c992c0f29442e38937ddb4ba6cbbadefa81f4315
dschmelt
  Tue Dec 3 11:51:58 2019 -0800
Removing scripts #24290

diff --git src/utils/qa/trackQaHelper src/utils/qa/trackQaHelper
deleted file mode 100755
index 82cc007..0000000
--- src/utils/qa/trackQaHelper
+++ /dev/null
@@ -1,166 +0,0 @@
-#!/bin/bash
-#TrackQaHelper guides some of the processes for QA.
-#Written by Daniel Schmelter 7/5/19
-
-echo ""
-echo "Welcome to trackQA helper!"
-echo "-------------------------------------------"
-# Check track Description
-#input path of html file
-echo "Step 1: Spellcheck and htmlCheck, no output is good (unfortunately)"
-read -p "Do you wish to run spell check on the track HTML (y/n)?" yn #could be condensed into yn7
-if [ "$yn" != "${yn#[Yy]}" ] ; then
-   read -p "Please enter the path of the html file (in trackDb)" htmlPath
-   #Spell check, html check
-   aspell check $htmlPath
-   echo "Spell check completed!"
-   echo ""
-   sleep 2
-   echo "Step 2.1: Comensing htmlCheck checkLinks"
-   htmlCheck checkLinks $htmlPath 2>&1 >/dev/null | grep -v 'db\|getaddr\|hgTables'
-   echo ""
-   echo "Step 2.2: htmlCheck validate, checks tags and tables"
-   htmlCheck validate $htmlPath 2>&1 >/dev/null | grep -v BODY
-fi
-echo ""
-
-#Push to Tables Beta
-#Input Tables
-read -p "Do you have tables to push to beta (y/n)?" yn2
-if [ "$yn2" != "${yn2#[Yy]}" ] ; then
-   echo "Step 3: Pushing tables and files to beta"
-   read -p "Please input your db: " db
-   read -p "Please input a file path to your table list: " tableList
-   echo "Thank you. These will now be pushed to beta"
-   bigPush.sh $db $tableList 
-fi
-echo ""
-
-#Push Gbdb files to beta
-#Ask and push gbDb files to beta 
-read -p "Do you need to push any gbDb files to beta (y/n)?" yn3
-if [ "$yn3" != "${yn3#[Yy]}" ] ; then
-   sudo gbdbPush
-fi
-
-echo ""
-
-#Make beta
-read -p "Want to make beta (y/n)?" yn4
-if [ "$yn4" != "${yn4#[Yy]}" ] ; then
-   if [ -z "$db" ] ; then
-         read -p "Please input your db" db
-   fi
-   echo "Making beta for your db"
-   sleep 2
-   cd /cluster/home/$USER/kent/src/hg/makeDb/trackDb
-   make beta DBS=$db
-fi
-echo ""
-
-#Run QAgbTracks, Only works on Tables
-read -p "Would you like to run qaGbTracks and joinerCheck on the tables (y/n)?" yn5
-if [ "$yn5" != "${yn5#[Yy]}" ] ; then
-   echo "Step 4: Run qaGbTracks and joinerCheck scripts on the tables"
-   if [ -z "$db" ] ; then
-      read -p "Please input your db" db
-   fi
-   if [ -z "$tableList" ] ; then
-      read -p "Please input your tableList file path: "  tableList
-   fi
-   cd ~/trackQA
-   cat $tableList | while read $table; do echo $tabe; qaGbTracks $db $table $table; done
-   #Review script output
-   echo "Step 5: Review script output"
-   echo "Database	Table	Type	Row count	featureBits	Overlap with gap	Errors"
-   cat ~/trackQA/*.summary
-   cat ~/trackQA/*.log | grep -B1 ERROR
-   echo "Apologies for that chaos"
-   sleep 2
-fi
-echo ""
-
-#Test the API
-echo "The API only works on barChart, bed, bigBed, bigNarrowPeak,
-bigWig, chain, genePred, interact, narrowPeak, peptideMapping, 
-psl, rmsk - repeat masker, wig"
-read -p "Would you like to test the API, note bigGePred doesnt' work (y/n)?" yn6
-if [ "$yn6" != "${yn6#[Yy]}" ] ; then
-   if [ -z "$db" ] ; then
-      read -p "Please input your db" db
-   fi
-   read -p "Please enter the url name or shortLabel of the file: " trackName
-   echo "Go to the following link:"
-   echo "http://api.genome.ucsc.edu/getData/track?genome=$db;track=$trackName;maximumItemsOutput=2"
-fi
-
-
-#Test Data Integrator and GBIB
-echo "Check DI and GBIB"
-
-#check TB schema table descriptions
-read -p "Would you like to check the track description and Table schema (y/n)?" yn7
-if [ "$yn7" != "${yn7#[Yy]}" ] ; then
-   echo "Please check tableDescriptions on beta"
-   if [ -z "$db" ] ; then
-         read -p "Please input your db" db
-   fi
-   if [ -z "$trackName" ] ; then
-         read -p "Please input your trackName from URL: " trackName
-   fi
-   echo "Go to the following link and look at 
-      \nrow count \nupdate time \nformat description \ncolumn descriptions"
-   echo "https://hgwbeta.soe.ucsc.edu/cgi-bin/hgTables?db=$db&hgta_track=$trackName&hgta_doSchema=describe+table+schema"
-   echo "Go to the following link and read the description: "
-   echo "https://hgwbeta.soe.ucsc.edu/cgi-bin/hgTrackUi?g=$trackName"
-fi
-
-#BETA COMPLETED
-echo " If the previous steps are done, then BETA QA is completed!!"
-
-#Check release tags and make public
-echo "Ready for RR?"
-read -p "Modify Release tags manually, push files/tables, make (y/n)?" yn8
-if [ "$yn8" != "${yn8#[Yy]}" ] ; then
-   echo "Please check and modify release tags for RR release MANUALLY"
-   echo "Add pennantIcon saying that the track is new or updated"
-   if [ -z "$db" ] ; then
-         read -p "Please input your db" db
-   fi
-   read -p "Are the release tags set for RR release (y/n)? make alpha and beta" yn10
-   if [ "$yn1-" != "${yn10#[Yy]}" ] ; then
-      cd /cluster/home/$USER/kent/src/hg/makeDb/trackDb
-      make alpha DBS=$db
-      make beta DBS=$db
-   fi
-   echo ""
-   echo "Send push request for Tables or GbDb files to the RR"
-   echo ""
-   echo "Send a make public warning for hg19, hg38, and mm10"
-   echo "Making public $db"
-   echo "<EOM>"
-   read -p "Ready to make public (y/n)?" yn9
-   if [ "$yn9" != "${yn9#[Yy]}" ] ; then
-      cd /cluster/home/$USER/kent/src/hg/makeDb/trackDb
-      make public DBS=$db
-      if [ -z "$trackName" ] ; then
-         read -p "Please input your trackName from URL: " trackName
-      fi
-      echo "Check beta public at the following link: "
-      echo "https://hgwbeta-public.soe.ucsc.edu/cgi-bin/hgTrackUi?g=$trackName"
-      sleep 5
-      echo "Send push trackDb and Friends Push request"
-   fi
-fi
-
-
-
-#Check download files (after the release?) Broken?
-echo "Check download files in the cue at this directory: "
-echo "/usr/local/apache/htdocs-hgdownload/goldenPath/*"
-
-
-#Prepare push requests to RR
-echo "Push request tables, gbdb files, and trackDb n friends"
-echo "Auto generated push requests still to come"
-