50d467281f8b23157c18f32327de0dc3703338a1
galt
  Thu Feb 13 15:31:03 2020 -0800
The rest of the changes for cirm from index.html to cirmIndex.html

diff --git src/hg/cirm/gateway/htdocs/README src/hg/cirm/gateway/htdocs/README
index 93a30e7..9b7e2dc 100644
--- src/hg/cirm/gateway/htdocs/README
+++ src/hg/cirm/gateway/htdocs/README
@@ -1,93 +1,93 @@
 
 
 USING htmlCheck and setRoot:
 
 Note that you can use htmlCheck with several useful commands either directly on the .html files in the 
 location where we edit the .html files (kent/src/hg/cirm/gateway/htdocs),
 
 or by using a url like 
- https://cirm-01-galt.cirm/index.html
+ https://cirm-01-galt.cirm/cirmIndex.html
 
 You can also login to cirmdcm from hgwdev with your password for testing:
- https://galt%40soe.ucsc.edu:mypassword@cirmdcm.soe.ucsce.edu/index.html
+ https://galt%40soe.ucsc.edu:mypassword@cirmdcm.soe.ucsce.edu/cirmIndex.html
 
 It is helpful to run htmlCheck with both the validate and strictTagNestCheck commands since they cover different things.
 This will find errors in the html syntax.
 
 htmlCheck getLinks is very handy for displaying all of the links and making sure they are properly formed and properly relative.
 To be properly relative, they should not start with the slash / character because that is an absolute path.
 
 This error is harmless:
-https://cirm-01-galt.cirm/index.html# doesn't exist
+https://cirm-01-galt.cirm/cirmIndex.html# doesn't exist
 It just means that the menu method employed has some dummy URLs "#" in dropdowns.
 
 This one filters out the internal # tags and off-site links to focus on the rest 
 and make sure they are correct and relative.
 htmlCheck getLinks 'https://cirm-01-galt.cirm/projects.html' | egrep -v '(http|^#)'
 
 
 Specific domain that is unwanted:
 Also, you should not use a domain in the URL like cirmdcm.soe.ucsc.edu because we do not need it and also it will fail when pushed to the public server.
 
 Obviously, if the link is something that is going completely off-site, then a protocol and domain are needed.
 
 Also, if it is a special case like a link labelled as taking the user specifically and only to the public site,
 then it would be ok to specify https://cirm.ucsc.edu.
 
 
 SETROOT SSI SOLUTION
 setRoot is an effective and efficient method for detecting how many levels deep a static page is below htdoc/ dir.
 
 setRoot.html is a small SSI command that sets what the $ROOT location is.
 At the highest level like htdoc itself, it is just an empty string.
 Each directory below that which contains .html files should have a setRoot.html too.
 And in fact, all the setRoot.html files BELOW the top level are identical.
 And they are all however different from the top level htdocs/ version.
 Basically, for all levels below htdocs, it just takes the value of ROOT from its parent directory
 and then appends "../" to the env variable.
 
 If you have a missing setRoot.html in one of the directories,
 you will see this error on the page:
 
 [an error occurred while processing this directive]
 
 The great thing about setRoot approach is that it automatically calculates
 the root from whatever directly you may be in without maintenance.
 If you move something into a subdirectory, the links should continue to work
 automatically with no new programming required.  All you have to do when making
 a new subdir for use with html is to copy the setRoot.html from a sibling directory,
 or a parent dir if it is not the htdocs root.
 
 There are 2 ways in which links on a page can be working and correct:
 1. You get the simple boilerplate of a couple of lines at the top which are identical in all .html files
 even the root too. And it never requires further editing as you move things around.
 It makes the included page header and footer work right no what directory they are being included from.
 2. You can change other internal relative links in the page to use 
 Instead of having somthing like 
 ../../../image/somePic.jpg
 <!--#echo var='ROOT'-->image/somePic.jpg
 Then it will never need changing again, even if you move the html file to another directory.
 Note that there is NO TRAILING SLASH after echoing ROOT.
 This takes a little more work but is usually worth it.
 The only exception would probably be for things that are on the very same level in the same directory.
 i.e. things that are basically topically related and in a nearby directory.
 Whereas resources that need to go to the top like /image/ or /js/ should have the ROOT variable instead.
 
 Note that I use single quotes around the 'ROOT' in the echo above precisely
 because I want to be able to run htmlCheck on the local .html file, even without going through SSI and apache
 which will replace them with the value at runtime.
 
 Note that if you are commenting out a section of code that is using the SSI command,
 you will have to change the <!-- and --> in the SSI command to <!~~ and ~~>
 especially if you want to be able to run htmlCheck on the local file.
 Because html does not allow nested comments.
 If you later decide to uncomment the SSI command, just replace the ~~ with --.
 
 Note that the checkLinks command is very useful, but it only works properly 
 on the non-local html file, i.e. you are specifying a full URL, not just a local path.
 Once you have run htmCheck on the local file, and are satisfied you found no errors,
 then you can run make in the htdocs dir to send it out to
 the apache area. Then rum checkLinks on the full URL as a final verification.