
+   if [[ $jobname == "sample-matrix" ]]; then
+	   echo "<cheRTeX> -----------------------------------------------------------"
+      echo "<cheRTeX> sample-matrix: update SHINY, run knit() + markdownToHTML()"
+      echo "<cheRTeX> -----------------------------------------------------------"
+      
+      # Before starting new shiny process, kill any previous instances
+      pkill -f "shiny::runApp"
+      bash -c "/home/taha/chepec/chetex/common/bash/shiny-matrix.sh" & 
+      Rscript -e "library(knitr); knit(input='$jobname.Rmd', output='$jobname.md')"
+      Rscript -e "library(markdown); markdownToHTML('$jobname.md', '$jobname.html', stylesheet = 'custom.css')"
+      echo "<cheRTeX> Terminating..."
+      /home/taha/chepec/chetex/common/bash/simpledelay.sh 14
+   	exit 1
+   fi
+	
+	
+   ## Handle knitr or pgfSweave jobs (each requires separate treatment)
    ## But how should we tell the difference between them?
    ## There is no obvious way to tell the difference (apart from reading the *.Rnw file)
    ## IN ALL KNITR DIRECTORIES, CREATE A FILE NAMED: .knitme
@@ -119,23 +140,6 @@ if [ $# -eq 1 ]; then
 	   latexmk -pdf -bibtex $jobname
    fi
 
-   ## THIS IS A QUICK-AND-DIRTY FIX FOR SAMPLE-MATRIX
-   # If $jobname is sample-matrix, run knitr and markdown
-   if [[ $jobname == "sample-matrix" ]]; then
-      echo "<cheRTeX> -----------------------------------------------------------"
-      echo "<cheRTeX> sample-matrix: update SHINY, run knit() + markdownToHTML()"
-      echo "<cheRTeX> -----------------------------------------------------------"
-      
-      # Old attempts, never worked 
-      #PORT=$(</home/taha/chepec/chetex/sample-matrix/shinyapp/shiny.port)
-      #bash -c "R -e 'shiny::runApp(\"/home/taha/chepec/chetex/sample-matrix/shinyapp\", port = $PORT)'"
-      # Before starting new shiny process, kill any previous instances
-      pkill -f "shiny::runApp"
-      bash -c "/home/taha/chepec/chetex/common/bash/shiny-matrix.sh" & 
-      Rscript -e "library(knitr); knit(input='$jobname.Rmd', output='$jobname.md')"
-      Rscript -e "library(markdown); markdownToHTML('$jobname.md', '$jobname.html', stylesheet = 'custom.css')"
-   fi
-
 else
 	# Either no arguments, or more than one argument
 	if [ $# -eq 0 ]; then
diff --git a/chrome-with-tabs.sh b/chrome-with-tabs.sh
index c23dee3..637ef7a 100755
--- a/chrome-with-tabs.sh
+++ b/chrome-with-tabs.sh
@@ -6,11 +6,13 @@
 a="https://mail.google.com"
 b="https://rememberthemilk.com"
 c="https://chepec.timetask.com"
+d="https://keep.google.com/keep/"
+
 # open shiny sample-matrix
 # find current port number by reading shiny.port file
 PORT=$(</home/taha/chepec/chetex/sample-matrix/shinyapp/shiny.port)
-d="localhost:$PORT"
+s="localhost:$PORT"
 
-google-chrome $a $b $c $d
+google-chrome $a $b $c $d $s
 
 exit 1
diff --git a/sendfromgmail.py b/sendfromgmail.py
old mode 100644
new mode 100755
index e0500ab..6784b36
--- a/sendfromgmail.py
+++ b/sendfromgmail.py
@@ -3,7 +3,6 @@ import os, re
 import sys
 import smtplib
 
-# I have commented out the parts that allow sending of attachments...
 # I got this code from user hakermania at http://ubuntuforums.org/showthread.php?t=1472520
  
 #from email.mime.image import MIMEImage
@@ -17,15 +16,16 @@ SMTP_SERVER = 'smtp.gmail.com'
 SMTP_PORT = 587
 
  
-sender = 'taha.sol@gmail.com'
-password = "OKWS:pled2XO"
+# this may no longer work due to two-factor auth enabled for this account
+sender = 'doktorandnamnden@gmail.com'
+password = ""
 recipient = sys.argv[1]
-subject = ''
+subject = sys.argv[2] # "Inbjudan till DNs sommarmingel - test" # 
 message = sys.argv[3]
  
 def main():
     msg = MIMEMultipart()
-    msg['Subject'] = sys.argv[2]
+    msg['Subject'] = subject
     msg['To'] = recipient
     msg['From'] = sender
     
@@ -42,21 +42,20 @@ def main():
     
     session.login(sender, password)
 
-    #fp = open(sys.argv[4], 'rb')
-    #msgq = MIMEBase('audio', 'audio')
-    #msgq.set_payload(fp.read())
-    #fp.close()
+    fp = open(sys.argv[4], 'rb')
+    msgq = MIMEBase('application', 'pdf') # MIMEBase('audio', 'audio')
+    msgq.set_payload(fp.read())
+    fp.close()
     # Encode the payload using Base64
-    #encoders.encode_base64(msgq)
+    encoders.encode_base64(msgq)
     # Set the filename parameter
-    #filename=sys.argv[4]
-    #msgq.add_header('Content-Disposition', 'attachment', filename=filename)
-    #msg.attach(msgq)
+    filename=sys.argv[4]
+    msgq.add_header('Content-Disposition', 'attachment', filename=filename)
+    msg.attach(msgq)
     # Now send or store the message
     qwertyuiop = msg.as_string()
 
 
-
     session.sendmail(sender, recipient, qwertyuiop)
     
     session.quit()