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2013-10-15Before getting rid of query_string in DecodeUserSam
2013-10-15Changed templates to call the header macroZachary Sloan
Correlation page now works with Non-BXD (or whatever group) or All Samples options
2013-10-15* Redid mail sending service to set a ping showing it's aliveSam
* Redid server so it wouldn't start unless mail service recently pinged * Wrote a bunch of forgot password code * Refactored sending email about verification and forgotten passwords
2013-10-11Merge /home/sam/geneLei Yan
2013-10-11Merge /home/sam/geneZachary Sloan
2013-10-11Small changes around logging inSam
2013-10-11Merge /home/lei/geneZachary Sloan
Conflicts: wqflask/maintenance/quick_search_table.py
2013-10-10Almost have correlation working for non-primary strain/groupLei Yan
There's just some issue with parents/f1s not being included if you select non-BXD (or whatever the group is). All Samples, however does work.
2013-10-09Improved some of the code related to the correlation pageLei Yan
For example, changed the two functions getting gene symbols and ids for a dataset into one function that can take a column name as a parameter
2013-10-08Literature correlation works when it is selected as the sortedLei Yan
correlation type (that is, when it is run again all traits in a database) Added a function to data_set.py that gets all the gene_ids in the data set. Not sure if having a separate function for getting the gene_ids and another for getting the gene symbols makes sense.
2013-10-08Did some work with interval mapping page; will use qtl reaper to doZachary Sloan
the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl
2013-10-07Worked on logins, session_ids, flash messages, etc.Sam
2013-10-06Before writing login codeSam
2013-10-03Much more progess on logging in:Sam
* Verifying emails now works * Redid user manager
2013-10-02Half the verification code for email addresses is doneSam
2013-09-27Downloaded the TableTools library so tables can be exported/savedLei Yan
2013-09-27Added trait links to correlation resultsLei Yan
Began adding the code that does the initial sort by literature correlation
2013-09-27User registration beginning to work (at least the first stage)Sam
2013-09-27Before fixing an issue in pbkdf2Sam
2013-09-24Did some work towards doing the tissue correlation for all traitsroot
in a dataset (in order to sort by tissue correlation instead of sample correlation).
2013-09-24before deleting more of the security flask stuffSam
2013-09-24Just committing a few additions to the interval mapping codeZachary Sloan
2013-09-24Fixed the db_tools import in mrna_assay_tissue_data.pyZachary Sloan
Added file for the interval mapping page and wrote code that gets/sets some parameters
2013-09-20Tissue correlation results work for sample r/rho correlation pageLei Yan
and are written to the template
2013-09-13Merge /home/lei/geneZachary Sloan
2013-09-13Added file that will convert genofiles to plink ped/map filesZachary Sloan
2013-09-13Merge https://github.com/zsloan/genenetworkLei Yan
Resolved conflicts: wqflask/base/trait.py wqflask/wqflask/correlation/correlationFunction.py wqflask/wqflask/correlation/correlation_function.py wqflask/wqflask/correlation/correlation_functions.py wqflask/wqflask/correlation/show_corr_results.py
2013-09-06Registration form validaiton without js worksSam
2013-09-05Missed some files in last checkin so adding them nowSam
2013-09-05Switched registration form to no longer be modal, but instead it's own pageSam
Added validation of form using parsley.js Added password strength indicator using zxcvbn
2013-09-05Adjusting to using our own registariton packageSam
2013-09-04Trying to trace through filesSam
2013-08-28Various changes to track down what happens with security modulesSam
2013-08-23Finally figured out where to put flask_security into the codeSam
Various registration template changes
2013-08-23Working on user registration and added nginx conf for my branchSam
2013-08-21Fixed an issue where correlationFunction was being importedZachary Sloan
instead of its updated name correlation_function
2013-08-21Just removed a couple print statementsZachary Sloan
2013-08-15Removed the markers with no variance (and thus no p-values) from theZachary Sloan
manhattan plot
2013-08-14Merge branch 'master' of https://github.com/zsloan/genenetworkZachary Sloan
2013-08-14Made some changes related to getting marker regression working forZachary Sloan
some datasets
2013-08-14Removed some duplicate files in the maintenance folderZachary Sloan
2013-08-13Added several test files and the file with the class thatZachary Sloan
they import (browser_test.py)
2013-08-08Fixed issue where points in marker regression manhattan plotZachary Sloan
weren't positioned on the x-axis
2013-08-07Fixed things with the dataset dropdowns and mRNA datasetsZachary Sloan
Improved the templates for a couple pages related to changing user password, etc
2013-08-02Fixed a bug related to groups with genofiles (not sure if it makes senseZachary Sloan
for them not to have genofiles yet)
2013-07-30Just added some print statements to debug an issue with LMM codeZachary Sloan
Also added some to notes
2013-07-23Fixed a couple issues with he quick_search_table.py scriptZachary Sloan
Added notes on using percona to optimise mysql to gn_installation_notes.txt Started moving "get_trait_data" to DataSet since it is the same regardless of the particular DataSet subclass (PhenotypeDataSet, MrnaAssayDataSet, etc)
2013-07-19Finished integrating code that reads sample list from geno filesZachary Sloan
withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page
2013-07-19Created file gen_group_samplelists that iterates through all genofilesZachary Sloan
and builds each groups' samplelist
2013-07-18Added Amelie's rat data genotypesZachary Sloan
Got human mapping mostly working Fixed dataset dropdown menus
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