"Biotools Pipeline" function
- Implement access control, most operations require owner or admin.
- N-1 relations partically done.
Dev Log 2004-12-31
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Monthly Archives: December 2004
Dev Log 2004-12-30
"Biotools Pipeline" function
- User are not allowed to configure a step unless all previous steps
have been configured. (check it in biotools.protocol.step.php) - Input/Sequence type parameters are not allowed for configuration in pipeDesign
- biotoolConfPage class is refined for inPipeDesgin and normal jobs
- The [DEFAULT] radio button for Excl type is removed, I do not think
it necessary as if it is not mandatory, the radio won't be selected - Step
configuration can be saved!! with all the parameter values, my main
purpose of using a new class to replace XSLT is achieve! woooo… - In fact, the ability to save configuration could also be applied for individual jobs, but so far I do not think it necessary.
- Saved configuration can be discarded.
- 1-1, 1-N relationship is done.
- Next step should be N-1 relation and run pipeline job.
Dev Log 2004-12-29
Dec 28-29, 2004
- previously I used a highly hacked XSLT to render the XML file, XSLT
is good for static page, though I have given it some flexibilities with
passed-in parameters and post-process with regular-expression, but soon
I found out it still becomes the bottoleneck especially when I am
trying to build a web-configureable pipeline. In the end, I decide to
spend a few day to convert the XSLT function into this class that indeed does the same thing, but more. - on
Dec 29, the transition is done almost perfectly. (at least the oringal
XSLT work could be prefectly duplicated with new class) - The
previous biotoolXML class is removed and changed to biotoolThinXml
which only convert the fat Pise XML to a thin version to be used in my
job. - biotoolThinXML is merged with biotoolCommand class in biotools.converter.php
- A few files are updated because of the file/class update.
- Now we are ready to move on with pipeline stuffs.
Dev Log 2004-12-27
Dev Log 2004-12-26
"Biotools pipeline" function
- Delete step barely work.
- Progress is slowed down a little bit. May try to speed up ASAP.
Dev Log 2004-12-25
"Biotools pipeline" function
- Pipeline steps are merged with pipeline for edit action.
- New class biotoolsProtocolStep and biotoolsProtocol
- We must distinguish protocol from pipeline job
- Adding new pipeStep almost done. Relations between each step is barely organized.
Network Privacy Protected
Got a great software/solution to anonymize TCP access.
- Get Tor and install it for SOCKS proxy
- Get Privoxy for HTTP/HTTPS proxy
- Edit /Libaray/Privoxy/config, add forward-socks4a / localhost:9050 . to the first line
- Start Tor
- Start Privoxy (/Libaray/Privoxy/StartPrivoxy.command)
- Edit proxy configure for HTTP (127.0.0.1:8118), or SOCKS (127.0.0.1:9105)
Great work!!
Dev Log 2004-12-22
"Biotools" function
- Finally figured out a better design of pipeline management (implementation may takes quite some time)
- Fixed a bug in job submission where tmp folder is not clean when request is duplicated.
- Move commonly used javascript to a seperate file
- Pipeline :: pipe task entry function implemented
- Pipeline :: newPipe, editPipe, cancelNewPipe implemented
- Pipeline :: cp_biotools_pise class implemented
Fink Fails
My attempts of moving from darwinport to fink fails … it wastes my entire day.
One uncomfortable thing about fink is its building mechansim. Fink
removes its working folder if the installation fails and this results
in re-building from scratch for every attemp. While darwinports can
keep the working environment even installation fails …
At least the restoration takes only 20 minutes as I backup everything before migration. Sigh…
From Darwinport to Fink
I am trying to move my unix libraries from darwinports to fink
package management. It is really time consuming, maybe just a relax for
next week.
The apache server and mysql will be using Fink for installation and
management, but I still need to hack the info file for my required
parameter, especially for mysql to provide UTF-8 support.