helpFound

dim

@@ -2,7 +2,7 @@
 #dim: control display brightness from terminal
 #usage: dim x
 #where x is an integer for a new display brightness within the [min,max] range of [0,100]
-#user should be part of the video user group to run this wcd ithout sudo
+#user should be part of the video user group to run this without sudo
 #James B. Ackman 2019-02-06T15:55:20-08:00
 
 #check kernel backlight driver names on your machine: `ls -l /sys/class/backlight/*`

mv2figs.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-#mv2figs: used by the <cmd-z> screenshot shortcut set in .config/i3/config
+#mv2figs: used by the <ctrl-z> screenshot shortcut set in .config/i3/config
 
 #default image location
 blobFolder=$HOME/figures

pdf2bib.sh

@@ -1,31 +1,49 @@
 #!/bin/bash
-#pdf2bib
-# usage:
-#  pdf2bib.sh file.pdf
-# depends: 
-#  xsltproc - xml processor, from GNOME project
-#  pubmed2bibtex.xsl - xml processor stylesheet
-#James Ackman 2018-11-07T14:41:53-08:00
+if [ "$1" == "-h" ] ; then
+    echo "
+        pdf2bib - search for a doi within a pdf, query pubmed, and append bibtex entry with pdf to your local bib database file. Last two steps are identical to sdoi.sh
+
+         usage:
+          pdf2bib.sh file.pdf
+
+         depends:
+          pdftotext - from ghostscript or poppler or texlive ?
+          xsltproc - xml processor, from GNOME project
+          pubmed2bibtex.xsl - xml processor stylesheet
+
+         defaults:
+          Set the three required default file locations (xsl file, bib file, pdf directory)
+          "
+    exit 0
+fi
 
 #Setup defaults
-styleSheet="$HOME/bin/pubmed2bibtex.xsl"
-bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
-pdfPathOut="$HOME/projects/bibd/papers"
+styleSheet=${pubmedStyleSheet:-$HOME/bin/pubmed2bibtex.xsl}
+bibdFileOut=${bibdFileOut:-$HOME/projects/bibd/OMEGA.bib}
+pdfPathOut=${pdfPathOut:-$HOME/projects/bibd/papers}
 relPath=$(basename $pdfPathOut)
 fn=$1
 
 set -e #exit if an error
+
 echo "using $pdfPathOut"
 echo "using $bibdFileOut"
 
 #try to extract doi from pdf and retrieve a pubmed id
+#for 'DOI:' syntax
 doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i doi: --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#doi:(.+)#\1#")
 
+#for 'https://doi.org' syntax
+if [ -z "$doi" ]; then
+  doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i "doi.org/" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#.+doi\.org\/(.+)#\1#")
+fi
+
 if [ -z "$doi" ]; then
   echo "doi not found"
   exit 1
 fi
 
+
 ## TODO: dedupe this with sdoi.sh
 uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s#<Id>([0-9]+)</Id>#\1#")
 

reveal.sh

@@ -1,6 +1,18 @@
 #!/bin/bash
-#installation: place in home directory and make this file executable `chmod u=rwX,go= reveal.sh`
-#usage example: `./reveal.sh neuroanatomy1.md`
+if [ "$1" == "-h" ] ; then
+    echo "
+              reveal - helper app for opening reveal.js markdown presentations 
+              Useful for serving markdown text files locally with reveal.js
+              
+              Usage: reveal.sh neuroanatomy1.md
+
+    "
+    echo "$(tput setaf 6)$EDITOR $(tput setaf 7)is currently set as editor"
+    exit 0
+fi
+
+set -e
+
 
 appPath="$HOME/projects/dev/reveal.js"
 

sdoi.sh

@@ -1,12 +1,26 @@
 #!/bin/bash
-#sdoi - search for doi and append bibtex entry to db
-# usage:
-#  sdoi.sh 'doi.string'
+if [ "$1" == "-h" ] ; then
+    echo "
+        sdoi - search for doi guid on pubmed and append bibtex entry to bibtex db. Optionally import a downloaded pdf.
+
+         usage:
+          sdoi.sh 'doi'
+          sdoi.sh 'doi' download.pdf
+
+         depends: 
+          xsltproc - xml processor, from GNOME project
+          pubmed2bibtex.xsl - xml processor stylesheet
+
+         defaults:
+          Set the three required default file locations (xsl file, bib file, pdf directory)
+          "
+    exit 0
+fi 
 
 #Setup defaults
-styleSheet="$HOME/bin/pubmed2bibtex.xsl"
-bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
-pdfPathOut="$HOME/projects/bibd/papers"
+styleSheet=${pubmedStyleSheet:-$HOME/bin/pubmed2bibtex.xsl}
+bibdFileOut=${bibdFileOut:-$HOME/projects/bibd/OMEGA.bib}
+pdfPathOut=${pdfPathOut:-$HOME/projects/bibd/papers}
 relPath=$(basename $pdfPathOut)
 doi=$1
 fn=$2

shrinkpdf.sh

@@ -20,6 +20,7 @@ set -e
 #Setup defaults
 fn=$1
 fn2=$2
+
 set -e #exit if an error
 
 #decide whether to use a provided new file name or too write over the original filename

spmid.sh

@@ -1,13 +1,26 @@
 #!/bin/bash
-#spmid - search for pubmed id and append bibtex entry to db
-# usage:
-#  spmid.sh '12345678'
-#  spmid.sh '12345678' download.pdf
+if [ "$1" == "-h" ] ; then
+    echo "
+        spmid - search for pubmed guid and append bibtex entry to bibtex db. Optionally import an associated pdf.
+         usage:
+          spmid.sh '12345678'
+          spmid.sh '12345678' download.pdf
+
+         depends: 
+          xsltproc - xml processor, from GNOME project
+          pubmed2bibtex.xsl - xml processor stylesheet
+
+         defaults:
+          Set the three required default file locations (xsl file, bib file, pdf directory)
+ 
+    "
+    exit 0
+fi
 
 #Setup defaults
-styleSheet="$HOME/bin/pubmed2bibtex.xsl"
-bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
-pdfPathOut="$HOME/projects/bibd/papers"
+styleSheet=${pubmedStyleSheet:-$HOME/bin/pubmed2bibtex.xsl}
+bibdFileOut=${bibdFileOut:-$HOME/projects/bibd/OMEGA.bib}
+pdfPathOut=${pdfPathOut:-$HOME/projects/bibd/papers}
 relPath=$(basename $pdfPathOut)
 uid=$1
 fn=$2

spubmed.sh

@@ -1,14 +1,29 @@
 #!/bin/bash
-#spubmed.sh - search for pubmed for author, journal, year
-# usage:
-#  spubmed.sh 'kaas' 'trends+neurosci' '1995'
-#  spubmed.sh 'rakic' 'j+comp+neurol' '1972'
+if [ "$1" == "-h" ] ; then
+    echo "
+        spubmed.sh - search for pubmed for author, journal, year
+
+         usage:
+          spubmed.sh 'kaas' 'trends+neurosci' '1995'
+          spubmed.sh 'rakic' 'j+comp+neurol' '1972'
+
+         depends: 
+          xsltproc - xml processor, from GNOME project
+          pubmed2bibtex.xsl - xml processor stylesheet
+
+         defaults:
+          Set the three required default file locations (xsl file, bib file, pdf directory)
+ 
+    "
+    exit 0
+fi
 
 #Setup defaults
-styleSheet="$HOME/bin/pubmed2bibtex.xsl"
-bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
-pdfPathOut="$HOME/projects/bibd/papers"
+styleSheet=${pubmedStyleSheet:-$HOME/bin/pubmed2bibtex.xsl}
+bibdFileOut=${bibdFileOut:-$HOME/projects/bibd/OMEGA.bib}
+pdfPathOut=${pdfPathOut:-$HOME/projects/bibd/papers}
 relPath=$(basename $pdfPathOut)
+
 author=$1
 journal=$2
 year=$3

woola

@@ -1,7 +1,25 @@
 #!/bin/bash
+if [ "$1" == "-h" ] ; then
+    echo "
+              woola shell script - a helper app to invoke the woola markdown content build or server programs
+    
+              Usage: woola
+                     woola build
+             
+              Takes an optional flag that can be 'build' to build website files instead of serving.
+              By default this app will serve files from the current directory by default using woola.
+
+              Installation: place in home directory and make this file executable chmod: u=rwX,go= woola
+    "
+    exit 0
+fi
+
+set -e
+
 #helper startup script for woola
 appPath="$HOME/projects/dev/woola"
 configFile=$HOME/.config/woola/config.js
+optFlag=${1:-serve}
 
 if [[ -e $configFile ]] && [[ ! -e config.js ]]; then
     ln -s $configFile config.js
@@ -18,5 +36,9 @@ fi
 #if [[ ! -d figures ]]; then
 #    ln -s $HOME/figures figures
 #fi
-node $appPath/lib/index.js
+if [[ "$optFlag" == "build" ]]; then
+    node $appPath/lib/index --build
+else
+    node $appPath/lib/index.js 
+fi