| Age | Commit message (Expand) | Author |
|---|
| 2013-08-13 | Added several test files and the file with the class that...they import (browser_test.py)
| Zachary Sloan |
| 2013-08-07 | Fixed things with the dataset dropdowns and mRNA datasets...Improved the templates for a couple pages related to changing user
password, etc
| Zachary Sloan |
| 2013-08-02 | Fixed a bug related to groups with genofiles (not sure if it makes sense...for them not to have genofiles yet)
| Zachary Sloan |
| 2013-07-30 | Just added some print statements to debug an issue with LMM code...Also added some to notes
| Zachary Sloan |
| 2013-07-23 | Fixed a couple issues with he quick_search_table.py script...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)
| Zachary Sloan |
| 2013-07-19 | Finished integrating code that reads sample list from geno files...withouot using reaper and caches results so it doesn't need
to read the file every single time someone loads a page
| Zachary Sloan |
| 2013-07-19 | Created file gen_group_samplelists that iterates through all genofiles...and builds each groups' samplelist
| Zachary Sloan |
| 2013-07-16 | Wrote code that can get a dataset's type for every single GN...dataset; previously we could not view traits in datasets that
were not in the DBType table in the database
| Zachary Sloan |
| 2013-06-27 | Created a group manager page where user administrators can create...groups of datasets to give/add read privileges to
| Zachary Sloan |
| 2013-06-26 | Moved code creating DataSets object to a function in dataset.py...Added caching to creating DataSets object
| Zachary Sloan |
| 2013-06-26 | Got code that creates DataSets object running...Fixed one genofile that had extra quotation marks
in the comments that caused an error
Defaults mb_graph_interval to 1 for species without chromosome
lengths in megabases
| Zachary Sloan |
| 2013-06-25 | Added DataSets class to dataset.py that will be used to create list of...confidential datasets
| Zachary Sloan |
| 2013-06-21 | Fixed bug where cursor was still being used in query | Zachary Sloan |
| 2013-06-19 | Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask...Conflicts:
wqflask/base/data_set.py
wqflask/wqflask/views.py
Fixed a couple conflicts to merge Lei's code related to the correlation page
| Zachary Sloan |
| 2013-06-13 | Fixed issue where too much memory was used as a result of creating a...dataset object for each trait in the correlation results
Added new fields/columns for each trait in the correlation result table
(max LRS, max LRS location, mean expression)
Fixed error if trait doesn't have these fields
| Lei Yan |
| 2013-06-12 | Fixed a couple issues with the template that caused the...regular search results and show trait page to not display
| Zachary Sloan |
| 2013-06-11 | Put trait info for correlation results page into a dictionary instead...of storing list of GeneralTrait objects
Added print statements to track memory usage
| Lei Yan |
| 2013-05-30 | Rewrote some code in get_trait_info in dataset.py...Added spearman correlation to show_corr_results and template
| Lei Yan |
| 2013-05-28 | Have correlation values appearing in a table in the template...Use scipy to calculate pearson correlation instead of old GN code
| Lei Yan |
| 2013-05-23 | Worked on rewriting the function in data_set.py that gets the sample...values for each trait
| Lei Yan |
| 2013-05-23 | Changed the way the query that gets sample ids is generated | Lei Yan |
| 2013-05-23 | Now calculates correlation values for traits, but not yet in template | Lei Yan |
| 2013-05-09 | Just added some print statements so I can show matrix/vector...shapes to Tony
| Zachary Sloan |
| 2013-05-08 | Worked on correlation page...Wrote function in dataset.py that gets all the traits in a dataset
and their sample values
| Lei Yan |
| 2013-04-09 | Nick's code works fine with human data...Added option to limit results based on lod score (which also
changes the y-axis of the plot)
| Zachary Sloan |
| 2013-04-05 | Made changes to get pylmm code working with HMDP datasets | Zachary Sloan |
| 2013-04-02 | Committing before splitting code that runs pylmm with plink files...and code that runs it with json
| Zachary Sloan |
| 2013-04-02 | pylmm code is running for human data (plink .bed genotype files) | Zachary Sloan |
| 2013-03-19 | Searches work for the full access human datasets with mRNA assay...searches, and the trait page can be loaded
Need to get marker regression page working with human data now
| Zachary Sloan |
| 2013-03-12 | Got cashing working with pickle | Zachary Sloan |
| 2013-03-07 | Progress bar is now completely working...Still need to figure out the problem that occurred
with negative p-values after I refactored the LMM
code
| Zachary Sloan |
| 2013-03-02 | Created generate_probesetfreeze_file to create the..."probesetfreeze data matrix" file corresponding with the
muscle dataset Evan was having trouble with
| Zachary Sloan |
| 2013-02-14 | Have marker regression results displaying as a scatterplot (just the points)...using d3.js
| Zachary Sloan |
| 2013-02-13 | Fixed some bugs related to getting the marker regression page working...with Nick's code
| Zachary Sloan |
| 2013-02-12 | Edited marker_regression.py and data_set.py to store the p-values...and their corresponding markers to be used in the table of qtl results
and other figures
| Zachary Sloan |
| 2013-01-31 | Changed fd to kw in search_results.py, commented out some lines...related to fd
| Zachary Sloan |
| 2013-01-18 | Renamed CorrelationPage.py to show_corr_results.py...Worked with correlation code; got to the code that
begins to do the actual correlations
Created a function "get_dataset_and_trait" in
the new file "helper_functions.py" because the
code initializing the dataset and trait objects
was repeated in multiple places
| Zachary Sloan |
| 2013-01-03 | Began working on marker_regression.py and created Chromosomes class...in species.py
| Zachary Sloan |
| 2013-01-03 | Created template for marek regression page and made the compute button direct...to it
added asbolute_import in data_set.py and trait.py
Made several minor changes and deleted commented out code in trait.py
| Zachary Sloan |
| 2012-12-18 | Created new file species.py and species class object TheSpecies...Converted html for the mapping tabs to bootstrap and redid html inside of
the Interval Mapping tab
Added text input for # of permutation tests and bootstrap tests
| Zachary Sloan |
| 2012-12-06 | Added minimum/maximum to basic statistics table...Continued bug-shooting related to getting show_trait running
with phenotype traits
| Zachary Sloan |
| 2012-12-06 | Got show_trait running again for MrnaAssay traits | Zachary Sloan |
| 2012-12-06 | Made many small changes to show_trait/data_set/search_results/trait to...remove use of the formData object and cursor
| Zachary Sloan |
| 2012-12-05 | Renamed webqtlTrait.py to trait.py...Renamed webqtlTrait class to GeneralTrait
Began process of removing fd from show_trait.py
Created DatasetGroup object in data_set.py (this may end up becoming
its own file later if it becomes big enough)
| Zachary Sloan |
| 2012-12-05 | Continued to make changes related to getting rid of cursor/db_conn...and using simple sqlalchemy
Got Pheno/MrnaAssay dataset searches working again
| Zachary Sloan |
| 2012-12-04 | Changed parser to allow quotes (i.e. name="rw williams")...Renamed webqtlTrait to GeneralTrait and began rewriting parts
Changed database code in many places to use simple sqlalchemy
| Zachary Sloan |
| 2012-12-04 | Began changing references to cursor/db_conn to use sqlalchemy...Wrote function for phenotype author searches
| Zachary Sloan |
| 2012-11-30 | Added example of escaping strings now that trasitioning to simple SQLAlchemy | Zachary Sloan |
| 2012-11-30 | Started switching to using basic sqlalchemy to handle db connection/queries...Began fixing bugs related to this fix, still in progress
| Zachary Sloan |
| 2012-11-29 | Changed a number of variables (riset to group, db to dataset)...Put most of the code for cisLRS and transLRS searches into the class
CisTransLrsSearch (might change this name to something else later)
Simplified escape code for searches in do_search.py
Got search_results working again after some changes
| Zachary Sloan |
