diff options
| author | Zachary Sloan | 2013-08-14 17:25:52 -0500 |
|---|---|---|
| committer | Zachary Sloan | 2013-08-14 17:25:52 -0500 |
| commit | 26b1883a8fe4053b59833178f44e047157f2fc9c (patch) | |
| tree | d2359e5952f6062d75ba1f43f1804a7b6df284c9 | |
| parent | eea1c38a9851f31011787b27c14365211a06ea51 (diff) | |
| parent | 6379959af53b2ec595b85ccdc099c6f14adf0381 (diff) | |
| download | genenetwork2-26b1883a8fe4053b59833178f44e047157f2fc9c.tar.gz | |
Merge branch 'master' of https://github.com/zsloan/genenetwork
78 files changed, 10220 insertions, 691 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt index bad21226..6329586f 100644 --- a/misc/gn_installation_notes.txt +++ b/misc/gn_installation_notes.txt @@ -1,6 +1,37 @@ +UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration + +Enable UFW: +sudo ufw enable +Check status of UFW: +sudo ufw status verbose + +Limit ssh: +sudo ufw limit ssh + +Enable http, https: +sudo ufw allow http +sudo ufw allow https + +=========================================== + +http://evilrouters.net/2011/02/18/using-etckeeper-with-git-on-ubuntu/ + +Install etckeeper: +sudo apt-get install etckeeper + +Edit /etc/etckeeper/etckeeper.conf to comment out VCS="bzr" and comment in VCS="git" + +Initialize repository: +sudo etckeeper init + +Do initial commit: +sudo etckeeper commit "Initial commit." + +=========================================== + Get git: -sudo apt-get install git-core +sudo apt-get install git =========================================== @@ -16,9 +47,10 @@ git pull origin flask(or whatever the branch is) Search for package with a specified file that can be installed with apt-get apt-file search _______ -Install from requirements.txt: -pip install -r gene/wqflask/requirements.txt -t ve27 +============================================ +Create trash directory: +mkdir ~/.trash ============================================ @@ -29,19 +61,6 @@ dpkg -l | less =========================================== -Using Yolk - -Install Yolk: -pip install yolk - -Check packages installed in this virtual environment: -yolk -l - -Checks packages that have updates available: -yolk -U - -=========================================== - Installing virtualenv: sudo pip install virtualenv @@ -53,20 +72,31 @@ source ~/ve27/bin/activate =========================================== -Installing yaml +Install libmysqlclient-dev (Mysql-Python dependency) +sudo apt-get install libmysqlclient-dev -Install libyaml-dev: -sudo apt-get install libyaml-dev +Install python-dev (numpy dependency) +sudo apt-get install python-dev -Install yaml: -pip install pyyaml +Install scipy dependencies: +sudo apt-get install libatlas-base-dev gfortran g++ =========================================== -Install MySQL Client +Install pip: +sudo apt-get install python-pip -To fix error "mysql_config not found" while installing packages with pip: -sudo apt-get install libmysqlclient-dev +REMEMBER TO SOURCE VE BEFORE INSTALLING + +Comment out in requirements.txt: +Reaper +numarray + +Before installing from requirements.txt, install numpy separately: +pip install numpy==1.7.0 (or whatever version we're using) + +Install from requirements.txt (after activating virtualenv): +pip install -r gene/misc/requirements.txt =========================================== @@ -75,10 +105,7 @@ Installing QTL Reaper wget http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb mv -v qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb qtlreaper-1.1.1.tar.gz tar xvf qtlreaper-1.1.1.tar.gz (to unzip) -python setup.py build -sudo mkdir /home/zas1024/ve27/include/python2.7/Reaper -sudo chown /home/zas1024/ve27/include/python2.7/Reaper (or whereever the directory is; the problem -involved the fact that doing "sudo python setup.py install" doesn't install within the virtualenv) +mkdir /home/zas1024/ve27/include/python2.7/Reaper python setup.py install =========================================== @@ -92,6 +119,153 @@ sudo python setup.py install =========================================== +Installing nginx + +sudo -s +nginx=stable # use nginx=development for latest development version +echo "deb http://ppa.launchpad.net/nginx/$nginx/ubuntu lucid main" > /etc/apt/sources.list.d/nginx-$nginx-lucid.list +apt-key adv --keyserver keyserver.ubuntu.com --recv-keys C300EE8C +apt-get update +apt-get install nginx + +Create configuration file in ~/gene/wqflask/other_config/nginx_conf/ (modeled off of the others) +Create symbolic link to config file in /etc/nginx/sites-enabled/: +ln -s dir_to_link_to linking_dir + +Run nginx: +sudo /usr/sbin/nginx + +============================================ + +Copy over zach_settings.py to /home/zas1024 directory (or whatever is home directory) + +export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located) + +============================================ + +Install MySQL Server + +sudo apt-get install mysql-server + +mkdir /mnt/big +fdisk /dev/sdb +m: for help +n: new partion +... +w: write to table and exit + +Start MySQL server: +service mysql start + +Stop MySQL server: +service mysql stop + +Change root password: +mysql> UPDATE mysql.user SET Password=PASSWORD('your password') WHERE User='root'; + +Setup accounts in MySQL (first need to delete anonymous/non-root accounts): +#; use mysql; +#; select * from user; +#; delete from user where Host!="localhost"; +#; delete from user where User!="root"; +#; update user set Password = Password('yourpassword') where User='root'; +#; GRANT ALL ON *.* TO 'yourusername'@'%' IDENTIFIED BY 'yourpassword'; +#; select * from user; + +Use Percona to optimise my.cfg file: +https://tools.percona.com/wizard + +To check # CPUs: +grep -c processor /proc/cpuinfo + +To check memory, can use htop + +============================================ + +Check RSA key: +ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key + +03:2c:d7:01:01:f0:31:3a:c8:df:e4:98:62:2c:59:d2 root@penguin (RSA) + +============================================ + +Installing redis server + +In the dls directory: +$ wget http://redis.googlecode.com/files/redis-2.6.14.tar.gz +$ tar xzf redis-2.6.14.tar.gz +$ cd redis-2.6.14 +$ make + +Run redis (from inside redis-2.6.14 directory): +src/redis-server + +For the rest of the installation instructions, refer to: +http://redis.io/topics/quickstart + +To continue installation (from the README): + +In order to install Redis binaries into /usr/local/bin just use: + + % make install + +Make install will just install binaries in your system, but will not configure +init scripts and configuration files in the appropriate place. This is not +needed if you want just to play a bit with Redis, but if you are installing +it the proper way for a production system, we have a script doing this +for Ubuntu and Debian systems: + + % cd utils + % ./install_server + +The script will ask you a few questions and will setup everything you need +to run Redis properly as a background daemon that will start again on +system reboots. + +In the redis config file (/etc/redis/6379.conf) uncomment the following line: +bind 127.0.0.1 + +This is so only the local computer has access + +============================================ + +Check RSA key: +ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key + +03:2c:d7:01:01:f0:31:3a:c8:df:e4:98:62:2c:59:d2 root@penguin (RSA) + +============================================ + +Using Yolk + +Install Yolk: +pip install yolk + +Check packages installed in this virtual environment: +yolk -l + +Checks packages that have updates available: +yolk -U + +=========================================== + +Installing yaml + +Install libyaml-dev: +sudo apt-get install libyaml-dev + +Install yaml: +pip install pyyaml + +=========================================== + +Install MySQL Client + +To fix error "mysql_config not found" while installing packages with pip: +sudo apt-get install libmysqlclient-dev + +=========================================== + Installing R sudo apt-get install r-base-dev @@ -132,7 +306,7 @@ Start up virtual environment: source ~/ve27/bin/activate To set WQFLASK_SETTINGS environment variable: -export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located) +export WQFLASK_SETTINGS=~/zach_settings.py (or wherever file is located) To change screen environment variable (if man not working or to get color, for example): export TERM=screen @@ -146,4 +320,9 @@ Run web server: Run server: python runserver.py +=========================================== + +To do full upgrade (as opposed to apt-get upgrade) +sudo aptitude full-upgrade + ===========================================
\ No newline at end of file diff --git a/misc/notes.txt b/misc/notes.txt index 621d95d3..ede8176b 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -1,5 +1,3 @@ -fubar - Clone code from git repository: git clone http://github.com/zsloan/genenetwork.git gene @@ -10,8 +8,7 @@ Add all files in current directory branch to be staged to be committed git add -A Git push to my github repository -git push https://github.com/zsloan/genenetwork.git flask - +git push https://github.com/zsloan/genenetwork.git master Get the default path being used when a command is typed: which _______ @@ -95,6 +92,15 @@ python runserver.py =========================================== +UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration + +Enable UFW: +sudo ufw enable +Check status of UFW: +sudo ufw status verbose + +=========================================== + Update user password: use mysql; UPDATE user SET password=PASSWORD('whatever') WHERE user='webqtl'; @@ -120,7 +126,7 @@ pylint --help Start screen session: -If "no option -R": +If "no option -R" or running for first time: byobu-select-backend 2. screen @@ -239,6 +245,11 @@ To iterate through dictionary items: for X, Y in MyDictionary.items(): =========================================== +Change import path from command line +export PYTHONPATH=~/gene/wqflask (or whatever) + +=========================================== + Create symbolic link: ln -s dir_to_link_to linking_dir @@ -258,7 +269,26 @@ grep -ir (search string) (directory) =========================================== +Change owner/group: + +chown zas1024 somefile (change owner of somefile to zas1024) +chown zas1024: somefile (change owner and group of somefile to zas1024) +sudo chown root: somefile (change owner/group of somefile to root) + +Change permissions: + +chmod g-wr (remove write/read privileges for group) +chmod g+w (add write privileges for group) +chmod u+rwx (add read, write, and execute privileges for user) +etc. + +=========================================== + MySQL Things - Create fulltext (MATCH AGAINST syntax) index: CREATE FULLTEXT INDEX __________ ON Table (Column); + +If <4 character searches not working: +Add ft_min_word_len = 2 (to make te minimum characters 2) to config file +Rebuild relevant tables with fulltext indexes with "REPAIR TABLE _______ QUICK" diff --git a/misc/requirements.txt b/misc/requirements.txt new file mode 100644 index 00000000..ec02a2c2 --- /dev/null +++ b/misc/requirements.txt @@ -0,0 +1,34 @@ +BeautifulSoup==3.2.1 +Flask==0.9 +Flask-Login==0.1.3 +Flask-Mail==0.7.6 +Flask-Principal==0.3.4 +Flask-SQLAlchemy==0.16 +Flask-Security==1.6.0 +Flask-WTF==0.8.3 +Jinja2==2.6 +MySQL-python==1.2.4 +PyYAML==3.10 +#Reaper==1.0 +Reindent==0.1.1 +SQLAlchemy==0.8.0 +WTForms==1.0.3 +Werkzeug==0.8.3 +apache-libcloud==0.12.3 +argparse==1.2.1 +blinker==1.2 +itsdangerous==0.17 +logging-tree==1.2 +logilab-astng==0.24.3 +logilab-common==0.59.1 +#numarray==1.5.2 +numpy==1.7.0 +passlib==1.6.1 +pp==1.6.3 +pylint==0.27.0 +redis==2.7.2 +requests==1.1.0 +scipy==0.11.0 +simplejson==3.0.7 +wsgiref==0.1.2 +yolk==0.4.3 diff --git a/web/genotypes/B6D2F2-PSU.geno b/web/genotypes/B6D2F2-PSU.geno index 2c8876a0..a0c1728f 100755 --- a/web/genotypes/B6D2F2-PSU.geno +++ b/web/genotypes/B6D2F2-PSU.geno @@ -1,5 +1,5 @@ -"#This is B6D2F2-PSU genotype file, it should be tab-delimited"
-"#the first three/four columns should be ""Chr, Locus, cM, [Mb]"" (case sensitive)"
+#This is B6D2F2-PSU genotype file, it should be tab-delimited
+#the first three/four columns should be ""Chr, Locus, cM, [Mb]"" (case sensitive)
#please save as Unix format text file.
#comment line always start with a '#'
#type riset or intercross
@@ -8,9 +8,9 @@ #abbreviation of maternal or paternal parents
@mat:B
@pat:D
-"#heterozygous , optional, default is ""H"""
+#heterozygous , optional, default is ""H""
@het:H
-"#Unknown , optional, default is ""U"""
+#Unknown , optional, default is ""U""
@unk:U
Chr Locus cM Mb PSU0001 PSU0004 PSU0007 PSU0022 PSU0024 PSU0042 PSU0044 PSU0045 PSU0046 PSU0048 PSU0049 PSU0050 PSU0052 PSU0053 PSU0054 PSU0055 PSU0056 PSU0057 PSU0058 PSU0059 PSU0060 PSU0061 PSU0062 PSU0063 PSU0066 PSU0067 PSU0068 PSU0069 PSU0070 PSU0071 PSU0072 PSU0074 PSU0077 PSU0079 PSU0080 PSU0082 PSU0083 PSU0084 PSU0085 PSU0086 PSU0087 PSU0089 PSU0090 PSU0091 PSU0092 PSU0093 PSU0094 PSU0095 PSU0096 PSU0097 PSU0098 PSU0099 PSU0100 PSU0102 PSU0103 PSU0104 PSU0107 PSU0108 PSU0109 PSU0110 PSU0112 PSU0113 PSU0114 PSU0116 PSU0117 PSU0118 PSU0119 PSU0122 PSU0124 PSU0126 PSU0128 PSU0130 PSU0131 PSU0132 PSU0133 PSU0134 PSU0135 PSU0136 PSU0137 PSU0138 PSU0139 PSU0140 PSU0141 PSU0142 PSU0143 PSU0146 PSU0147 PSU0148 PSU0152 PSU0153 PSU0155 PSU0158 PSU0159 PSU0163 PSU0164 PSU0165 PSU0166 PSU0167 PSU0168 PSU0169 PSU0170 PSU0172 PSU0173 PSU0174 PSU0175 PSU0177 PSU0178 PSU0179 PSU0180 PSU0182 PSU0183 PSU0187 PSU0188 PSU0190 PSU0191 PSU0193 PSU0194 PSU0196 PSU0197 PSU0198 PSU0199 PSU0205 PSU0206 PSU0207 PSU0208 PSU0209 PSU0210 PSU0211 PSU0212 PSU0213 PSU0214 PSU0216 PSU0218 PSU0219 PSU0220 PSU0222 PSU0223 PSU0225 PSU0226 PSU0227 PSU0229 PSU0230 PSU0231 PSU0234 PSU0235 PSU0236 PSU0238 PSU0239 PSU0241 PSU0242 PSU0243 PSU0244 PSU0246 PSU0247 PSU0248 PSU0250 PSU0251 PSU0255 PSU0257 PSU0258 PSU0260 PSU0261 PSU0262 PSU0263 PSU0264 PSU0271 PSU0272 PSU0273 PSU0274 PSU0275 PSU0276 PSU0278 PSU0280 PSU0282 PSU0283 PSU0285 PSU0286 PSU0287 PSU0288 PSU0289 PSU0291 PSU0292 PSU0293 PSU0295 PSU0296 PSU0299 PSU0300 PSU0301 PSU0302 PSU0304 PSU0305 PSU0306 PSU0308 PSU0309 PSU0310 PSU0311 PSU0312 PSU0313 PSU0314 PSU0315 PSU0316 PSU0317 PSU0318 PSU0319 PSU0320 PSU0321 PSU0323 PSU0325 PSU0326 PSU0327 PSU0328 PSU0329 PSU0330 PSU0331 PSU0334 PSU0336 PSU0337 PSU0338 PSU0339 PSU0340 PSU0341 PSU0342 PSU0343 PSU0344 PSU0346 PSU0349 PSU0351 PSU0352 PSU0353 PSU0355 PSU0356 PSU0357 PSU0358 PSU0359 PSU0360 PSU0361 PSU0362 PSU0363 PSU0366 PSU0367 PSU0369 PSU0370 PSU0371 PSU0372 PSU0373 PSU0374 PSU0375 PSU0376 PSU0378 PSU0379 PSU0381 PSU0382 PSU0383 PSU0384 PSU0385 PSU0388 PSU0390 PSU0391 PSU0392 PSU0393 PSU0395 PSU0397 PSU0399 PSU0400 PSU0401 PSU0403 PSU0405 PSU0406 PSU0408 PSU0410 PSU0412 PSU0413 PSU0414 PSU0416 PSU0417 PSU0418 PSU0420 PSU0421 PSU0423 PSU0425 PSU0426 PSU0430 PSU0431 PSU0434 PSU0435 PSU0437 PSU0438 PSU0441 PSU0445 PSU0449 PSU0450 PSU0451 PSU0452 PSU0454 PSU0455 PSU0458 PSU0461 PSU0462 PSU0464 PSU0466 PSU0468 PSU0470 PSU0472 PSU0478 PSU0479 PSU0480 PSU0482 PSU0483 PSU0487 PSU0488 PSU0490 PSU0492 PSU0493 PSU0494 PSU0495 PSU0499 PSU0501 PSU0502 PSU0503 PSU0504 PSU0505 PSU0506 PSU0508 PSU0511 PSU0513 PSU0514 PSU0517 PSU0519 PSU0521 PSU0522 PSU0523 PSU0524 PSU0527 PSU0529 PSU0531 PSU0533 PSU0535 PSU0536 PSU0537 PSU0540 PSU0542 PSU0543 PSU0545 PSU0546 PSU0549 PSU0551 PSU0553 PSU0554 PSU0557 PSU0561 PSU0562 PSU0565 PSU0566 PSU0568 PSU0569 PSU0570 PSU0571 PSU0575 PSU0576 PSU0586 PSU0593 PSU0597 PSU0598 PSU0603 PSU0604 PSU0606 PSU0609 PSU0610 PSU0612 PSU0616 PSU0617 PSU0620 PSU0621 PSU0623 PSU0624 PSU0626 PSU0629 PSU0630 PSU0631 PSU0632 PSU0634 PSU0637 PSU0639 PSU0641 PSU0642 PSU0643 PSU0645 PSU0646 PSU0647 PSU0648 PSU0649 PSU0650 PSU0651 PSU0652 PSU0654 PSU0655 PSU0659 PSU0661 PSU0662 PSU0663 PSU0665 PSU0667 PSU0668 PSU0669 PSU0671 PSU0672 PSU0673 PSU0674 PSU0675 PSU0677 PSU0680 PSU0682 PSU0683 PSU0684 PSU0686 PSU0687 PSU0689 PSU0690 PSU0691 PSU0696 PSU0697 PSU0699 PSU0701 PSU0702 PSU0704 PSU0705 PSU0706 PSU0709 PSU0710 PSU0712 PSU0714 PSU0716 PSU0717 PSU0718 PSU0719 PSU0720 PSU0721 PSU0724 PSU0725 PSU0727 PSU0728 PSU0729 PSU0730 PSU0731 PSU0733 PSU0734 PSU0736 PSU0737 PSU0738 PSU0741 PSU0742 PSU0743 PSU0744 PSU0745 PSU0749 PSU0750 PSU0751 PSU0753 PSU0756 PSU0757 PSU0758 PSU0759 PSU0760 PSU0763 PSU0764 PSU0765 PSU0766 PSU0767 PSU0769 PSU0770 PSU0771 PSU0772 PSU0773 PSU0776 PSU0780 PSU0781 PSU0782 PSU0783 PSU0784 PSU0787 PSU0788 PSU0789 PSU0790 PSU0791 PSU0792 PSU0794 PSU0798 PSU0799 PSU0804 PSU0806 PSU0807 PSU0808 PSU0810 PSU0811 PSU0813 PSU0814 PSU0815 PSU0816 PSU0818 PSU0821 PSU0822 PSU0824 PSU0825 PSU0828 PSU0830 PSU0831 PSU0833 PSU0834 PSU0837 PSU0840 PSU0843 PSU0844 PSU0847 PSU0849 PSU0851 PSU0853 PSU0855 PSU0856 PSU0858 PSU0860 PSU0862 PSU0863 PSU0864 PSU1060 PSU1095 PSU1372 PSU1373 PSU1374 PSU1381 PSU1392 PSU1399 PSU1414 PSU1421 PSU1422 PSU1430 PSU1432 PSU1470 PSU1473 PSU1490 PSU1526 PSU1540 PSU1549 PSU1553 PSU1556 PSU1561 PSU1564 PSU1576 PSU1591 PSU1609 PSU1613 PSU1625 PSU1626 PSU1630 PSU1638 PSU1639
1 rs13475697 0.01 3.385827 U H H H H B D B H B H H D H H H H H H H H B H H H H D H D B B D H H B H D H B H H H B B B D B H H D H D B H H H B H B B B B B B H H B D D H H D D H D D H H B D D B B D B B D B B H B B H D B H H H D H D B D B D H H D B D D H H H D B H B H D H D H D B D D D H H D H B B H H B H B H B D H D D D D H D H H H D B D H D H H D B D B B B D H H B D H H H H D H D H D H D H D D B H D B H D H D D H H H H H D D B H H D B H H H H D H H H D H B D D D H H H H B D H H H D H B B B D B H H H H B H H B H B D D D D H D H D H D B H H H B B B B B H U B H H B D H D H D H H B B B H H H H H D B H H H B H D H D B B D B H H B D H H H B B H H H D H B H B D H B H D B H B H H H B H B H D D B H D B H H D H H D D H H H H B B H D H D H H D D B D D H H D D H H B H H H H B H H D H D H B H D D H H D D B H H H H H H D B D H H B H B H H H H H D H B B D H H D D D B B H H B H H B H B B H B D H H H B B H D B B B D D B D H H B H D D H H H B H H D B D H B H D D B H H D H D H B H H H H H D H B D B H H H D H H B H H B D H D D B H D H D B H H H D H D H D D H B B D B H D B H D H H B B H H H H B H D H H B D B D H D D H B D H B H H H D D H D H
diff --git a/web/genotypes/HSNIH.geno.gz b/web/genotypes/HSNIH.geno.gz Binary files differnew file mode 100644 index 00000000..96584768 --- /dev/null +++ b/web/genotypes/HSNIH.geno.gz diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 07fe9cd9..091433a6 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -16,8 +16,6 @@ # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # -#we -# # This module is used by GeneNetwork project (www.genenetwork.org) from __future__ import absolute_import, print_function, division @@ -27,8 +25,13 @@ import string import collections import json +import gzip +import cPickle as pickle import itertools +from redis import Redis +Redis = Redis() + from flask import Flask, g import reaper @@ -40,35 +43,101 @@ from utility import webqtlUtil from utility.benchmark import Bench from wqflask.my_pylmm.pyLMM import chunks +from maintenance import get_group_samplelists + from MySQLdb import escape_string as escape from pprint import pformat as pf # Used by create_database to instantiate objects +# Each subclass will add to this DS_NAME_MAP = {} -def create_dataset(dataset_name): - #print("dataset_name:", dataset_name) +def create_dataset(dataset_name, dataset_type = None): + if not dataset_type: + dataset_type = Dataset_Getter(dataset_name) + #dataset_type = get_dataset_type_from_json(dataset_name) - query = """ - SELECT DBType.Name - FROM DBList, DBType - WHERE DBList.Name = '{}' and - DBType.Id = DBList.DBTypeId - """.format(escape(dataset_name)) - #print("query is: ", pf(query)) - dataset_type = g.db.execute(query).fetchone().Name + print("dataset_type is:", dataset_type) + #query = """ + # SELECT DBType.Name + # FROM DBList, DBType + # WHERE DBList.Name = '{}' and + # DBType.Id = DBList.DBTypeId + # """.format(escape(dataset_name)) + #dataset_type = g.db.execute(query).fetchone().Name - #dataset_type = cursor.fetchone()[0] - #print("[blubber] dataset_type:", pf(dataset_type)) dataset_ob = DS_NAME_MAP[dataset_type] - #dataset_class = getattr(data_set, dataset_ob) - #print("dataset_ob:", dataset_ob) - #print("DS_NAME_MAP:", pf(DS_NAME_MAP)) - dataset_class = globals()[dataset_ob] return dataset_class(dataset_name) + +#def get_dataset_type_from_json(dataset_name): + +class Dataset_Types(object): + + def __init__(self): + self.datasets = {} + file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" + with open(file_name, 'r') as fh: + data = json.load(fh) + + print("*" * 70) + for species in data['datasets']: + for group in data['datasets'][species]: + for dataset_type in data['datasets'][species][group]: + for dataset in data['datasets'][species][group][dataset_type]: + print("dataset is:", dataset) + + short_dataset_name = dataset[0] + if dataset_type == "Phenotypes": + new_type = "Publish" + elif dataset_type == "Genotypes": + new_type = "Geno" + else: + new_type = "ProbeSet" + self.datasets[short_dataset_name] = new_type + + def __call__(self, name): + return self.datasets[name] + +# Do the intensive work at startup one time only +Dataset_Getter = Dataset_Types() + +# +#print("Running at startup:", get_dataset_type_from_json("HBTRC-MLPFC_0611")) + + +def create_datasets_list(): + key = "all_datasets" + result = Redis.get(key) + + if result: + print("Cache hit!!!") + datasets = pickle.loads(result) + + else: + datasets = list() + with Bench("Creating DataSets object"): + type_dict = {'Publish': 'PublishFreeze', + 'ProbeSet': 'ProbeSetFreeze', + 'Geno': 'GenoFreeze'} + + for dataset_type in type_dict: + query = "SELECT Name FROM {}".format(type_dict[dataset_type]) + for result in g.db.execute(query).fetchall(): + #The query at the beginning of this function isn't necessary here, but still would + #rather just reuse it + #print("type: {}\tname: {}".format(dataset_type, result.Name)) + dataset = create_dataset(result.Name, dataset_type) + datasets.append(dataset) + + Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*60) + + return datasets + + def create_in_clause(items): """Create an in clause for mysql""" in_clause = ', '.join("'{}'".format(x) for x in mescape(*items)) @@ -99,7 +168,8 @@ class Markers(object): for marker, p_value in itertools.izip(self.markers, p_values): marker['p_value'] = p_value - print("p_value is:", marker['p_value']) + if math.isnan(marker['p_value']): + print("p_value is:", marker['p_value']) marker['lod_score'] = -math.log10(marker['p_value']) #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 @@ -167,8 +237,8 @@ class DatasetGroup(object): self.incparentsf1 = False self.allsamples = None - - + + def get_markers(self): #print("self.species is:", self.species) if self.species == "human": @@ -177,7 +247,7 @@ class DatasetGroup(object): marker_class = Markers self.markers = marker_class(self.name) - + def get_f1_parent_strains(self): try: @@ -190,7 +260,29 @@ class DatasetGroup(object): self.f1list = [f1, f12] if maternal and paternal: self.parlist = [maternal, paternal] - + + def get_samplelist(self): + key = "samplelist:v4:" + self.name + print("key is:", key) + with Bench("Loading cache"): + result = Redis.get(key) + + if result: + print("Sample List Cache hit!!!") + print("Before unjsonifying {}: {}".format(type(result), result)) + self.samplelist = json.loads(result) + print(" type: ", type(self.samplelist)) + print(" self.samplelist: ", self.samplelist) + else: + print("Cache not hit") + try: + self.samplelist = get_group_samplelists.get_samplelist(self.name + ".geno") + except IOError: + self.samplelist = None + print("after get_samplelist") + Redis.set(key, json.dumps(self.samplelist)) + Redis.expire(key, 60*5) + def read_genotype_file(self): '''Read genotype from .geno file instead of database''' #if self.group == 'BXD300': @@ -205,7 +297,18 @@ class DatasetGroup(object): # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) - genotype_1.read(full_filename) + if os.path.isfile(full_filename): + print("Reading file: ", full_filename) + genotype_1.read(full_filename) + print("File read") + else: + try: + full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno')) + #print("Reading file") + genotype_1.read(full_filename) + #print("File read") + except IOError: + print("File doesn't exist!") if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) @@ -222,6 +325,27 @@ class DatasetGroup(object): self.samplelist = list(genotype.prgy) +#class DataSets(object): +# """Builds a list of DataSets""" +# +# def __init__(self): +# self.datasets = list() +# + + + #query = """SELECT Name FROM ProbeSetFreeze + # UNION + # SELECT Name From PublishFreeze + # UNION + # SELECT Name From GenoFreeze""" + # + #for result in g.db.execute(query).fetchall(): + # dataset = DataSet(result.Name) + # self.datasets.append(dataset) + +#ds = DataSets() +#print("[orange] ds:", ds.datasets) + class DataSet(object): """ DataSet class defines a dataset in webqtl, can be either Microarray, @@ -234,6 +358,8 @@ class DataSet(object): assert name, "Need a name" self.name = name self.id = None + self.shortname = None + self.fullname = None self.type = None self.setup() @@ -243,7 +369,7 @@ class DataSet(object): self.retrieve_other_names() self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype - self.group.read_genotype_file() + self.group.get_samplelist() self.species = species.TheSpecies(self) @@ -277,7 +403,6 @@ class DataSet(object): # return self._group - def retrieve_other_names(self): """ If the data set name parameter is not found in the 'Name' field of the data set table, @@ -293,7 +418,7 @@ class DataSet(object): self.name, self.name, self.name)) - #print("query_args are:", query_args) + print("query_args are:", query_args) #print(""" # SELECT Id, Name, FullName, ShortName @@ -301,22 +426,109 @@ class DataSet(object): # WHERE public > %s AND # (Name = '%s' OR FullName = '%s' OR ShortName = '%s') # """ % (query_args)) + + try: + self.id, self.name, self.fullname, self.shortname = g.db.execute(""" + SELECT Id, Name, FullName, ShortName + FROM %s + WHERE public > %s AND + (Name = '%s' OR FullName = '%s' OR ShortName = '%s') + """ % (query_args)).fetchone() + except TypeError: + print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) + pass + + def get_trait_data(self): + self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list + query = """ + SELECT Strain.Name, Strain.Id FROM Strain, Species + WHERE Strain.Name IN {} + and Strain.SpeciesId=Species.Id + and Species.name = '{}' + """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) + results = dict(g.db.execute(query).fetchall()) + sample_ids = [results[item] for item in self.samplelist] + + # MySQL limits the number of tables that can be used in a join to 61, + # so we break the sample ids into smaller chunks + # Postgres doesn't have that limit, so we can get rid of this after we transition + chunk_size = 50 + number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) + trait_sample_data = [] + for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): - self.id, self.name, self.fullname, self.shortname = g.db.execute(""" - SELECT Id, Name, FullName, ShortName - FROM %s - WHERE public > %s AND - (Name = '%s' OR FullName = '%s' OR ShortName = '%s') - """ % (query_args)).fetchone() + #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId + #tempTable = None + #if GeneId and db.type == "ProbeSet": + # if method == "3": + # tempTable = self.getTempLiteratureTable(species=species, + # input_species_geneid=GeneId, + # returnNumber=returnNumber) + # + # if method == "4" or method == "5": + # tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol, + # TissueProbeSetFreezeId=tissueProbeSetFreezeId, + # method=method, + # returnNumber=returnNumber) + + if self.type == "Publish": + dataset_type = "Phenotype" + else: + dataset_type = self.type + temp = ['T%s.value' % item for item in sample_ids_step] + if self.type == "Publish": + query = "SELECT {}XRef.Id,".format(escape(self.type)) + else: + query = "SELECT {}.Name,".format(escape(dataset_type)) + data_start_pos = 1 + query += string.join(temp, ', ') + query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type, + self.type, + self.type)) + + for item in sample_ids_step: + query += """ + left join {}Data as T{} on T{}.Id = {}XRef.DataId + and T{}.StrainId={}\n + """.format(*mescape(self.type, item, item, self.type, item, item)) + + if self.type == "Publish": + query += """ + WHERE {}XRef.PublicationId = {}Freeze.Id + and {}Freeze.Name = '{}' + and {}.Id = {}XRef.{}Id + order by {}.Id + """.format(*mescape(self.type, self.type, self.type, self.type, + self.name, dataset_type, self.type, self.type, dataset_type)) + else: + query += """ + WHERE {}XRef.{}FreezeId = {}Freeze.Id + and {}Freeze.Name = '{}' + and {}.Id = {}XRef.{}Id + order by {}.Id + """.format(*mescape(self.type, self.type, self.type, self.type, + self.name, dataset_type, self.type, self.type, dataset_type)) + results = g.db.execute(query).fetchall() + trait_sample_data.append(results) - #self.cursor.execute(query) - #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone() + trait_count = len(trait_sample_data[0]) + self.trait_data = collections.defaultdict(list) + # put all of the separate data together into a dictionary where the keys are + # trait names and values are lists of sample values + for trait_counter in range(trait_count): + trait_name = trait_sample_data[0][trait_counter][0] + for chunk_counter in range(int(number_chunks)): + self.trait_data[trait_name] += ( + trait_sample_data[chunk_counter][trait_counter][data_start_pos:]) class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' def setup(self): + + print("IS A PHENOTYPEDATASET") + # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', @@ -387,14 +599,24 @@ class PhenotypeDataSet(DataSet): def get_trait_info(self, trait_list, species = ''): for this_trait in trait_list: if not this_trait.haveinfo: - this_trait.retrieveInfo(QTL=1) + this_trait.retrieve_info(get_qtl_info=True) description = this_trait.post_publication_description + + #If the dataset is confidential and the user has access to confidential + #phenotype traits, then display the pre-publication description instead + #of the post-publication description if this_trait.confidential: continue # for now - if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): + + if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( + privilege=self.privilege, + userName=self.userName, + authorized_users=this_trait.authorized_users): + description = this_trait.pre_publication_description - this_trait.description_display = unicode(description, "utf8") + + this_trait.description_display = description if not this_trait.year.isdigit(): this_trait.pubmed_text = "N/A" @@ -632,73 +854,73 @@ class MrnaAssayDataSet(DataSet): #print("After retrieve_sample_data") return trait_data - def get_trait_data(self): - self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list - query = """ - SELECT Strain.Name, Strain.Id FROM Strain, Species - WHERE Strain.Name IN {} - and Strain.SpeciesId=Species.Id - and Species.name = '{}' - """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) - results = dict(g.db.execute(query).fetchall()) - sample_ids = [results[item] for item in self.samplelist] - - # MySQL limits the number of tables that can be used in a join to 61, - # so we break the sample ids into smaller chunks - # Postgres doesn't have that limit, so we can get rid of this after we transition - chunk_size = 50 - number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) - trait_sample_data = [] - for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): - - #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId - #tempTable = None - #if GeneId and db.type == "ProbeSet": - # if method == "3": - # tempTable = self.getTempLiteratureTable(species=species, - # input_species_geneid=GeneId, - # returnNumber=returnNumber) - # - # if method == "4" or method == "5": - # tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol, - # TissueProbeSetFreezeId=tissueProbeSetFreezeId, - # method=method, - # returnNumber=returnNumber) - - temp = ['T%s.value' % item for item in sample_ids_step] - query = "SELECT {}.Name,".format(escape(self.type)) - data_start_pos = 1 - query += string.join(temp, ', ') - query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type, - self.type, - self.type)) - - for item in sample_ids_step: - query += """ - left join {}Data as T{} on T{}.Id = {}XRef.DataId - and T{}.StrainId={}\n - """.format(*mescape(self.type, item, item, self.type, item, item)) - - query += """ - WHERE {}XRef.{}FreezeId = {}Freeze.Id - and {}Freeze.Name = '{}' - and {}.Id = {}XRef.{}Id - order by {}.Id - """.format(*mescape(self.type, self.type, self.type, self.type, - self.name, self.type, self.type, self.type, self.type)) - results = g.db.execute(query).fetchall() - trait_sample_data.append(results) - - trait_count = len(trait_sample_data[0]) - self.trait_data = collections.defaultdict(list) - - # put all of the separate data together into a dictionary where the keys are - # trait names and values are lists of sample values - for trait_counter in range(trait_count): - trait_name = trait_sample_data[0][trait_counter][0] - for chunk_counter in range(int(number_chunks)): - self.trait_data[trait_name] += ( - trait_sample_data[chunk_counter][trait_counter][data_start_pos:]) + #def get_trait_data(self): + # self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list + # query = """ + # SELECT Strain.Name, Strain.Id FROM Strain, Species + # WHERE Strain.Name IN {} + # and Strain.SpeciesId=Species.Id + # and Species.name = '{}' + # """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) + # results = dict(g.db.execute(query).fetchall()) + # sample_ids = [results[item] for item in self.samplelist] + # + # # MySQL limits the number of tables that can be used in a join to 61, + # # so we break the sample ids into smaller chunks + # # Postgres doesn't have that limit, so we can get rid of this after we transition + # chunk_size = 50 + # number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) + # trait_sample_data = [] + # for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): + # + # #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId + # #tempTable = None + # #if GeneId and db.type == "ProbeSet": + # # if method == "3": + # # tempTable = self.getTempLiteratureTable(species=species, + # # input_species_geneid=GeneId, + # # returnNumber=returnNumber) + # # + # # if method == "4" or method == "5": + # # tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol, + # # TissueProbeSetFreezeId=tissueProbeSetFreezeId, + # # method=method, + # # returnNumber=returnNumber) + # + # temp = ['T%s.value' % item for item in sample_ids_step] + # query = "SELECT {}.Name,".format(escape(self.type)) + # data_start_pos = 1 + # query += string.join(temp, ', ') + # query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type, + # self.type, + # self.type)) + # + # for item in sample_ids_step: + # query += """ + # left join {}Data as T{} on T{}.Id = {}XRef.DataId + # and T{}.StrainId={}\n + # """.format(*mescape(self.type, item, item, self.type, item, item)) + # + # query += """ + # WHERE {}XRef.{}FreezeId = {}Freeze.Id + # and {}Freeze.Name = '{}' + # and {}.Id = {}XRef.{}Id + # order by {}.Id + # """.format(*mescape(self.type, self.type, self.type, self.type, + # self.name, self.type, self.type, self.type, self.type)) + # results = g.db.execute(query).fetchall() + # trait_sample_data.append(results) + # + # trait_count = len(trait_sample_data[0]) + # self.trait_data = collections.defaultdict(list) + # + # # put all of the separate data together into a dictionary where the keys are + # # trait names and values are lists of sample values + # for trait_counter in range(trait_count): + # trait_name = trait_sample_data[0][trait_counter][0] + # for chunk_counter in range(int(number_chunks)): + # self.trait_data[trait_name] += ( + # trait_sample_data[chunk_counter][trait_counter][data_start_pos:]) def get_trait_info(self, trait_list=None, species=''): @@ -779,14 +1001,14 @@ class MrnaAssayDataSet(DataSet): #Max LRS and its Locus location if this_trait.lrs and this_trait.locus: - self.cursor.execute(""" + query = """ select Geno.Chr, Geno.Mb from Geno, Species - where Species.Name = '%s' and - Geno.Name = '%s' and + where Species.Name = '{}' and + Geno.Name = '{}' and Geno.SpeciesId = Species.Id - """ % (species, this_trait.locus)) - result = self.cursor.fetchone() - + """.format(species, this_trait.locus) + result = g.db.execute(query).fetchone() + if result: #if result[0] and result[1]: # lrs_chr = result[0] @@ -940,6 +1162,5 @@ def geno_mrna_confidentiality(ob): authorized_users) = result.fetchall()[0] if confidential: - # Allow confidential data later - NoConfindetialDataForYouTodaySorry + return True diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 191f4535..ebc2bfed 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -56,6 +56,7 @@ class Chromosomes(object): InbredSet.Name = %s Order by OrderId """, self.dataset.group.name).fetchall() + print("group: ", self.dataset.group.name) print("bike:", results) for item in results: @@ -68,9 +69,14 @@ class Chromosomes(object): def set_mb_graph_interval(self): """Empirical megabase interval""" + if self.chromosomes: + self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) + else: + self.mb_graph_interval = 1 + #if self.chromosomes: - assert self.chromosomes, "Have to add some code back in apparently to set it to 1" - self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) + #assert self.chromosomes, "Have to add some code back in apparently to set it to 1" + #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) #else: #self.mb_graph_interval = 1 diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index db76ddea..c893c887 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -319,8 +319,11 @@ class GeneralTrait(object): #XZ: assign SQL query result to trait attributes. for i, field in enumerate(self.dataset.display_fields): - print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i])) - setattr(self, field, trait_info[i]) + #print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i])) + holder = trait_info[i] + if isinstance(trait_info[i], basestring): + holder = unicode(trait_info[i], "utf8", "ignore") + setattr(self, field, holder) if self.dataset.type == 'Publish': self.confidential = 0 @@ -329,9 +332,9 @@ class GeneralTrait(object): self.homologeneid = None - print("self.geneid is:", self.geneid) - print(" type:", type(self.geneid)) - print("self.dataset.group.name is:", self.dataset.group.name) + #print("self.geneid is:", self.geneid) + #print(" type:", type(self.geneid)) + #print("self.dataset.group.name is:", self.dataset.group.name) if self.dataset.type == 'ProbeSet' and self.dataset.group and self.geneid: #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. #XZ: So I have to test if geneid is number before execute the query. @@ -600,4 +603,4 @@ class GeneralTrait(object): else: ZValue = 0.5*log((1.0+self.correlation)/(1.0-self.correlation)) ZValue = ZValue*sqrt(self.overlap-3) - self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue))) + self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))
\ No newline at end of file diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index a811c3cd..23d32233 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -1,4 +1,3 @@ -from webqtlConfigLocal import * #########################################' # Environment Variables - public ######################################### @@ -36,7 +35,7 @@ NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrie UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s" OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s" -UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s" +UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"; HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s" PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit" @@ -49,15 +48,17 @@ UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit" ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" + +GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'web/' -PYLMM_PATH = '/home/zas1024/' -SNP_PATH = '/mnt/xvdf1/snps/' +PYLMM_PATH = '/home/zas1024/plink/' +SNP_PATH = '/home/zas1024/snps/' IMGDIR = HTMLPATH +'image/' IMAGESPATH = HTMLPATH + 'images/' UPLOADPATH = IMAGESPATH + 'upload/' -TMPDIR = HTMLPATH + 'tmp/' +TMPDIR = '/tmp/' GENODIR = HTMLPATH + 'genotypes/' NEWGENODIR = HTMLPATH + 'new_genotypes/' GENO_ARCHIVE_DIR = GENODIR + 'archive/' diff --git a/wqflask/base/webqtlConfigLocal.py b/wqflask/base/webqtlConfigLocal.py deleted file mode 100755 index abaeff93..00000000 --- a/wqflask/base/webqtlConfigLocal.py +++ /dev/null @@ -1,20 +0,0 @@ -#########################################' -# Environment Variables - private -######################################### - -MYSQL_SERVER = 'gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com' -DB_NAME = 'db_webqtl' -DB_USER = 'webqtl' -DB_PASSWD = 'f2ZypIflRM' - -MYSQL_UPDSERVER = 'gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com' -DB_UPDNAME = 'db_webqtl' -DB_UPDUSER = 'webqtl' -DB_UPDPASSWD = 'f2ZypIflRM' - -GNROOT = '/home/zas1024/gene/' -ROOT_URL = 'http://50.16.251.170' -PythonPath = '/usr/bin/python' -PIDDLE_FONT_PATH = '/usr/lib/python2.4/site-packages/piddle/truetypefonts/' - -TEXTUI=1 # XZ: This is to protect GN production server. If set to 0, no text UI is allowed. diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py index 96f7f1a5..e638a9c0 100644 --- a/wqflask/cfg/default_settings.py +++ b/wqflask/cfg/default_settings.py @@ -13,3 +13,5 @@ SECURITY_REGISTERABLE = True SECURITY_RECOVERABLE = True SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org" + +SECURITY_POST_LOGIN_VIEW = "/thank_you" diff --git a/wqflask/maintenance/__init__.py b/wqflask/maintenance/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/maintenance/__init__.py diff --git a/wqflask/maintenance/browser_test.py b/wqflask/maintenance/browser_test.py new file mode 100644 index 00000000..ecf8e1ca --- /dev/null +++ b/wqflask/maintenance/browser_test.py @@ -0,0 +1,60 @@ +from __future__ import print_function, division, absolute_import + +from time import sleep + +import selenium +from selenium import webdriver +from selenium.common.exceptions import NoSuchElementException, ElementNotVisibleException +from selenium.webdriver.common.keys import Keys + +class Test(object): + def __init__(self): + self.browser = webdriver.Chrome('/home/gn2/gn2/webtests/chromedriver') + + def get(self, url): + self.browser.get(url) + sleep(5) + self.title() + + def click(self, xpath_selector): + el = self.browser.find_element_by_xpath(xpath_selector) + text = el.text.strip() or el.get_attribute("value").strip() + el.click() + print("clicked:", text) + sleep(2) + + def click_option(self, xpath_selector, option_text): + el = self.browser.find_element_by_xpath(xpath_selector) + for option in el.find_elements_by_tag_name('option'): + if option.text == option_text: + option.click() # select() in earlier versions of webdriver + break + sleep(2) + + def enter_text(self, xpath_selector, text): + el = self.browser.find_element_by_xpath(xpath_selector) + sleep(10) + el.send_keys(text) + sleep(5) + # Just in case things get mangled by JavaScript, etc. we print the text for testing + self.get_text(xpath_selector) + + def get_text(self, xpath_selector): + el = self.browser.find_element_by_xpath(xpath_selector) + text = el.text.strip() or el.get_attribute("value").strip() + print("text:", text) + + def switch_window(self): + self.browser.switch_to_window(self.browser.window_handles[-1]) + sleep(2) + self.title() + sleep(2) + + + def title(self): + print("title:", self.browser.title) + + +#if __name__ == '__main__': +# import doctest +# doctest.testmod()
\ No newline at end of file diff --git a/wqflask/maintenance/correlation_matrix_test.py b/wqflask/maintenance/correlation_matrix_test.py new file mode 100644 index 00000000..2983a76b --- /dev/null +++ b/wqflask/maintenance/correlation_matrix_test.py @@ -0,0 +1,117 @@ +""" + +Test Correlation matrix + +>>> test = Test() +>>> test.get("http://genenetwork.org/") +title: GeneNetwork + +Choose the type +>>> test.click_option('''//*[@id="tissue"]''', 'Hippocampus mRNA') + +Enter the Get Any +>>> test.enter_text('''//*[@id="tfor"]''', 'grin2b') +text: grin2b + +Search +>>> test.click('//*[@id="btsearch"]') + +Select the first 4 records +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[2]/td/input''') +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[3]/td/input''') +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[4]/td/input''') +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[5]/td/input''') + +>>> sleep(5) + +Add to collection page +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[1]/td/table/tbody/tr[1]/td[4]/a''') + +>>> sleep(5) + +A new window is created, so we switch to it +>>> test.switch_window() +title: BXD Trait Collection + +Select all records +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/table/tbody/tr/td/table/tbody/tr/td/table/tbody/tr/td/a/img''') + +Click Matrix +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/table/tbody/tr/td/table/tbody/tr[2]/td/table/tbody/tr/td[2]/a/img''') + +Another new window +>>> test.switch_window() +title: Correlation Matrix + +Sleep a bunch because this can take a while +>>> sleep(10) + +Ensure that the correlation between Trait3 (HC_M2_0606_P::1457003_at) and Trait4 (HC_M2_0606_P::1422223_at) is 0.608 +>>> test.get_text('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/blockquote/table/tbody/tr[5]/td[5]/a/font''') +text: 0.608 + +""" + +from __future__ import print_function, division, absolute_import + +from time import sleep + +import selenium +from selenium import webdriver +from selenium.common.exceptions import NoSuchElementException, ElementNotVisibleException +from selenium.webdriver.common.keys import Keys + +from browser_test import Test +# +#class Test(object): +# def __init__(self): +# self.browser = webdriver.Chrome('/home/gn2/gn2/webtests/chromedriver') +# +# def get(self, url): +# self.browser.get(url) +# sleep(5) +# self.title() +# +# def click(self, xpath_selector): +# el = self.browser.find_element_by_xpath(xpath_selector) +# #text = el.text.strip() or el.get_attribute("value").strip() +# el.click() +# #print("clicked:", text) +# sleep(2) +# +# def click_option(self, xpath_selector, option_text): +# el = self.browser.find_element_by_xpath(xpath_selector) +# for option in el.find_elements_by_tag_name('option'): +# if option.text == option_text: +# option.click() # select() in earlier versions of webdriver +# break +# sleep(2) +# +# def enter_text(self, xpath_selector, text): +# el = self.browser.find_element_by_xpath(xpath_selector) +# sleep(10) +# el.send_keys(text) +# sleep(5) +# # Just in case things get mangled by JavaScript, etc. we print the text for testing +# self.get_text(xpath_selector) +# +# def get_text(self, xpath_selector): +# el = self.browser.find_element_by_xpath(xpath_selector) +# text = el.text.strip() or el.get_attribute("value").strip() +# print("text:", text) +# +# def switch_window(self): +# self.browser.switch_to_window(self.browser.window_handles[-1]) +# sleep(2) +# self.title() +# sleep(2) +# +# +# def title(self): +# print("title:", self.browser.title) +# +# +# +if __name__ == '__main__': + import doctest + doctest.testmod() diff --git a/wqflask/maintenance/correlation_test.py b/wqflask/maintenance/correlation_test.py new file mode 100644 index 00000000..aaf3f7df --- /dev/null +++ b/wqflask/maintenance/correlation_test.py @@ -0,0 +1,110 @@ +""" +Test calculate correlations + +>>> test = Test() +>>> test.get("http://genenetwork.org") +title: GeneNetwork + +Choose the type +>>> test.click_option('''//*[@id="tissue"]''', 'Hippocampus mRNA') + +Enter the Get Any +>>> test.enter_text('''//*[@id="tfor"]''', 'ssh') +text: ssh + +Search +>>> test.click('//*[@id="btsearch"]') +clicked: Search + +Choose the first result +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[2]/td[2]/a''') +clicked: 1455854_a_at + +A new window is created, so we switch to it +>>> test.switch_window() +title: Hippocampus M430v2 BXD 06/06 PDNN : 1455854_a_at: Display Trait + +Click on Calculate Correlations +>>> test.click('''//*[@id="title3"]''') +clicked: Calculate Correlations + +Click on Compute +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p[6]/table/tbody/tr/td/div/div/span/table/tbody/tr/td/input[3]''') +clicked: Compute + +Another new window +>>> test.switch_window() +title: Correlation + +Sleep a bunch because this can take a while +>>> sleep(60) + +Ensure the Sample rho is the exepcted 1.000 because it should be the same record +>>> test.get_text('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/table/tbody/tr[2]/td/div/table/tbody/tr[2]/td[9]/a''') +text: 1.000 + +""" + +from __future__ import print_function, division, absolute_import + +from time import sleep + + +import selenium +from selenium import webdriver +from selenium.common.exceptions import NoSuchElementException, ElementNotVisibleException +from selenium.webdriver.common.keys import Keys + + +class Test(object): + def __init__(self): + self.browser = webdriver.Chrome('/home/gn2/gn2/webtests/chromedriver') + + def get(self, url): + self.browser.get(url) + sleep(5) + self.title() + + def click(self, xpath_selector): + el = self.browser.find_element_by_xpath(xpath_selector) + text = el.text.strip() or el.get_attribute("value").strip() + el.click() + print("clicked:", text) + sleep(2) + + def click_option(self, xpath_selector, option_text): + el = self.browser.find_element_by_xpath(xpath_selector) + for option in el.find_elements_by_tag_name('option'): + if option.text == option_text: + option.click() # select() in earlier versions of webdriver + break + sleep(2) + + def enter_text(self, xpath_selector, text): + el = self.browser.find_element_by_xpath(xpath_selector) + sleep(10) + el.send_keys(text) + sleep(5) + # Just in case things get mangled by JavaScript, etc. we print the text for testing + self.get_text(xpath_selector) + + def get_text(self, xpath_selector): + el = self.browser.find_element_by_xpath(xpath_selector) + text = el.text.strip() or el.get_attribute("value").strip() + print("text:", text) + + def switch_window(self): + self.browser.switch_to_window(self.browser.window_handles[-1]) + sleep(2) + self.title() + sleep(2) + + + def title(self): + print("title:", self.browser.title) + + + +if __name__ == '__main__': + import doctest + doctest.testmod() diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 4c544192..ad560659 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -29,25 +29,47 @@ It needs to be run manually when database has been changed. from __future__ import print_function, division -import sys +#from flask import config +# +#cdict = {} +#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS') +#print("cdict is:", cdict) -sys.path.insert(0, "..") +import our_settings import MySQLdb import simplejson as json +import urlparse -from pprint import pformat as pf -from base import webqtlConfig +#import sqlalchemy as sa + +from pprint import pformat as pf +#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI) # build MySql database connection -Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, - host=webqtlConfig.MYSQL_SERVER, - user=webqtlConfig.DB_USER, - passwd=webqtlConfig.DB_PASSWD) -Cursor = Con.cursor() + +#conn = Engine.connect() + + + + + +def parse_db_uri(db_uri): + """Converts a database URI to the db name, host name, user name, and password""" + + parsed_uri = urlparse.urlparse(our_settings.DB_URI) + + db_conn_info = dict( + db = parsed_uri.path[1:], + host = parsed_uri.hostname, + user = parsed_uri.username, + passwd = parsed_uri.password) + + return db_conn_info + def get_species(): @@ -77,12 +99,14 @@ def get_groups(species): def get_types(groups): """Build types list""" types = {} + print("Groups: ", pf(groups)) for species, group_dict in groups.iteritems(): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")] types[species][group_name] += build_types(species, group_name) + return types @@ -93,17 +117,32 @@ def build_types(species, group): (all types except phenotype/genotype are tissues) """ - Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') + + print("""select distinct Tissue.Name + from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species + where Species.Name = '{}' and Species.Id = InbredSet.SpeciesId and + InbredSet.Name = '{}' and + ProbeFreeze.TissueId = Tissue.Id and + ProbeFreeze.InbredSetId = InbredSet.Id and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeSetFreeze.public > 0 + order by Tissue.Name""".format(species, group)) + Cursor.execute("""select distinct Tissue.Name from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and InbredSet.Name = %s and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and - ProbeSetFreeze.public > %s - order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH)) - return Cursor.fetchall() - + ProbeSetFreeze.public > 0 + order by Tissue.Name""", (species, group)) + + results = [] + for result in Cursor.fetchall(): + if len(result): + results.append((result[0], result[0])) + + return results def get_datasets(types): """Build datasets list""" @@ -111,9 +150,10 @@ def get_datasets(types): for species, group_dict in types.iteritems(): datasets[species] = {} for group, type_list in group_dict.iteritems(): + print("type_list: ", type_list) datasets[species][group] = {} - for type_name, _type_full_name in type_list: - datasets[species][group][type_name] = build_datasets(species, group, type_name) + for type_name in type_list: + datasets[species][group][type_name[0]] = build_datasets(species, group, type_name[0]) return datasets @@ -134,20 +174,30 @@ def build_datasets(species, group, type_name): if dataset_value: return [(dataset_value, dataset_text)] else: + print("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from + ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where + Species.Name = '{}' and Species.Id = InbredSet.SpeciesId and + InbredSet.Name = '{}' and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '{}' + and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = + InbredSet.Id and ProbeSetFreeze.public > 0 order by + ProbeSetFreeze.CreateTime desc""".format(species, group, type_name)) Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and InbredSet.Name = %s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = - InbredSet.Id and ProbeSetFreeze.public > %s order by - ProbeSetFreeze.CreateTime desc""", ( - species, group, type_name, webqtlConfig.PUBLICTHRESH)) + InbredSet.Id and ProbeSetFreeze.public > 0 order by + ProbeSetFreeze.CreateTime desc""", (species, group, type_name)) return Cursor.fetchall() def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" + + parse_db_uri(our_settings.DB_URI) + species = get_species() groups = get_groups(species) types = get_types(groups) @@ -167,6 +217,8 @@ def main(): datasets=datasets, ) + print("data:", data) + output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" with open(output_file, 'w') as fh: @@ -182,5 +234,7 @@ def _test_it(): datasets = build_datasets("Mouse", "BXD", "Hippocampus") print("build_datasets:", pf(datasets)) -if __name__ == '__main__': +if __name__ == '__main__': + Conn = MySQLdb.Connect(**parse_db_uri(our_settings.DB_URI)) + Cursor = Conn.cursor() main() diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py new file mode 100644 index 00000000..c9ec3872 --- /dev/null +++ b/wqflask/maintenance/get_group_samplelists.py @@ -0,0 +1,43 @@ +from __future__ import absolute_import, print_function, division + +import os +import glob +import gzip + +from base import webqtlConfig + + +def process_genofiles(geno_dir=webqtlConfig.GENODIR): + print("Yabba") + #sys.exit("Dabba") + os.chdir(geno_dir) + for geno_file in glob.glob("*"): + if geno_file.lower().endswith(('.geno', '.geno.gz')): + #group_name = genofilename.split('.')[0] + sample_list = get_samplelist(geno_file) + + +def get_samplelist(geno_file): + genofilename = os.path.join(webqtlConfig.GENODIR, geno_file) + if os.path.isfile(genofilename + '.gz'): + genofilename += '.gz' + genofile = gzip.open(genofilename) + else: + genofile = open(genofilename) + + for line in genofile: + line = line.strip() + if not line: + continue + if line.startswith(("#", "@")): + continue + break + + headers = line.split() + + if headers[3] == "Mb": + samplelist = headers[4:] + else: + samplelist = headers[3:] + return samplelist + diff --git a/wqflask/maintenance/marker_regression_test.py b/wqflask/maintenance/marker_regression_test.py new file mode 100644 index 00000000..f4840bd7 --- /dev/null +++ b/wqflask/maintenance/marker_regression_test.py @@ -0,0 +1,118 @@ +""" +Test calculate correlations + +>>> test = Test() +>>> test.get("http://genenetwork.org") +title: GeneNetwork + +Choose the type +>>> test.click_option('''//*[@id="tissue"]''', 'Liver mRNA') +clicked: Liver mRNA + +Enter the Get Any +>>> test.enter_text('''//*[@id="tfor"]''', 'grin2b') +text: grin2b + +Search +>>> test.click('//*[@id="btsearch"]') +clicked: Search + +Choose the second result +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[3]/td[2]/a''') +clicked: 1431700_at_A + +A new window is created, so we switch to it +>>> test.switch_window() +title: GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA : 1431700_at_A: Display Trait + +Click on Mapping Tools +>>> test.click('''//*[@id="title4"]''') +clicked: Mapping Tools + +Click on Marker Regression tab +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p[8]/table/tbody/tr/td/div/ul/li[2]/a''') +clicked: Marker Regression + +Click on Compute +>>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p[8]/table/tbody/tr/td/div/div[2]/span/table/tbody/tr/td/input''') +clicked: Compute + +Another new window +>>> test.switch_window() +title: Genome Association Result + +Sleep a bunch because this can take a while +>>> sleep(60) + +Ensure that the LRS of the top record is the exepcted value +>>> test.get_text('''/html/body/table/tbody/tr[3]/td/table/tbody/tr[4]/td/table/tbody/tr/td/div/table/tbody/tr[2]/td[2]''') +text: 11.511 + +""" + +from __future__ import print_function, division, absolute_import + +from browser_test import Test + +# +#from time import sleep +# +# +#import selenium +#from selenium import webdriver +#from selenium.common.exceptions import NoSuchElementException, ElementNotVisibleException +#from selenium.webdriver.common.keys import Keys +# +# +#class Test(object): +# def __init__(self): +# self.browser = webdriver.Chrome('/home/gn2/gn2/webtests/chromedriver') +# +# def get(self, url): +# self.browser.get(url) +# sleep(5) +# self.title() +# +# def click(self, xpath_selector): +# el = self.browser.find_element_by_xpath(xpath_selector) +# text = el.text.strip() or el.get_attribute("value").strip() +# el.click() +# print("clicked:", text) +# sleep(2) +# +# def click_option(self, xpath_selector, option_text): +# el = self.browser.find_element_by_xpath(xpath_selector) +# for option in el.find_elements_by_tag_name('option'): +# if option.text == option_text: +# option.click() # select() in earlier versions of webdriver +# break +# sleep(2) +# +# def enter_text(self, xpath_selector, text): +# el = self.browser.find_element_by_xpath(xpath_selector) +# sleep(10) +# el.send_keys(text) +# sleep(5) +# # Just in case things get mangled by JavaScript, etc. we print the text for testing +# self.get_text(xpath_selector) +# +# def get_text(self, xpath_selector): +# el = self.browser.find_element_by_xpath(xpath_selector) +# text = el.text.strip() or el.get_attribute("value").strip() +# print("text:", text) +# +# def switch_window(self): +# self.browser.switch_to_window(self.browser.window_handles[-1]) +# sleep(2) +# self.title() +# sleep(2) +# +# +# def title(self): +# print("title:", self.browser.title) + + + +if __name__ == '__main__': + import doctest + doctest.testmod() diff --git a/wqflask/maintenance/our_settings.py b/wqflask/maintenance/our_settings.py new file mode 120000 index 00000000..14efe407 --- /dev/null +++ b/wqflask/maintenance/our_settings.py @@ -0,0 +1 @@ +../../../zach_settings.py
\ No newline at end of file diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py index b07e7656..9cd792ef 100644 --- a/wqflask/maintenance/quick_search_table.py +++ b/wqflask/maintenance/quick_search_table.py @@ -71,9 +71,10 @@ class PublishXRef(Base): values['the_key'] = json.dumps([pub_row.Id, pub_row.InbredSetId]) values['terms'] = cls.get_unique_terms(pub_row.Id, pub_row.InbredSetId) print("terms is:", values['terms']) - values['result_fields'] = cls.get_result_fields(pub_row.Id, pub_row.InbredSetId) - ins = QuickSearch.insert().values(**values) - conn.execute(ins) + if values['terms']: + values['result_fields'] = cls.get_result_fields(pub_row.Id, pub_row.InbredSetId) + ins = QuickSearch.insert().values(**values) + conn.execute(ins) counter += 1 print("Done:", counter) @@ -100,28 +101,30 @@ class PublishXRef(Base): inbredset_id=inbredset_id).all() unique = set() - for item in results[0]: - #print("locals:", locals()) - if not item: - continue - for token in item.split(): - if token.startswith(('(','[')): - token = token[1:] - if token.endswith((')', ']')): - token = token[:-1] - if token.endswith(';'): - token = token[:-1] - if len(token) > 2: - try: - # This hopefully ensures that the token is utf-8 - token = token.encode('utf-8') - print(" ->", token) - except UnicodeDecodeError: - print("\n-- UDE \n") - # Can't get it into utf-8, we won't use it - continue - - unique.add(token) + print("results: ", results) + if len(results): + for item in results[0]: + #print("locals:", locals()) + if not item: + continue + for token in item.split(): + if token.startswith(('(','[')): + token = token[1:] + if token.endswith((')', ']')): + token = token[:-1] + if token.endswith(';'): + token = token[:-1] + if len(token) > 2: + try: + # This hopefully ensures that the token is utf-8 + token = token.encode('utf-8') + print(" ->", token) + except UnicodeDecodeError: + print("\n-- UDE \n") + # Can't get it into utf-8, we won't use it + continue + + unique.add(token) #print("\nUnique terms are: {}\n".format(unique)) return " ".join(unique) @@ -467,8 +470,8 @@ QuickSearch = sa.Table("QuickSearch", Metadata, mysql_engine = 'MyISAM', ) -#QuickSearch.drop(Engine, checkfirst=True) -#Metadata.create_all(Engine) +QuickSearch.drop(Engine, checkfirst=True) +Metadata.create_all(Engine) def row2dict(row): @@ -495,9 +498,10 @@ def main(): Add all items from the ProbeSetXRef, GenoXRef, and PublishXRef tables to the QuickSearch tables. """ + + GenoXRef.run() + PublishXRef.run() ProbeSetXRef.run() - #GenoXRef.run() - #PublishXRef.run() if __name__ == "__main__": main()
\ No newline at end of file diff --git a/wqflask/other_config/nginx_conf/penguin.conf b/wqflask/other_config/nginx_conf/penguin.conf new file mode 100644 index 00000000..822556d3 --- /dev/null +++ b/wqflask/other_config/nginx_conf/penguin.conf @@ -0,0 +1,42 @@ +server { + # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/ + listen 80; + + server_name penguin.uthsc.edu; + + access_log /var/log/nginx/access.log; + error_log /var/log/nginx/error.log; + + location ^~ /css/ { + root /gene/wqflask/wqflask/static/; + } + + location ^~ /javascript/ { + root /gene/wqflask/wqflask/static/; + } + +# location ^~ /image/ { +# root /gene/wqflask/wqflask/static/; +# } + + location ^~ /images/ { + root /gene/wqflask/wqflask/static/; + } + + ### New - added by Sam + #location ^~ /static/ { + # root /gene/wqflask/wqflask/static/; + #} + + location / { + proxy_pass http://127.0.0.1:5000/; + proxy_redirect off; + + proxy_set_header Host $host; + proxy_set_header X-Real-IP $remote_addr; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + + proxy_read_timeout 40m; + } +} + diff --git a/wqflask/other_config/wqflask-nginx.conf b/wqflask/other_config/wqflask-nginx.conf deleted file mode 100644 index 4e6fd0d9..00000000 --- a/wqflask/other_config/wqflask-nginx.conf +++ /dev/null @@ -1,83 +0,0 @@ -server { - # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/ - listen 80; - - server_name gn2python.genenetwork.org; - - access_log /var/log/nginx/access.log; - error_log /var/log/nginx/error.log; - - location ^~ /css/ { - root /gene/wqflask/wqflask/static/; - } - - location ^~ /javascript/ { - root /gene/wqflask/wqflask/static/; - } - -# location ^~ /image/ { -# root /gene/wqflask/wqflask/static/; -# } - - location ^~ /images/ { - root /gene/wqflask/wqflask/static/; - } - - ### New - added by Sam - #location ^~ /static/ { - # root /gene/wqflask/wqflask/static/; - #} - - location / { - proxy_pass http://127.0.0.1:5000/; - proxy_redirect off; - - proxy_set_header Host $host; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - - proxy_read_timeout 40m; - } -} - -server { - # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/ - listen 80; - - server_name gn2python_lei.genenetwork.org; - - access_log /var/log/nginx/lei_access.log; - error_log /var/log/nginx/lei_error.log; - - location ^~ /css/ { - root /gene/wqflask/wqflask/static/; - } - - location ^~ /javascript/ { - root /gene/wqflask/wqflask/static/; - } - -# location ^~ /image/ { -# root /gene/wqflask/wqflask/static/; -# } - - location ^~ /images/ { - root /gene/wqflask/wqflask/static/; - } - - ### New - added by Sam - #location ^~ /static/ { - # root /gene/wqflask/wqflask/static/; - #} - - location / { - proxy_pass http://127.0.0.1:5001/; - proxy_redirect off; - - proxy_set_header Host $host; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - - proxy_read_timeout 40m; - } -} diff --git a/wqflask/requirements.txt b/wqflask/requirements.txt deleted file mode 100644 index 4449c0e7..00000000 --- a/wqflask/requirements.txt +++ /dev/null @@ -1,17 +0,0 @@ -Flask==0.9 -Jinja2==2.6 -#MySQL-python==1.2.3 -Piddle==0.1-dev -PyYAML==3.10 -SQLAlchemy==0.7.9 -Werkzeug==0.8.3 -logging-tree==1.1 -nose==1.2.1 -numpy==1.6.2 -pp==1.6.3 -requests==0.13.3 -rpy2==2.3.1 -scipy==0.11.0 -simplejson==2.6.2 -wsgiref==0.1.2 -yolk==0.4.3 diff --git a/wqflask/secure_server.py b/wqflask/secure_server.py index 3487f35b..2abfdb05 100644 --- a/wqflask/secure_server.py +++ b/wqflask/secure_server.py @@ -4,12 +4,10 @@ from wqflask import app from flask import Flask, render_template - # Setup mail from flask.ext.mail import Mail mail = Mail(app) - from wqflask.model import * # Create a user to test with @@ -19,7 +17,6 @@ from wqflask.model import * # user_datastore.create_user(email='matt@example.com', password='notebook') # db.session.commit() - import logging file_handler = logging.FileHandler(app.config['LOGFILE']) file_handler.setLevel(logging.DEBUG) diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index d76a32ce..44f5321e 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -8,11 +8,14 @@ from base.species import TheSpecies def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" self.dataset = data_set.create_dataset(start_vars['dataset']) + print("After creating dataset") self.species = TheSpecies(dataset=self.dataset) + print("After creating species") self.this_trait = GeneralTrait(dataset=self.dataset, name=start_vars['trait_id'], cellid=None) + print("After creating trait") #if read_genotype: - self.dataset.group.read_genotype_file() + #self.dataset.group.read_genotype_file() #self.genotype = self.dataset.group.genotype diff --git a/wqflask/wqflask/correlation/correlationFunction.py b/wqflask/wqflask/correlation/correlation_function.py index 7d4b58a9..7d4b58a9 100644 --- a/wqflask/wqflask/correlation/correlationFunction.py +++ b/wqflask/wqflask/correlation/correlation_function.py diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 1410ae0c..07d70897 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -52,6 +52,8 @@ import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlationFunction from utility.benchmark import Bench +from MySQLdb import escape_string as escape + from pprint import pformat as pf METHOD_SAMPLE_PEARSON = "1" @@ -101,13 +103,14 @@ class CorrelationResults(object): self.sample_data = {} self.corr_method = start_vars['corr_sample_method'] + self.return_number = 500 #The two if statements below append samples to the sample list based upon whether the user #rselected Primary Samples Only, Other Samples Only, or All Samples primary_samples = (self.dataset.group.parlist + - self.dataset.group.f1list + - self.dataset.group.samplelist) + self.dataset.group.f1list + + self.dataset.group.samplelist) #If either BXD/whatever Only or All Samples, append all of that group's samplelist if corr_samples_group != 'samples_other': @@ -137,8 +140,6 @@ class CorrelationResults(object): this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values( this_trait_vals, target_vals) - print("num_overlap:", num_overlap) - if self.corr_method == 'pearson': sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals) else: @@ -153,13 +154,15 @@ class CorrelationResults(object): #self.correlation_data_slice = collections.OrderedDict() - for trait_counter, trait in enumerate(self.correlation_data.keys()[:300]): + for trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): trait_object = GeneralTrait(dataset=self.dataset, name=trait, get_qtl_info=True) trait_object.sample_r = self.correlation_data[trait][0] trait_object.sample_p = self.correlation_data[trait][1] - trait_object_num_overlap = self.correlation_data[trait][2] + trait_object.num_overlap = self.correlation_data[trait][2] self.correlation_results.append(trait_object) + + #self.correlation_data_slice[trait] = self.correlation_data[trait] #self.correlation_data_slice[trait].append(trait_object) #if self.dataset.type == 'ProbeSet': @@ -524,9 +527,13 @@ class CorrelationResults(object): #XZ, 09/23/2008: In tissue correlation tables, there is no record of GeneId1 == GeneId2 #XZ, 09/24/2008: Note that the correlation value can be negative. - def getTempTissueCorrTable(self, primaryTraitSymbol="", TissueProbeSetFreezeId=0, method="", returnNumber=0): + def get_temp_tissue_corr_table(self, + tissue_probesetfreeze_id=0, + method="", + return_number=0): + - def cmpTissCorrAbsoluteValue(A, B): + def cmp_tisscorr_absolute_value(A, B): try: if abs(A[1]) < abs(B[1]): return 1 elif abs(A[1]) == abs(B[1]): @@ -535,26 +542,27 @@ class CorrelationResults(object): except: return 0 - symbolCorrDict, symbolPvalueDict = self.calculateCorrOfAllTissueTrait(primaryTraitSymbol=primaryTraitSymbol, TissueProbeSetFreezeId=TISSUE_MOUSE_DB, method=method) + symbol_corr_dict, symbol_pvalue_dict = self.calculate_corr_for_all_tissues( + tissue_dataset_id=TISSUE_MOUSE_DB) - symbolCorrList = symbolCorrDict.items() + symbol_corr_list = symbol_corr_dict.items() - symbolCorrList.sort(cmpTissCorrAbsoluteValue) - symbolCorrList = symbolCorrList[0 : 2*returnNumber] + symbol_corr_list.sort(cmp_tisscorr_absolute_value) + symbol_corr_list = symbol_corr_list[0 : 2*return_number] - tmpTableName = webqtlUtil.genRandStr(prefix="TOPTISSUE") + tmp_table_name = webqtlUtil.genRandStr(prefix="TOPTISSUE") - q1 = 'CREATE TEMPORARY TABLE %s (Symbol varchar(100) PRIMARY KEY, Correlation float, PValue float)' % tmpTableName + q1 = 'CREATE TEMPORARY TABLE %s (Symbol varchar(100) PRIMARY KEY, Correlation float, PValue float)' % tmp_table_name self.cursor.execute(q1) - for one_pair in symbolCorrList: + for one_pair in symbol_corr_list: one_symbol = one_pair[0] one_corr = one_pair[1] - one_p_value = symbolPvalueDict[one_symbol] + one_p_value = symbol_pvalue_dict[one_symbol] self.cursor.execute( "INSERT INTO %s (Symbol, Correlation, PValue) VALUES ('%s',%f,%f)" % (tmpTableName, one_symbol, float(one_corr), float(one_p_value)) ) - return tmpTableName + return tmp_table_name #XZ, 01/09/2009: This function was created by David Crowell. Xiaodong cleaned up and modified it. @@ -584,37 +592,50 @@ class CorrelationResults(object): return litCorrDict + def fetch_tissue_correlations(self): + """Comments Possibly Out of Date!!!!! + + + Uses getTempTissueCorrTable to generate table of tissue correlations + + This function then gathers that data and pairs it with the TraitID string. + Takes as its arguments a formdata instance, and a database instance. + Returns a dictionary of 'TraitID':(tissueCorr, tissuePValue) + for the requested correlation + + Used when the user selects the tissue correlation method; i.e. not for the + column that is appended to all probeset trait correlation tables + + """ - #XZ, 01/09/2009: Xiaodong created this function. - def fetchTissueCorrelations(self, db, primaryTraitSymbol="", TissueProbeSetFreezeId=0, method="", returnNumber = 0): - """Uses getTempTissueCorrTable to generate table of tissue correlations. This function then gathers that data and - pairs it with the TraitID string. Takes as its arguments a formdata instance, and a database instance. - Returns a dictionary of 'TraitID':(tissueCorr, tissuePValue) for the requested correlation""" - - - tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=primaryTraitSymbol, TissueProbeSetFreezeId=TISSUE_MOUSE_DB, method=method, returnNumber=returnNumber) + # table name string + temp_table = self.get_temp_tissue_corr_table(tissue_probesetfreeze_id=TISSUE_MOUSE_DB, + method=method) - query = "SELECT ProbeSet.Name, %s.Correlation, %s.PValue" % (tempTable, tempTable) - query += ' FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)' - query += ' LEFT JOIN %s ON %s.Symbol=ProbeSet.Symbol ' % (tempTable,tempTable) - query += "WHERE ProbeSetFreeze.Name = '%s' and ProbeSetFreeze.Id=ProbeSetXRef.ProbeSetFreezeId and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSet.Symbol IS NOT NULL AND %s.Correlation IS NOT NULL" % (db.name, tempTable) + query = """SELECT ProbeSet.Name, {}.Correlation, {}.PValue + FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) + LEFT JOIN {} ON {}.Symbol=ProbeSet.Symbol + WHERE ProbeSetFreeze.Name = '{}' + and ProbeSetFreeze.Id=ProbeSetXRef.ProbeSetFreezeId + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSet.Symbol IS NOT NULL + and {}.Correlation IS NOT NULL""".format(dataset.mescape( + temp_table, temp_table, temp_table, temp_table, + self.dataset.name, temp_table)) - self.cursor.execute(query) - results = self.cursor.fetchall() + results = g.db.execute(query).fetchall() - tissueCorrDict = {} + tissue_corr_dict = {} for entry in results: - traitName, tissueCorr, tissuePValue = entry - tissueCorrDict[traitName] = (tissueCorr, tissuePValue) + trait_name, tissue_corr, tissue_pvalue = entry + tissue_corr_dict[trait_name] = (tissue_corr, tissue_pvalue) - self.cursor.execute('DROP TEMPORARY TABLE %s' % tempTable) - - return tissueCorrDict + g.db.execute('DROP TEMPORARY TABLE {}'.format(escape(temp_table))) + return tissue_corr_dict - #XZ, 01/13/2008 def getLiteratureCorrelationByList(self, input_trait_mouse_geneid=None, species=None, traitList=None): tmpTableName = webqtlUtil.genRandStr(prefix="LITERATURE") @@ -665,7 +686,7 @@ class CorrelationResults(object): use_tissue_corr = False if self.method in TISSUE_METHODS: - tissue_corrs = self.fetchTissueCorrelations(db=self.db, primaryTraitSymbol=self.trait_symbol, TissueProbeSetFreezeId=TISSUE_MOUSE_DB, method=self.method, returnNumber = self.returnNumber) + tissue_corrs = self.fetch_tissue_correlations(method=self.method, return_number = self.return_number) use_tissue_corr = True DatabaseFileName = self.getFileName( target_db_name=self.target_db_name ) @@ -890,20 +911,28 @@ class CorrelationResults(object): return trait_list """ - def calculateCorrOfAllTissueTrait(self, primaryTraitSymbol=None, TissueProbeSetFreezeId=None, method=None): + def calculate_corr_for_all_tissues(self, tissue_dataset_id=None): - symbolCorrDict = {} - symbolPvalueDict = {} + symbol_corr_dict = {} + symbol_pvalue_dict = {} - primaryTraitSymbolValueDict = correlationFunction.getGeneSymbolTissueValueDictForTrait(cursor=self.cursor, GeneNameLst=[primaryTraitSymbol], TissueProbeSetFreezeId=TISSUE_MOUSE_DB) - primaryTraitValue = primaryTraitSymbolValueDict.values()[0] + primary_trait_symbol_value_dict = correlation_function.make_gene_tissue_value_dict( + GeneNameLst=[self.this_trait.symbol], + TissueProbeSetFreezeId=tissue_dataset_id) + primary_trait_value = primary_trait_symbol_value_dict.values()[0] - SymbolValueDict = correlationFunction.getGeneSymbolTissueValueDictForTrait(cursor=self.cursor, GeneNameLst=[], TissueProbeSetFreezeId=TISSUE_MOUSE_DB) + symbol_value_dict = correlation_function.make_gene_tissue_value_dict( + gene_name_list=[], + tissue_dataset_id=tissue_dataset_id) - if method in ["2","5"]: - symbolCorrDict, symbolPvalueDict = correlationFunction.batchCalTissueCorr(primaryTraitValue,SymbolValueDict,method='spearman') - else: - symbolCorrDict, symbolPvalueDict = correlationFunction.batchCalTissueCorr(primaryTraitValue,SymbolValueDict) + symbol_corr_dict, symbol_pvalue_dict = correlation_function.batch_cal_tissue_corr( + primaryTraitValue, + SymbolValueDict, + method=self.corr_method) + #else: + # symbol_corr_dict, symbol_pvalue_dict = correlation_function.batch_cal_tissue_corr( + # primaryTraitValue, + # SymbolValueDict) return (symbolCorrDict, symbolPvalueDict) diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 7b3e0869..5eb09aa1 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -36,7 +36,7 @@ class DoSearch(object): def execute(self, query): """Executes query and returns results""" query = self.normalize_spaces(query) - #print("in do_search query is:", pf(query)) + print("in do_search query is:", pf(query)) results = g.db.execute(query, no_parameters=True).fetchall() #results = self.cursor.fetchall() return results @@ -90,7 +90,7 @@ class QuickMrnaAssaySearch(DoSearch): AGAINST ('%s' IN BOOLEAN MODE)) """ % (escape(self.search_term[0])) - #print("final query is:", pf(query)) + print("final query is:", pf(query)) return self.execute(query) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 5bfc3a01..9a795c66 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -138,8 +138,8 @@ def run_human(pheno_vector, #print("***** Added to {} queue *****".format(key)) for snp, this_id in plink_input: #with Bench("part before association"): - if count > 2000: - break + #if count > 2000: + # break count += 1 percent_complete = (float(count) / total_snps) * 100 @@ -237,6 +237,9 @@ def run(pheno_vector, with Bench("Calculate Kinship"): kinship_matrix = calculate_kinship(genotype_matrix, temp_data) + print("kinship_matrix: ", pf(kinship_matrix)) + print("kinship_matrix.shape: ", pf(kinship_matrix.shape)) + with Bench("Create LMM object"): lmm_ob = LMM(pheno_vector, kinship_matrix) @@ -365,9 +368,9 @@ def GWAS(pheno_vector, if v.sum(): keep = True - v pheno_vector = pheno_vector[keep] - genotype_matrix = genotype_matrix[keep,:] - covariate_matrix = covariate_matrix[keep,:] - kinship_matrix = kinship_matrix[keep,:][:,keep] + #genotype_matrix = genotype_matrix[keep,:] + #covariate_matrix = covariate_matrix[keep,:] + #kinship_matrix = kinship_matrix[keep,:][:,keep] kinship_eigen_vals = [] kinship_eigen_vectors = [] @@ -459,9 +462,12 @@ class LMM: x = True - np.isnan(Y) #pdb.set_trace() if not x.sum() == len(Y): + print("Removing %d missing values from Y\n" % ((True - x).sum())) if self.verbose: sys.stderr.write("Removing %d missing values from Y\n" % ((True - x).sum())) Y = Y[x] - K = K[x,:][:,x] + print("x: ", len(x)) + print("K: ", K.shape) + #K = K[x,:][:,x] X0 = X0[x,:] Kva = [] Kve = [] diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index f76af374..702b646e 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -79,7 +79,13 @@ class SearchResultPage(object): print("kw is:", kw) #self.quick_search = False self.search_terms = kw['search_terms'] - self.dataset = create_dataset(kw['dataset']) + if kw['type'] == "Phenotypes": + dataset_type = "Publish" + elif kw['type'] == "Genotypes": + dataset_type = "Geno" + else: + dataset_type = "ProbeSet" + self.dataset = create_dataset(kw['dataset'], dataset_type) self.search() self.gen_search_result() @@ -162,8 +168,6 @@ class SearchResultPage(object): import redis Redis = redis.Redis() - - #def get_group_species_tree(self): # self.species_groups = collections.default_dict(list) # for key in self.results: diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 60e42afb..b0c96c56 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -41,7 +41,7 @@ class ShowTrait(object): helper_functions.get_species_dataset_trait(self, kw) - self.dataset.group.read_genotype_file() + #self.dataset.group.read_genotype_file() # Todo: Add back in the ones we actually need from below, as we discover we need them hddn = OrderedDict() @@ -1204,10 +1204,12 @@ class ShowTrait(object): other_sample_names.append(sample) if other_sample_names: - parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list + if self.dataset.group.parlist and self.dataset.group.f1list: + parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list other_sample_names.sort() #Sort other samples - other_sample_names = parent_f1_samples + other_sample_names + if parent_f1_samples: + other_sample_names = parent_f1_samples + other_sample_names other_samples = SampleList(dataset=self.dataset, sample_names=other_sample_names, diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 88bdcb11..43575a18 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -62,7 +62,7 @@ "QSM Genotypes" ] ], - "Leaf": [ + "Leaf mRNA": [ [ "B1LI0809M5", "Barley1 Leaf INOC TTKS (Aug09) MAS5" @@ -88,7 +88,7 @@ ] }, "SXM": { - "Embryo": [ + "Embryo mRNA": [ [ "B139_K_1206_R", "Barley1 Embryo gcRMA SCRI (Dec06)" @@ -108,7 +108,7 @@ "SXM Genotypes" ] ], - "Leaf": [ + "Leaf mRNA": [ [ "B30_K_1206_M", "Barley1 Leaf MAS 5.0 SCRI (Dec06)" @@ -144,7 +144,7 @@ "DGRP Published Phenotypes" ] ], - "Whole Body": [ + "Whole Body mRNA": [ [ "NCSU_DrosWB_LC_RMA_0111", "NCSU Drosophila Whole Body (Jan11) RMA" @@ -164,7 +164,7 @@ "Oregon-R_x_2b3 Published Phenotypes" ] ], - "Whole Body": [ + "Whole Body mRNA": [ [ "UAB_DrosWB_LC_RMA_1009", "UAB Whole body D.m. mRNA control (Oct09) RMA" @@ -178,7 +178,7 @@ }, "human": { "AD-cases-controls": { - "Brain": [ + "Brain mRNA": [ [ "GSE5281_F_RMA_N_0709", "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" @@ -210,7 +210,7 @@ ] }, "AD-cases-controls-Myers": { - "Brain": [ + "Brain mRNA": [ [ "GSE15222_F_N_RI_0409", "GSE15222 Human Brain Normal Myers (Apr09) RankInv" @@ -244,10 +244,20 @@ "CANDLE Genotypes" ] ], - "Newborn Cord Blood": [ + "Methylation": [ + [ + "CANDLE_Meth27_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) **" + ], + [ + "CANDLE_Meth_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) Z-Score **" + ] + ], + "Newborn Cord Blood mRNA": [ [ "CANDLE_NB_0711", - "CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT **" + "CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT" ] ], "Phenotypes": [ @@ -264,7 +274,7 @@ "CEPH-2004 Genotypes" ] ], - "Lymphoblast B-cell": [ + "Lymphoblast B-cell mRNA": [ [ "UT_CEPH_RankInv0909", "UTHSC CEPH B-cells Illumina (Sep09) RankInv" @@ -282,7 +292,7 @@ ] }, "HB": { - "Cerebellum": [ + "Cerebellum mRNA": [ [ "HBTRC-MLC_0611", "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" @@ -312,7 +322,7 @@ "HB Published Phenotypes" ] ], - "Prefrontal Cortex": [ + "Prefrontal Cortex mRNA": [ [ "HBTRC-MLPFC_0611", "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" @@ -330,7 +340,7 @@ "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" ] ], - "Primary Visual Cortex": [ + "Primary Visual Cortex mRNA": [ [ "HBTRC-MLVC_0611", "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" @@ -356,7 +366,7 @@ "HLC Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "HLC_0311", "GSE9588 Human Liver Normal (Mar11) Both Sexes" @@ -377,20 +387,52 @@ ] ] }, + "HLT": { + "Genotypes": [ + [ + "HLTGeno", + "HLT Genotypes" + ] + ], + "Lung mRNA": [ + [ + "GSE23546HLT0613", + "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ], + [ + "luCA_GSE23352HLT0613", + "UL/GSE23352 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA (Jun11) RMA" + ], + [ + "UBC-GSE23529HLT0613", + "UBC/GSE23529 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ], + [ + "GRNG-GSE23545HLT0613", + "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ] + ], + "Phenotypes": [ + [ + "HLTPublish", + "HLT Published Phenotypes" + ] + ] + }, "HSB": { - "Amygdala": [ + "Amygdala mRNA": [ [ "KIN_YSM_AMY_0711", "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Cerebellar Cortex": [ + "Cerebellar Cortex mRNA": [ [ "KIN_YSM_CBC_0711", "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Dorsolateral Prefrontal Cortex": [ + "Dorsolateral Prefrontal Cortex mRNA": [ [ "KIN_YSM_DFC_0711", "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" @@ -402,31 +444,31 @@ "HSB Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "KIN_YSM_HIP_0711", "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Inferior Temporal Cortex": [ + "Inferior Temporal Cortex mRNA": [ [ "KIN_YSM_ITC_0711", "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Medial Prefrontal Cortex": [ + "Medial Prefrontal Cortex mRNA": [ [ "KIN_YSM_MFC_0711", "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Mediodorsal Nucleus of Thalamus": [ + "Mediodorsal Nucleus of Thalamus mRNA": [ [ "KIN_YSM_MD_0711", "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Orbital Prefrontal Cortex": [ + "Orbital Prefrontal Cortex mRNA": [ [ "KIN_YSM_OFC_0711", "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" @@ -438,49 +480,49 @@ "HSB Published Phenotypes" ] ], - "Posterior Inferior Parietal Cortex": [ + "Posterior Inferior Parietal Cortex mRNA": [ [ "KIN_YSM_IPC_0711", "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Posterior Superior Temporal Cortex": [ + "Posterior Superior Temporal Cortex mRNA": [ [ "KIN_YSM_STC_0711", "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Primary Auditory (A1) Cortex": [ + "Primary Auditory (A1) Cortex mRNA": [ [ "KIN_YSM_A1C_0711", "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Primary Motor (M1) Cortex": [ + "Primary Motor (M1) Cortex mRNA": [ [ "KIN_YSM_M1C_0711", "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Primary Somatosensory (S1) Cortex": [ + "Primary Somatosensory (S1) Cortex mRNA": [ [ "KIN_YSM_S1C_0711", "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Primary Visual Cortex": [ + "Primary Visual Cortex mRNA": [ [ "KIN_YSM_V1C_0711", "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Striatum": [ + "Striatum mRNA": [ [ "KIN_YSM_STR_0711", "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Ventrolateral Prefrontal Cortex": [ + "Ventrolateral Prefrontal Cortex mRNA": [ [ "KIN_YSM_VFC_0711", "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" @@ -490,13 +532,13 @@ }, "macaque monkey": { "Macaca-fasicularis": { - "Amygdala": [ + "Amygdala mRNA": [ [ "INIA_MacFas_AMG_RMA_0110", "INIA Macaca fasicularis Amygdala (Jan10) RMA **" ] ], - "Brain": [ + "Brain mRNA": [ [ "INIA_MacFas_brain_RMA_0110", "INIA Macaca fasicularis Brain (Jan10) RMA **" @@ -508,13 +550,13 @@ "Macaca-fasicularis Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "INIA_MacFas_Hc_RMA_0110", "INIA Macaca fasicularis Hippocampus (Jan10) RMA **" ] ], - "Nucleus Accumbens": [ + "Nucleus Accumbens mRNA": [ [ "INIA_MacFas_Ac_RMA_0110", "INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA **" @@ -526,7 +568,7 @@ "Macaca-fasicularis Published Phenotypes" ] ], - "Prefrontal Cortex": [ + "Prefrontal Cortex mRNA": [ [ "INIA_MacFas_Pf_RMA_0110", "INIA Macaca fasicularis Prefrontal Cortex (Jan10) RMA **" @@ -542,7 +584,7 @@ "AKXD Genotypes" ] ], - "Mammary Tumors": [ + "Mammary Tumors mRNA": [ [ "NCI_Agil_Mam_Tum_RMA_0409", "NCI Mammary LMT miRNA v2 (Apr09) RMA" @@ -564,7 +606,13 @@ ] }, "AXBXA": { - "Eye": [ + "Bone Femur mRNA": [ + [ + "UCLA_AXB/BXA_Femur_0113_RSN", + "UCLA GSE27483 AXB/BXA Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN" + ] + ], + "Eye mRNA": [ [ "Eye_AXBXA_1008_RankInv", "Eye AXBXA Illumina V6.2(Oct08) RankInv Beta" @@ -576,7 +624,13 @@ "AXBXA Genotypes" ] ], - "Liver": [ + "Heart mRNA": [ + [ + "IRCM_AXBXA_HRI0213", + "IRCM AXB/BXA Mouse Heart ILM MouseRef-8 v2.0 (Feb13) RankInv" + ] + ], + "Liver mRNA": [ [ "GSE16780AB_UCLA_ML0911", "GSE16780 UCLA Mouse AXB/BXA Liver Affy HT M430A (Sep11) RMA" @@ -596,7 +650,7 @@ "B6BTBRF2 Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "LVF2_M_0704_M", "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" @@ -614,11 +668,7 @@ ] }, "B6D2F2": { - "Brain": [ - [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], + "Brain mRNA": [ [ "BRF2_M_0805_P", "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" @@ -628,6 +678,10 @@ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" ], [ + "BRF2_M_0805_M", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" + ], + [ "BRF2_M_0304_P", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" ], @@ -660,10 +714,22 @@ "B6D2F2-PSU Genotypes" ] ], - "Muscle": [ + "Muscle mRNA": [ [ "PSU-B6D2F2_0812", "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA **" + ], + [ + "PSU-B6D2F2_F0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Females **" + ], + [ + "PSU-B6D2F2_M0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males **" + ], + [ + "PSU-B6D2F2_M2000812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males Aged 200 **" ] ], "Phenotypes": [ @@ -680,7 +746,7 @@ "B6D2RI Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "UTHSC_B6D2RI_H_0912", "UTHSC B6D2RI Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA **" @@ -700,7 +766,7 @@ "BDF2-1999 Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "UCLA_BDF2_LIVER_1999", "UCLA BDF2 Liver (1999) mlratio" @@ -726,7 +792,7 @@ "BDF2-2005 Published Phenotypes" ] ], - "Striatum": [ + "Striatum mRNA": [ [ "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" @@ -742,7 +808,7 @@ ] }, "BHF2": { - "Adipose": [ + "Adipose mRNA": [ [ "UCLA_BHF2_ADIPOSE_FEMALE", "UCLA BHF2 Adipose Female mlratio" @@ -756,7 +822,7 @@ "UCLA BHF2 Adipose (June05) mlratio" ] ], - "Brain": [ + "Brain mRNA": [ [ "UCLA_BHF2_BRAIN_FEMALE", "UCLA BHF2 Brain Female mlratio" @@ -776,7 +842,7 @@ "BHF2 Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "UCLA_BHF2_LIVER_FEMALE", "UCLA BHF2 Liver Female mlratio" @@ -790,7 +856,7 @@ "UCLA BHF2 Liver (June05) mlratio" ] ], - "Muscle": [ + "Muscle mRNA": [ [ "UCLA_BHF2_MUSCLE_FEMALE", "UCLA BHF2 Muscle Female mlratio **" @@ -812,7 +878,7 @@ ] }, "BHHBF2": { - "Adipose": [ + "Adipose mRNA": [ [ "UCLA_BHHBF2_ADIPOSE_2005", "UCLA BHHBF2 Adipose (2005) mlratio" @@ -826,7 +892,7 @@ "UCLA BHHBF2 Adipose Female Only" ] ], - "Brain": [ + "Brain mRNA": [ [ "UCLA_BHHBF2_BRAIN_2005", "UCLA BHHBF2 Brain (2005) mlratio" @@ -846,7 +912,7 @@ "BHHBF2 Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "UCLA_BHHBF2_LIVER_2005", "UCLA BHHBF2 Liver (2005) mlratio" @@ -860,7 +926,7 @@ "UCLA BHHBF2 Liver Female Only" ] ], - "Muscle": [ + "Muscle mRNA": [ [ "UCLA_BHHBF2_MUSCLE_2005", "UCLA BHHBF2 Muscle (2005) mlratio" @@ -882,17 +948,25 @@ ] }, "BXD": { - "Adrenal Gland": [ + "Adrenal Gland mRNA": [ [ "INIA_Adrenal_RMA_0612", "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA" ], [ + "INIA_Adrenal_RMA_F_0612", + "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA Females" + ], + [ + "INIA_Adrenal_RMA_M_0612", + "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA Males" + ], + [ "INIA_Adrenal_RMA_Ex_0612", "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA Exon Level" ] ], - "Amygdala": [ + "Amygdala mRNA": [ [ "INIA_AmgCoh_0311", "INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA" @@ -914,7 +988,25 @@ "INIA Amygdala Exon Affy MoGene 1.0 ST (Nov10) RMA" ] ], - "Brain": [ + "Bone Femur mRNA": [ + [ + "UCLA_BXD_Femur_0113_RSN", + "UCLA GSE27483 BXD Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN" + ], + [ + "UCLA_BXD-on_Femur_0113_RSN", + "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v2.0 (Jan13) RSN" + ] + ], + "Brain mRNA": [ + [ + "UTHSC_BXD_WB_RNASeqEx1112", + "UTHSC Mouse BXD Whole Brain RNA Sequence Exon Level (Nov12) RPKM" + ], + [ + "UTHSC_BXD_WB_RNASeq1112", + "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM" + ], [ "BR_M2_1106_R", "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" @@ -924,10 +1016,6 @@ "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], - [ "BR_U_0805_P", "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" ], @@ -936,11 +1024,15 @@ "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" ], [ + "BR_U_0805_R", + "UTHSC Brain mRNA U74Av2 (Aug05) RMA" + ], + [ "CB_M_0204_P", "INIA Brain mRNA M430 (Feb04) PDNN" ] ], - "Cartilage": [ + "Cartilage mRNA": [ [ "UCLA_BXDBXH_CARTILAGE_V2", "UCLA BXD and BXH Cartilage v2" @@ -954,7 +1046,7 @@ "UCLA BXD Cartilage" ] ], - "Cerebellum": [ + "Cerebellum mRNA": [ [ "CB_M_1004_R", "SJUT Cerebellum mRNA M430 (Oct04) RMA" @@ -970,9 +1062,65 @@ [ "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" + ], + [ + "CMMTUBCBXDCerILM0513", + "UBC/CMMT BXD Cerebellum All Ages Combined ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDG12CerILM0513", + "UBC/CMMT BXD E12 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDG15CerILM0513", + "UBC/CMMT BXD E15 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDG18CerILM0513", + "UBC/CMMT BXD E18 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDP00CerILM0513", + "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDP03CerILM0513", + "UBC/CMMT BXD P3 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDP06CerILM0513", + "UBC/CMMT BXD P6 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDP09CerILM0513", + "UBC/CMMT BXD P9 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "GenEx_BXD_CerebEt_RMA_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes **" + ], + [ + "GenEx_BXD_CerebEt_RMA_F_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Females **" + ], + [ + "GenEx_BXD_CerebEt_RMA_M_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Males **" + ], + [ + "GenEx_BXD_CerebSal_RMA_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes **" + ], + [ + "GenEx_BXD_CerebSal_RMA_F_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Females **" + ], + [ + "GenEx_BXD_CerebSal_RMA_M_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Males **" ] ], - "Eye": [ + "Eye mRNA": [ [ "Eye_M2_0908_R", "Eye M430v2 (Sep08) RMA" @@ -990,10 +1138,6 @@ "Eye M430v2 WT Gpnmb (Sep08) RMA **" ], [ - "Eye_M2_0908_R_MT", - "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" - ], - [ "Eye_M2_0908_WTWT", "Eye M430v2 WT WT (Sep08) RMA **" ], @@ -1002,6 +1146,14 @@ "Eye M430v2 WT Tyrp1 (Sep08) RMA **" ], [ + "DBA2J-ONH-1212", + "ONH BXD Glaucoma Affy M430 2.0 Trial (Dec12) RMA **" + ], + [ + "Eye_M2_0908_R_MT", + "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" + ], + [ "BXD_GLA_0911", "BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **" ] @@ -1012,7 +1164,7 @@ "BXD Genotypes" ] ], - "Hematopoietic Cells": [ + "Hematopoietic Cells mRNA": [ [ "UMCG_0907_HemaStem_ori", "UMCG Stem Cells ILM6v1.1 (Apr09) original" @@ -1050,7 +1202,7 @@ "GNF Stem Cells U74Av2 (Mar04) RMA" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "HC_M2_0606_P", "Hippocampus Consortium M430v2 (Jun06) PDNN" @@ -1064,6 +1216,30 @@ "Hippocampus Consortium M430v2 (Jun06) RMA" ], [ + "UT_ILM_BXD_hipp_5T_1112", + "UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_NON_1112", + "UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_NOS_1112", + "UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_NOE_1112", + "UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_RSS_1112", + "UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_RSE_1112", + "UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv" + ], + [ "UMUTAffyExon_0209_RMA", "UMUTAffy Hippocampus Exon (Feb09) RMA" ], @@ -1096,7 +1272,7 @@ "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA Exon Level **" ] ], - "Hypothalamus": [ + "Hypothalamus mRNA": [ [ "INIA_Hyp_RMA_1110", "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)" @@ -1114,7 +1290,7 @@ "INIA Hypothalamus Exon Affy MoGene 1.0 ST (Nov10)" ] ], - "Kidney": [ + "Kidney mRNA": [ [ "MA_M2M_0706_R", "Mouse kidney M430v2 Male (Aug06) RMA" @@ -1140,59 +1316,101 @@ "Mouse Kidney M430v2 (Jul06) PDNN" ] ], - "Leucocytes": [ + "Leucocytes mRNA": [ [ "Illum_BXD_PBL_1108", "UWA Illumina PBL (Nov08) RSN **" ] ], - "Liver": [ + "Liver Proteome": [ + [ + "EPFLBXDprotRPN0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (May13) RPN **" + ], + [ + "EPFLBXDprotHFDRPN0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins HFD (May13) RPN **" + ], + [ + "EPFLBXDprotCDRPN0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD (May13) RPN **" + ], + [ + "EPFLBXDprot0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (May13) **" + ], + [ + "EPFLBXDprotHFD0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins HFD (May13) **" + ], + [ + "EPFLBXDprotCD0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD (May13) **" + ] + ], + "Liver mRNA": [ [ "GSE16780_UCLA_ML0911", "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" ], [ - "GenEx_BXD_liverEt_M5_0912", - "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes **" + "EPFLMouseLiverRMA0413", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA **" ], [ - "GenEx_BXD_liverEt_M5F_0912", - "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females **" + "EPFLMouseLiverHFDRMA0413", + "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA **" + ], + [ + "EPFLMouseLiverCDRMA0413", + "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA **" + ], + [ + "EPFLMouseLiverBothExRMA0413", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level **" + ], + [ + "GenEx_BXD_liverEt_M5_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes **" ], [ "GenEx_BXD_liverEt_M5M_0912", "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Males **" ], [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" + "GenEx_BXD_liverEt_M5F_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females **" ], [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" + "GenEx_BXD_liverEt_RMA_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" ], [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + "GenEx_BXD_liverEt_RMA_M_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" ], [ "GenEx_BXD_liverEt_RMA_F_0211", "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" ], [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" + "GenEx_BXD_liverSal_RMA_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" ], [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + "GenEx_BXD_liverSal_RMA_M_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" + ], + [ + "GenEx_BXD_liverSal_RMA_F_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" ], [ "SUH_Liv_RMA_0611", "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" ] ], - "Lung": [ + "Lung mRNA": [ [ "HZI_0408_R", "HZI Lung M430v2 (Apr08) RMA" @@ -1202,17 +1420,33 @@ "HZI Lung M430v2 (Apr08) MAS5" ], [ + "HZI_LTCF_0313", + "HZI Lung Time Course Flu PR8M (Mar13) Schughart **" + ], + [ "HZI_PR8M_Q_0612", "HZI PR8M-Infected Lungs Agilent4x44 (Apr12) Quantile Females **" ] ], - "Midbrain": [ + "Midbrain mRNA": [ [ "VUBXDMouseMidBrainQ0512", "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile **" ] ], - "Muscle": [ + "Muscle mRNA": [ + [ + "EPFLMouseMuscleRMA_Ex1112", + "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level **" + ], + [ + "EPFLMouseMuscleHFDRMAEx1112", + "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level **" + ], + [ + "EPFLMouseMuscleCDRMAEx1112", + "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level **" + ], [ "EPFLMouseMuscleRMA1211", "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" @@ -1226,7 +1460,7 @@ "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" ] ], - "Neocortex": [ + "Neocortex mRNA": [ [ "DevNeocortex_ILM6.2P3RInv_1111", "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" @@ -1256,12 +1490,24 @@ "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], - "Nucleus Accumbens": [ + "Nucleus Accumbens mRNA": [ [ "VCUSalo_1007_R", "VCU BXD NA Sal M430 2.0 (Oct07) RMA" ], [ + "VCU_NAc_AvE_0113_Ss", + "VCU BXD NAc EtOH vs CIE Air M430 2.0 (Jan13) Sscore **" + ], + [ + "VCU_NAc_Et_0113_R", + "VCU BXD NAc CIE EtOH M430 2.0 (Jan13) RMA **" + ], + [ + "VCU_NAc_Air_0113_R", + "VCU BXD NAc CIE Air M430 2.0 (Jan13) RMA **" + ], + [ "VCUEtOH_1007_R", "VCU BXD NA EtOH M430 2.0 (Oct07) RMA **" ], @@ -1276,49 +1522,57 @@ "BXD Published Phenotypes" ] ], - "Pituitary Gland": [ + "Pituitary Gland mRNA": [ [ "INIA_PG_RMA_0612", "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA" ], [ + "INIA_Pituitary_RMA_F_0612", + "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Females" + ], + [ + "INIA_Pituitary_RMA_M_0612", + "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Males" + ], + [ "INIA_PG_RMA_Ex_0612", "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Exon Level" ] ], - "Popliteal Lymph Node": [ + "Popliteal Lymph Node mRNA": [ [ "STJ_PLN_0912", "St Jude BXD Popliteal Lymph Node Affy HT MG-430 PM (Sep12) RMA **" ] ], - "Prefrontal Cortex": [ + "Prefrontal Cortex mRNA": [ [ "VCUSal_1206_R", "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" ], [ - "VCUSal_1006_R", - "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" - ], - [ "VCUEtOH_1206_R", "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" ], [ - "VCU_PF_Air_0111_R", - "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" + "VCUSal_1006_R", + "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + ], + [ + "VCU_PF_AvE_0111_Ss", + "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" ], [ "VCU_PF_Et_0111_R", "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **" ], [ - "VCU_PF_AvE_0111_Ss", - "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" + "VCU_PF_Air_0111_R", + "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" ] ], - "Retina": [ + "Retina mRNA": [ [ "G2NEI_ILM_Retina_BXD_RI0410", "Normal HEI Retina (April 2010) RankInv" @@ -1332,19 +1586,27 @@ "ONC HEI Retina (April 2012) RankInv" ], [ - "B6D2ONCILM_0412", - "B6D2 ONC Retina (April 2012) RankInv **" + "ONCRetMoGene2_0413", + "DoD TATRC Retina Affy MoGene 2.0 ST (Apr13) RMA **" ], [ - "HEIONCvsCRetILM6_0911", - "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **" + "ONCRetExMoGene2_0413", + "DoD TATRC Retina Affy MoGene 2.0 ST (Apr13) RMA Exon Level **" + ], + [ + "B6D2ONCILM_0412", + "B6D2 ONC Retina (April 2012) RankInv **" ], [ "G2HEIONCRetILM6_0911", "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" + ], + [ + "HEIONCvsCRetILM6_0911", + "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **" ] ], - "Spleen": [ + "Spleen mRNA": [ [ "UTHSC_SPL_RMA_1210", "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA" @@ -1358,6 +1620,10 @@ "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Females" ], [ + "UTHSC_SPL_RMAEx_1210", + "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Exon Level" + ], + [ "UTHSC_SPL_RMA_1010", "UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA" ], @@ -1374,14 +1640,14 @@ "UWA Illumina Spleen (Nov08) RSN **" ] ], - "Striatum": [ + "Striatum mRNA": [ [ - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" + "Striatum_Exon_1212", + "HQF Striatum Affy Mouse Exon 1.0ST Gene Level (Dec09) RMA" ], [ - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" + "Striatum_Exon_0209", + "HQF Striatum Affy Mouse Exon 1.0ST Exon Level (Dec09) RMA" ], [ "UTHSC_Striatum_RankInv_1210", @@ -1416,37 +1682,41 @@ "HBP Rosen Striatum M430V2 (Apr05) RMA Orig" ], [ - "Striatum_Exon_0209", - "HQF Striatum Exon (Feb09) RMA" + "DevStriatum_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" ], [ - "DevStriatum_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" + "DevStriatum_ILM6.2P14RInv_1111", + "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" ], [ "DevStriatum_ILM6.2P3RInv_1110", "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" + ], + [ + "DevStriatum_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" ] ], - "T Cell (helper)": [ + "T Cell (helper) mRNA": [ [ "RTHC_0211_R", "HZI Thelp M430v2 (Feb11) RMA" ] ], - "T Cell (regulatory)": [ + "T Cell (regulatory) mRNA": [ [ "RTC_1106_R", "HZI Treg M430v2 (Feb11) RMA" ] ], - "Thymus": [ + "Thymus mRNA": [ [ "Illum_BXD_Thy_1108", "UWA Illumina Thymus (Nov08) RSN **" ] ], - "Ventral Tegmental Area": [ + "Ventral Tegmental Area mRNA": [ [ "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **" @@ -1462,7 +1732,13 @@ ] }, "BXH": { - "Cartilage": [ + "Bone Femur mRNA": [ + [ + "UCLA_BXH_Femur_0113_RSN", + "UCLA GSE27483 BXH Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN" + ] + ], + "Cartilage mRNA": [ [ "UCLA_BXHBXD_CARTILAGE_V2", "UCLA BXH and BXD Cartilage v2" @@ -1482,7 +1758,7 @@ "BXH Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "GSE16780BXH_UCLA_ML0911", "GSE16780 UCLA Mouse BXH Liver Affy HT M430A (Sep11) RMA" @@ -1495,8 +1771,22 @@ ] ] }, + "C57BL-6JxC57BL-6NJF2": { + "Genotypes": [ + [ + "C57BL-6JxC57BL-6NJF2Geno", + "C57BL-6JxC57BL-6NJF2 Genotypes" + ] + ], + "Phenotypes": [ + [ + "C57BL-6JxC57BL-6NJF2Publish", + "C57BL-6JxC57BL-6NJF2 Published Phenotypes" + ] + ] + }, "CTB6F2": { - "Adipose": [ + "Adipose mRNA": [ [ "UCLA_CTB6B6CTF2_ADIPOSE_2005", "UCLA CTB6/B6CTF2 Adipose (2005) mlratio" @@ -1510,7 +1800,7 @@ "UCLA CTB6B6CTF2 Adipose Male mlratio **" ] ], - "Brain": [ + "Brain mRNA": [ [ "UCLA_CTB6B6CTF2_BRAIN_2005", "UCLA CTB6/B6CTF2 Brain (2005) mlratio" @@ -1530,7 +1820,7 @@ "CTB6F2 Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "UCLA_CTB6B6CTF2_LIVER_2005", "UCLA CTB6/B6CTF2 Liver (2005) mlratio" @@ -1544,7 +1834,7 @@ "UCLA CTB6B6CTF2 Liver Male mlratio **" ] ], - "Muscle": [ + "Muscle mRNA": [ [ "UCLA_CTB6B6CTF2_MUSCLE_2005", "UCLA CTB6/B6CTF2 Muscle (2005) mlratio" @@ -1572,7 +1862,7 @@ "CXB Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "HC_M2CB_1205_P", "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" @@ -1588,7 +1878,7 @@ "CXB Published Phenotypes" ] ], - "Spleen": [ + "Spleen mRNA": [ [ "STSPL_1107_R", "Stuart Spleen M430v2 (Nov07) RMA" @@ -1602,19 +1892,19 @@ "HS Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "OXUKHS_ILMHipp_RI0510", "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" ] ], - "Liver": [ + "Liver mRNA": [ [ "OXUKHS_ILMLiver_RI0510", "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" ] ], - "Lung": [ + "Lung mRNA": [ [ "OXUKHS_ILMLung_RI0510", "OX UK HS ILM6v1.1 Lung (May 2010) RankInv" @@ -1640,7 +1930,7 @@ "HS-CC Published Phenotypes" ] ], - "Striatum": [ + "Striatum mRNA": [ [ "OHSU_HS-CC_ILMStr_0211", "OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv" @@ -1654,7 +1944,7 @@ "LXS Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "Illum_LXS_Hipp_loess0807", "Hippocampus Illumina (Aug07) LOESS" @@ -1684,10 +1974,6 @@ "Hippocampus Illumina (May07) RankInv" ], [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" - ], - [ "Illum_LXS_Hipp_NOE_1008", "Hippocampus Illumina NOE (Oct08) RankInv beta" ], @@ -1702,6 +1988,10 @@ [ "Illum_LXS_Hipp_NON_1008", "Hippocampus Illumina NON (Oct08) RankInv beta" + ], + [ + "Illum_LXS_Hipp_RSE_1008", + "Hippocampus Illumina RSE (Oct08) RankInv beta" ] ], "Phenotypes": [ @@ -1710,7 +2000,7 @@ "LXS Published Phenotypes" ] ], - "Prefrontal Cortex": [ + "Prefrontal Cortex mRNA": [ [ "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" @@ -1726,13 +2016,25 @@ ] }, "MDP": { + "Bone Femur mRNA": [ + [ + "UCLA_MDP_Femur_0113_RSN", + "UCLA GSE27483 MDP Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN" + ] + ], + "Dorsal Root Ganglia mRNA": [ + [ + "TSRI-DRG-AffyMOE430_0113-MDP", + "TSRI DRG Affy Mouse Genome 430 2.0 (Jan13) RMA MDP **" + ] + ], "Genotypes": [ [ "MDPGeno", "MDP Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "HC_M2_0606_MDP", "Hippocampus Consortium M430v2 (Jun06) RMA MDP" @@ -1742,7 +2044,7 @@ "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" ] ], - "Liver": [ + "Liver mRNA": [ [ "GSE16780MDP_UCLA_ML0911", "GSE16780 UCLA Mouse MDP Liver Affy HT M430A (Sep11) RMA" @@ -1758,6 +2060,10 @@ [ "JAX_CSB_L_6C_0711", "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" + ], + [ + "JAX_liver_agil_MDP-0113", + "Harrill-Rusyn MDP Liver Acetaminophen Tox Study (G4121A, 2009)" ] ], "Phenotypes": [ @@ -1774,7 +2080,7 @@ "NZBXFVB-N2 Genotypes" ] ], - "Mammary Tumors": [ + "Mammary Tumors mRNA": [ [ "NCI_Mam_Tum_RMA_0409", "NCI Mammary M430v2 (Apr09) RMA" @@ -1786,11 +2092,63 @@ "NZBXFVB-N2 Published Phenotypes" ] ] + }, + "SOTNOT-OHSU": { + "Genotypes": [ + [ + "SOTNOT-OHSUGeno", + "SOTNOT-OHSU Genotypes" + ] + ], + "Phenotypes": [ + [ + "SOTNOT-OHSUPublish", + "SOTNOT-OHSU Published Phenotypes" + ] + ] + }, + "Scripps-2013": { + "Anterior Cingulate Cortex mRNA": [ + [ + "ScrBXDACC4G0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Gene Level **" + ], + [ + "ScrBXDACC4GEx0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Exon Level **" + ] + ], + "Genotypes": [ + [ + "Scripps-2013Geno", + "Scripps-2013 Genotypes" + ] + ], + "Phenotypes": [ + [ + "Scripps-2013Publish", + "Scripps-2013 Published Phenotypes" + ] + ] } }, "rat": { + "HSNIH": { + "Genotypes": [ + [ + "HSNIHGeno", + "HSNIH Genotypes" + ] + ], + "Phenotypes": [ + [ + "HSNIHPublish", + "HSNIH Published Phenotypes" + ] + ] + }, "HXBBXH": { - "Adrenal Gland": [ + "Adrenal Gland mRNA": [ [ "HXB_Adrenal_1208", "MDC/CAS/UCL Adrenal 230A (Dec08) RMA" @@ -1802,19 +2160,19 @@ "HXBBXH Genotypes" ] ], - "Heart": [ + "Heart mRNA": [ [ "HXB_Heart_1208", "MDC/CAS/UCL Heart 230_V2 (Dec08) RMA" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "UT_HippRatEx_RMA_0709", "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" ] ], - "Kidney": [ + "Kidney mRNA": [ [ "KI_2A_0405_M", "MDC/CAS/ICL Kidney 230A (Apr05) MAS5" @@ -1828,13 +2186,13 @@ "MDC/CAS/ICL Kidney 230A (Apr05) RMA" ] ], - "Liver": [ + "Liver mRNA": [ [ "HXB_Liver_1208", "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" ] ], - "Peritoneal Fat": [ + "Peritoneal Fat mRNA": [ [ "FT_2A_0805_M", "MDC/CAS/ICL Peritoneal Fat 230A (Aug05) MAS5" @@ -1852,7 +2210,7 @@ ] }, "SRxSHRSPF2": { - "Eye": [ + "Eye mRNA": [ [ "UIOWA_Eye_RMA_0906", "UIOWA Eye mRNA RAE230v2 (Sep06) RMA" @@ -1972,6 +2330,10 @@ "Human Liver Cohort (Merck)" ], [ + "HLT", + "Human Lung Transcriptome (Rosetta/Merck)" + ], + [ "HSB", "Human Brain Transcriptome (Yale/Kavli)" ] @@ -2032,6 +2394,10 @@ "BXH" ], [ + "C57BL-6JxC57BL-6NJF2", + "C57BL/6JxC57BL/6NJ F2 Cross" + ], + [ "CTB6F2", "CastB6/B6Cast F2 UCLA" ], @@ -2058,10 +2424,22 @@ [ "NZBXFVB-N2", "NZB/FVB N2 NCI" + ], + [ + "Scripps-2013", + "Scripps C57BL/6J" + ], + [ + "SOTNOT-OHSU", + "SOTNOT-OHSU" ] ], "rat": [ [ + "HSNIH", + "NIH Heterogeneous Stock" + ], + [ "HXBBXH", "HXB/BXH" ], @@ -2177,7 +2555,7 @@ "Genotypes" ], [ - "Leaf", + "Leaf mRNA", "Leaf mRNA" ] ], @@ -2191,11 +2569,11 @@ "Genotypes" ], [ - "Embryo", + "Embryo mRNA", "Embryo mRNA" ], [ - "Leaf", + "Leaf mRNA", "Leaf mRNA" ] ] @@ -2211,7 +2589,7 @@ "Genotypes" ], [ - "Whole Body", + "Whole Body mRNA", "Whole Body mRNA" ] ], @@ -2225,7 +2603,7 @@ "Genotypes" ], [ - "Whole Body", + "Whole Body mRNA", "Whole Body mRNA" ] ] @@ -2241,7 +2619,7 @@ "Genotypes" ], [ - "Brain", + "Brain mRNA", "Brain mRNA" ] ], @@ -2255,7 +2633,7 @@ "Genotypes" ], [ - "Brain", + "Brain mRNA", "Brain mRNA" ] ], @@ -2269,7 +2647,11 @@ "Genotypes" ], [ - "Newborn Cord Blood", + "Methylation", + "Methylation" + ], + [ + "Newborn Cord Blood mRNA", "Newborn Cord Blood mRNA" ] ], @@ -2283,7 +2665,7 @@ "Genotypes" ], [ - "Lymphoblast B-cell", + "Lymphoblast B-cell mRNA", "Lymphoblast B-cell mRNA" ] ], @@ -2297,15 +2679,15 @@ "Genotypes" ], [ - "Cerebellum", + "Cerebellum mRNA", "Cerebellum mRNA" ], [ - "Prefrontal Cortex", + "Prefrontal Cortex mRNA", "Prefrontal Cortex mRNA" ], [ - "Primary Visual Cortex", + "Primary Visual Cortex mRNA", "Primary Visual Cortex mRNA" ] ], @@ -2319,10 +2701,24 @@ "Genotypes" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ] ], + "HLT": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Lung mRNA", + "Lung mRNA" + ] + ], "HSB": [ [ "Phenotypes", @@ -2333,67 +2729,67 @@ "Genotypes" ], [ - "Amygdala", + "Amygdala mRNA", "Amygdala mRNA" ], [ - "Cerebellar Cortex", + "Cerebellar Cortex mRNA", "Cerebellar Cortex mRNA" ], [ - "Dorsolateral Prefrontal Cortex", + "Dorsolateral Prefrontal Cortex mRNA", "Dorsolateral Prefrontal Cortex mRNA" ], [ - "Hippocampus", + "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Inferior Temporal Cortex", + "Inferior Temporal Cortex mRNA", "Inferior Temporal Cortex mRNA" ], [ - "Medial Prefrontal Cortex", + "Medial Prefrontal Cortex mRNA", "Medial Prefrontal Cortex mRNA" ], [ - "Mediodorsal Nucleus of Thalamus", + "Mediodorsal Nucleus of Thalamus mRNA", "Mediodorsal Nucleus of Thalamus mRNA" ], [ - "Orbital Prefrontal Cortex", + "Orbital Prefrontal Cortex mRNA", "Orbital Prefrontal Cortex mRNA" ], [ - "Posterior Inferior Parietal Cortex", + "Posterior Inferior Parietal Cortex mRNA", "Posterior Inferior Parietal Cortex mRNA" ], [ - "Posterior Superior Temporal Cortex", + "Posterior Superior Temporal Cortex mRNA", "Posterior Superior Temporal Cortex mRNA" ], [ - "Primary Auditory (A1) Cortex", + "Primary Auditory (A1) Cortex mRNA", "Primary Auditory (A1) Cortex mRNA" ], [ - "Primary Motor (M1) Cortex", + "Primary Motor (M1) Cortex mRNA", "Primary Motor (M1) Cortex mRNA" ], [ - "Primary Somatosensory (S1) Cortex", + "Primary Somatosensory (S1) Cortex mRNA", "Primary Somatosensory (S1) Cortex mRNA" ], [ - "Primary Visual Cortex", + "Primary Visual Cortex mRNA", "Primary Visual Cortex mRNA" ], [ - "Striatum", + "Striatum mRNA", "Striatum mRNA" ], [ - "Ventrolateral Prefrontal Cortex", + "Ventrolateral Prefrontal Cortex mRNA", "Ventrolateral Prefrontal Cortex mRNA" ] ] @@ -2409,23 +2805,23 @@ "Genotypes" ], [ - "Amygdala", + "Amygdala mRNA", "Amygdala mRNA" ], [ - "Brain", + "Brain mRNA", "Brain mRNA" ], [ - "Hippocampus", + "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Nucleus Accumbens", + "Nucleus Accumbens mRNA", "Nucleus Accumbens mRNA" ], [ - "Prefrontal Cortex", + "Prefrontal Cortex mRNA", "Prefrontal Cortex mRNA" ] ] @@ -2441,7 +2837,7 @@ "Genotypes" ], [ - "Mammary Tumors", + "Mammary Tumors mRNA", "Mammary Tumors mRNA" ] ], @@ -2455,11 +2851,19 @@ "Genotypes" ], [ - "Eye", + "Bone Femur mRNA", + "Bone Femur mRNA" + ], + [ + "Eye mRNA", "Eye mRNA" ], [ - "Liver", + "Heart mRNA", + "Heart mRNA" + ], + [ + "Liver mRNA", "Liver mRNA" ] ], @@ -2473,7 +2877,7 @@ "Genotypes" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ] ], @@ -2487,7 +2891,7 @@ "Genotypes" ], [ - "Brain", + "Brain mRNA", "Brain mRNA" ] ], @@ -2501,7 +2905,7 @@ "Genotypes" ], [ - "Muscle", + "Muscle mRNA", "Muscle mRNA" ] ], @@ -2515,7 +2919,7 @@ "Genotypes" ], [ - "Hippocampus", + "Hippocampus mRNA", "Hippocampus mRNA" ] ], @@ -2529,7 +2933,7 @@ "Genotypes" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ] ], @@ -2543,7 +2947,7 @@ "Genotypes" ], [ - "Striatum", + "Striatum mRNA", "Striatum mRNA" ] ], @@ -2557,19 +2961,19 @@ "Genotypes" ], [ - "Adipose", + "Adipose mRNA", "Adipose mRNA" ], [ - "Brain", + "Brain mRNA", "Brain mRNA" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ], [ - "Muscle", + "Muscle mRNA", "Muscle mRNA" ] ], @@ -2583,19 +2987,19 @@ "Genotypes" ], [ - "Adipose", + "Adipose mRNA", "Adipose mRNA" ], [ - "Brain", + "Brain mRNA", "Brain mRNA" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ], [ - "Muscle", + "Muscle mRNA", "Muscle mRNA" ] ], @@ -2609,111 +3013,119 @@ "Genotypes" ], [ - "Adrenal Gland", + "Adrenal Gland mRNA", "Adrenal Gland mRNA" ], [ - "Amygdala", + "Amygdala mRNA", "Amygdala mRNA" ], [ - "Brain", + "Bone Femur mRNA", + "Bone Femur mRNA" + ], + [ + "Brain mRNA", "Brain mRNA" ], [ - "Cartilage", + "Cartilage mRNA", "Cartilage mRNA" ], [ - "Cerebellum", + "Cerebellum mRNA", "Cerebellum mRNA" ], [ - "Eye", + "Eye mRNA", "Eye mRNA" ], [ - "Hematopoietic Cells", + "Hematopoietic Cells mRNA", "Hematopoietic Cells mRNA" ], [ - "Hippocampus", + "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Hypothalamus", + "Hypothalamus mRNA", "Hypothalamus mRNA" ], [ - "Kidney", + "Kidney mRNA", "Kidney mRNA" ], [ - "Leucocytes", + "Leucocytes mRNA", "Leucocytes mRNA" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ], [ - "Lung", + "Liver Proteome", + "Liver Proteome" + ], + [ + "Lung mRNA", "Lung mRNA" ], [ - "Midbrain", + "Midbrain mRNA", "Midbrain mRNA" ], [ - "Muscle", + "Muscle mRNA", "Muscle mRNA" ], [ - "Neocortex", + "Neocortex mRNA", "Neocortex mRNA" ], [ - "Nucleus Accumbens", + "Nucleus Accumbens mRNA", "Nucleus Accumbens mRNA" ], [ - "Pituitary Gland", + "Pituitary Gland mRNA", "Pituitary Gland mRNA" ], [ - "Popliteal Lymph Node", + "Popliteal Lymph Node mRNA", "Popliteal Lymph Node mRNA" ], [ - "Prefrontal Cortex", + "Prefrontal Cortex mRNA", "Prefrontal Cortex mRNA" ], [ - "Retina", + "Retina mRNA", "Retina mRNA" ], [ - "Spleen", + "Spleen mRNA", "Spleen mRNA" ], [ - "Striatum", + "Striatum mRNA", "Striatum mRNA" ], [ - "T Cell (helper)", + "T Cell (helper) mRNA", "T Cell (helper) mRNA" ], [ - "T Cell (regulatory)", + "T Cell (regulatory) mRNA", "T Cell (regulatory) mRNA" ], [ - "Thymus", + "Thymus mRNA", "Thymus mRNA" ], [ - "Ventral Tegmental Area", + "Ventral Tegmental Area mRNA", "Ventral Tegmental Area mRNA" ] ], @@ -2727,14 +3139,28 @@ "Genotypes" ], [ - "Cartilage", + "Bone Femur mRNA", + "Bone Femur mRNA" + ], + [ + "Cartilage mRNA", "Cartilage mRNA" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ] ], + "C57BL-6JxC57BL-6NJF2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "CTB6F2": [ [ "Phenotypes", @@ -2745,19 +3171,19 @@ "Genotypes" ], [ - "Adipose", + "Adipose mRNA", "Adipose mRNA" ], [ - "Brain", + "Brain mRNA", "Brain mRNA" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ], [ - "Muscle", + "Muscle mRNA", "Muscle mRNA" ] ], @@ -2771,11 +3197,11 @@ "Genotypes" ], [ - "Hippocampus", + "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Spleen", + "Spleen mRNA", "Spleen mRNA" ] ], @@ -2789,15 +3215,15 @@ "Genotypes" ], [ - "Hippocampus", + "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ], [ - "Lung", + "Lung mRNA", "Lung mRNA" ] ], @@ -2811,7 +3237,7 @@ "Genotypes" ], [ - "Striatum", + "Striatum mRNA", "Striatum mRNA" ] ], @@ -2825,11 +3251,11 @@ "Genotypes" ], [ - "Hippocampus", + "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Prefrontal Cortex", + "Prefrontal Cortex mRNA", "Prefrontal Cortex mRNA" ] ], @@ -2843,11 +3269,19 @@ "Genotypes" ], [ - "Hippocampus", + "Bone Femur mRNA", + "Bone Femur mRNA" + ], + [ + "Dorsal Root Ganglia mRNA", + "Dorsal Root Ganglia mRNA" + ], + [ + "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ] ], @@ -2861,12 +3295,46 @@ "Genotypes" ], [ - "Mammary Tumors", + "Mammary Tumors mRNA", "Mammary Tumors mRNA" ] + ], + "SOTNOT-OHSU": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], + "Scripps-2013": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA" + ] ] }, "rat": { + "HSNIH": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "HXBBXH": [ [ "Phenotypes", @@ -2877,27 +3345,27 @@ "Genotypes" ], [ - "Adrenal Gland", + "Adrenal Gland mRNA", "Adrenal Gland mRNA" ], [ - "Heart", + "Heart mRNA", "Heart mRNA" ], [ - "Hippocampus", + "Hippocampus mRNA", "Hippocampus mRNA" ], [ - "Kidney", + "Kidney mRNA", "Kidney mRNA" ], [ - "Liver", + "Liver mRNA", "Liver mRNA" ], [ - "Peritoneal Fat", + "Peritoneal Fat mRNA", "Peritoneal Fat mRNA" ] ], @@ -2911,7 +3379,7 @@ "Genotypes" ], [ - "Eye", + "Eye mRNA", "Eye mRNA" ] ] diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js index 34fa7503..5c5b433a 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.4.0 +// Generated by CoffeeScript 1.6.1 (function() { $(function() { diff --git a/wqflask/wqflask/static/new/javascript/login.coffee b/wqflask/wqflask/static/new/javascript/login.coffee index c49353d5..15dafd9a 100644 --- a/wqflask/wqflask/static/new/javascript/login.coffee +++ b/wqflask/wqflask/static/new/javascript/login.coffee @@ -13,8 +13,8 @@ $ -> - - $(document).on("click", ".modalize", modalize) + $(document).one("click", ".modalize", modalize) + console.log("Modalized click!!!") form_success = (data) -> $.colorbox( @@ -39,4 +39,4 @@ $ -> ) - $("form").on("submit", submit_form) + $("#colorbox form").on("submit", submit_form) diff --git a/wqflask/wqflask/static/new/javascript/login.js b/wqflask/wqflask/static/new/javascript/login.js index 6c6120ec..f6fd1b2e 100644 --- a/wqflask/wqflask/static/new/javascript/login.js +++ b/wqflask/wqflask/static/new/javascript/login.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.4.0 +// Generated by CoffeeScript 1.6.1 (function() { $(function() { @@ -14,7 +14,8 @@ } }); }; - $(document).on("click", ".modalize", modalize); + $(document).one("click", ".modalize", modalize); + console.log("Modalized click!!!"); form_success = function(data) { return $.colorbox({ open: true, @@ -38,7 +39,7 @@ success: form_success }); }; - return $("form").on("submit", submit_form); + return $("#colorbox form").on("submit", submit_form); }); }).call(this); diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee index 2f8da6dc..2892987e 100644 --- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee +++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee @@ -15,6 +15,7 @@ $ -> console.time('Create coordinates') @create_coordinates() console.log("@x_coords: ", @x_coords) + console.log("@y_coords: ", @y_coords) console.timeEnd('Create coordinates') [@chr_lengths, @cumulative_chr_lengths] = @get_chr_lengths() @@ -24,6 +25,8 @@ $ -> #@x_max = d3.max(@x_coords) @x_max = @total_length + console.log("@x_max: ", @x_max) + console.log("@x_buffer: ", @x_buffer) @y_max = d3.max(@y_coords) * 1.2 @svg = @create_svg() @@ -52,6 +55,8 @@ $ -> ### + console.log("@chromosomes: ", @chromosomes) + cumulative_chr_lengths = [] chr_lengths = [] total_length = 0 @@ -60,8 +65,8 @@ $ -> chr_lengths.push(this_length) cumulative_chr_lengths.push(total_length + this_length) total_length += this_length - - #console.log("total length is:", total_length) + + console.log("chr_lengths: ", chr_lengths) return [chr_lengths, cumulative_chr_lengths] @@ -69,16 +74,20 @@ $ -> chr_lengths = [] chr_seen = [] for result in js_data.qtl_results - chr_length = @chromosomes[result.chr] + if result.chr == "X" + chr_length = parseFloat(@chromosomes[20]) + else + chr_length = parseFloat(@chromosomes[result.chr]) if not(result.chr in chr_seen) chr_seen.push(result.chr) chr_lengths.push(chr_length) if result.chr != "1" - @total_length += chr_lengths[chr_lengths.length - 2] + @total_length += parseFloat(chr_lengths[chr_lengths.length - 2]) @x_coords.push(@total_length + parseFloat(result.Mb)) @y_coords.push(result.lod_score) @marker_names.push(result.name) - @total_length += chr_lengths[chr_lengths.length-1] + @total_length += parseFloat(chr_lengths[chr_lengths.length-1]) + #console.log("chr_lengths: ", chr_lengths) show_marker_in_table: (marker_info) -> console.log("in show_marker_in_table") @@ -270,7 +279,7 @@ $ -> .enter() .append("circle") .attr("cx", (d) => - return @x_buffer + ((@plot_width-@x_buffer) * d[0]/@x_max) + return parseFloat(@x_buffer) + ((parseFloat(@plot_width)-parseFloat(@x_buffer)) * d[0]/parseFloat(@x_max)) ) .attr("cy", (d) => return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max) diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js index 50578125..ffcf1a75 100644 --- a/wqflask/wqflask/static/new/javascript/marker_regression.js +++ b/wqflask/wqflask/static/new/javascript/marker_regression.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.4.0 +// Generated by CoffeeScript 1.6.1 (function() { var __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }; @@ -21,11 +21,14 @@ console.time('Create coordinates'); this.create_coordinates(); console.log("@x_coords: ", this.x_coords); + console.log("@y_coords: ", this.y_coords); console.timeEnd('Create coordinates'); _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1]; this.x_buffer = this.plot_width / 30; this.y_buffer = this.plot_height / 20; this.x_max = this.total_length; + console.log("@x_max: ", this.x_max); + console.log("@x_buffer: ", this.x_buffer); this.y_max = d3.max(this.y_coords) * 1.2; this.svg = this.create_svg(); this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names); @@ -54,12 +57,13 @@ Manhattan_Plot.prototype.get_chr_lengths = function() { /* - Gets a list of both individual and cumulative (the position of one on the graph - is its own length plus the lengths of all preceding chromosomes) lengths in order - to draw the vertical lines separating chromosomes and the chromosome labels + Gets a list of both individual and cumulative (the position of one on the graph + is its own length plus the lengths of all preceding chromosomes) lengths in order + to draw the vertical lines separating chromosomes and the chromosome labels */ var chr_lengths, cumulative_chr_lengths, key, this_length, total_length; + console.log("@chromosomes: ", this.chromosomes); cumulative_chr_lengths = []; chr_lengths = []; total_length = 0; @@ -69,6 +73,7 @@ cumulative_chr_lengths.push(total_length + this_length); total_length += this_length; } + console.log("chr_lengths: ", chr_lengths); return [chr_lengths, cumulative_chr_lengths]; }; @@ -79,19 +84,23 @@ _ref = js_data.qtl_results; for (_i = 0, _len = _ref.length; _i < _len; _i++) { result = _ref[_i]; - chr_length = this.chromosomes[result.chr]; + if (result.chr === "X") { + chr_length = parseFloat(this.chromosomes[20]); + } else { + chr_length = parseFloat(this.chromosomes[result.chr]); + } if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) { chr_seen.push(result.chr); chr_lengths.push(chr_length); if (result.chr !== "1") { - this.total_length += chr_lengths[chr_lengths.length - 2]; + this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]); } } this.x_coords.push(this.total_length + parseFloat(result.Mb)); this.y_coords.push(result.lod_score); this.marker_names.push(result.name); } - return this.total_length += chr_lengths[chr_lengths.length - 1]; + return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]); }; Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) { @@ -247,7 +256,7 @@ Manhattan_Plot.prototype.add_plot_points = function() { var _this = this; return this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) { - return _this.x_buffer + ((_this.plot_width - _this.x_buffer) * d[0] / _this.x_max); + return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max)); }).attr("cy", function(d) { return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max); }).attr("r", 2).attr("id", function(d) { diff --git a/wqflask/wqflask/static/new/javascript/marker_regression_old.js b/wqflask/wqflask/static/new/javascript/marker_regression_old.js new file mode 100644 index 00000000..5dd5b508 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/marker_regression_old.js @@ -0,0 +1,226 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + + $(function() { + var Chromosome, Manhattan_Plot, Permutation_Histogram, sort_number; + sort_number = function(a, b) { + return a - b; + }; + Permutation_Histogram = (function() { + + function Permutation_Histogram() { + this.process_data(); + this.display_graph(); + } + + Permutation_Histogram.prototype.process_data = function() { + var bars, floored, key, keys, lrs, lrs_array, _i, _j, _len, _len1; + lrs_array = js_data.lrs_array; + bars = {}; + for (_i = 0, _len = lrs_array.length; _i < _len; _i++) { + lrs = lrs_array[_i]; + floored = Math.floor(lrs); + if (!(floored in bars)) { + bars[floored] = 0; + } + bars[floored] += 1; + } + keys = []; + for (key in bars) { + keys.push(key); + } + keys.sort(sort_number); + this.bars_ordered = []; + for (_j = 0, _len1 = keys.length; _j < _len1; _j++) { + key = keys[_j]; + this.bars_ordered.push([parseInt(key), bars[key]]); + } + console.log("bars is:", bars); + console.log("keys are:", keys); + return console.log("bars_ordered are:", this.bars_ordered); + }; + + Permutation_Histogram.prototype.display_graph = function() { + return $.jqplot('permutation_histogram', [this.bars_ordered], { + title: 'Permutation Histogram', + seriesDefaults: { + renderer: $.jqplot.BarRenderer, + rendererOptions: { + barWidth: 15 + }, + pointLabels: { + show: true + } + }, + axesDefaults: { + labelRenderer: $.jqplot.CanvasAxisLabelRenderer + }, + axes: { + xaxis: { + min: 0, + label: "LRS", + pad: 1.1 + }, + yaxis: { + min: 0, + label: "Frequency" + } + } + }); + }; + + return Permutation_Histogram; + + })(); + Chromosome = (function() { + + function Chromosome(name) { + this.name = name; + this.max_mb = 0; + this.plot_points = []; + } + + Chromosome.prototype.process_point = function(mb, lrs) { + if (mb > this.max_mb) { + this.max_mb = mb; + } + return this.plot_points.push([mb, lrs]); + }; + + Chromosome.prototype.display_graph = function(max_lrs) { + var div_name, plot_options, x_axis_max, x_axis_ticks, x_tick; + div_name = 'manhattan_plot_' + this.name; + console.log("div_name:", div_name); + x_axis_max = Math.ceil(this.max_mb / 25) * 25; + x_axis_ticks = []; + x_tick = 0; + while (x_tick <= x_axis_max) { + x_axis_ticks.push(x_tick); + x_tick += 25; + } + plot_options = { + title: this.name, + seriesDefaults: { + showLine: false, + markerRenderer: $.jqplot.MarkerRenderer, + markerOptions: { + style: "filledCircle", + size: 3 + } + }, + axesDefaults: { + tickRenderer: $.jqplot.CanvasAxisTickRenderer, + labelRenderer: $.jqplot.CanvasAxisLabelRenderer + }, + axes: { + xaxis: { + min: 0, + max: x_axis_max, + ticks: x_axis_ticks, + tickOptions: { + angle: 90, + showGridline: false, + formatString: '%d' + }, + label: "Megabases" + } + } + }; + if (this.name === "1") { + plot_options.axes.yaxis = { + min: 0, + max: Math.floor(max_lrs + 0.1 * max_lrs), + tickInterval: 1, + label: "LRS", + tickOptions: { + formatString: '%d', + showGridline: false + } + }; + } else { + plot_options.axes.yaxis = { + show: false, + min: 0, + max: Math.floor(max_lrs + 0.1 * max_lrs), + tickInterval: 1, + tickOptions: { + formatString: '%d', + showGridline: false + } + }; + } + return $.jqplot(div_name, [this.plot_points], plot_options); + }; + + return Chromosome; + + })(); + Manhattan_Plot = (function() { + + function Manhattan_Plot() { + this.max_lrs = 0; + this.chromosomes = {}; + this.build_chromosomes(); + this.display_graphs(); + } + + Manhattan_Plot.prototype.build_chromosomes = function() { + var chromosome, mb, result, _i, _len, _ref, _results; + _ref = js_data.qtl_results; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + result = _ref[_i]; + chromosome = result.locus.chromosome; + if (!(chromosome in this.chromosomes)) { + this.chromosomes[chromosome] = new Chromosome(chromosome); + } + mb = parseInt(result.locus.mb); + if (result.lrs > this.max_lrs) { + this.max_lrs = result.lrs; + } + _results.push(this.chromosomes[chromosome].process_point(mb, result.lrs)); + } + return _results; + }; + + Manhattan_Plot.prototype.display_graphs = function() { + /* Call display_graph for each chromosome + */ + + var extra_keys, html, key, keys, numbered_keys, this_class, _i, _len; + numbered_keys = []; + extra_keys = []; + for (key in this.chromosomes) { + if (isNaN(key)) { + extra_keys.push(key); + } else { + numbered_keys.push(key); + } + } + numbered_keys.sort(sort_number); + extra_keys.sort(); + keys = numbered_keys.concat(extra_keys); + console.log("keys are:", keys); + for (_i = 0, _len = keys.length; _i < _len; _i++) { + key = keys[_i]; + this_class = "manhattan_plot_segment"; + if (key !== "1") { + this_class += " no_y_axis"; + } + html = "<div id=\"manhattan_plot_" + key + "\" class=" + this_class + "></div>"; + console.log("html is:", html); + $("#manhattan_plots").append(html); + this.chromosomes[key].display_graph(this.max_lrs); + } + $('.jqplot-yaxis').hide(); + return $('#manhattan_plot_1').find('.jqplot-yaxis').show(); + }; + + return Manhattan_Plot; + + })(); + new Permutation_Histogram; + return new Manhattan_Plot; + }); + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/.bin/cake b/wqflask/wqflask/static/new/javascript/node_modules/.bin/cake new file mode 120000 index 00000000..d95f32af --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/.bin/cake @@ -0,0 +1 @@ +../coffee-script/bin/cake
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/node_modules/.bin/coffee b/wqflask/wqflask/static/new/javascript/node_modules/.bin/coffee new file mode 120000 index 00000000..b57f275d --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/.bin/coffee @@ -0,0 +1 @@ +../coffee-script/bin/coffee
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/.npmignore b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/.npmignore new file mode 100644 index 00000000..21e430d2 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/.npmignore @@ -0,0 +1,11 @@ +*.coffee +*.html +.DS_Store +.git* +Cakefile +documentation/ +examples/ +extras/coffee-script.js +raw/ +src/ +test/ diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CNAME b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CNAME new file mode 100644 index 00000000..faadabe5 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CNAME @@ -0,0 +1 @@ +coffeescript.org
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CONTRIBUTING.md b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CONTRIBUTING.md new file mode 100644 index 00000000..6390c68b --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CONTRIBUTING.md @@ -0,0 +1,9 @@ +## How to contribute to CoffeeScript + +* Before you open a ticket or send a pull request, [search](https://github.com/jashkenas/coffee-script/issues) for previous discussions about the same feature or issue. Add to the earlier ticket if you find one. + +* Before sending a pull request for a feature, be sure to have [tests](https://github.com/jashkenas/coffee-script/tree/master/test). + +* Use the same coding style as the rest of the [codebase](https://github.com/jashkenas/coffee-script/tree/master/src). If you're just getting started with CoffeeScript, there's a nice [style guide](https://github.com/polarmobile/coffeescript-style-guide). + +* In your pull request, do not add documentation to `index.html` or re-build the minified `coffee-script.js` file. We'll do those things before cutting a new release.
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/LICENSE b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/LICENSE new file mode 100644 index 00000000..dbe6b4e3 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/LICENSE @@ -0,0 +1,22 @@ +Copyright (c) 2009-2012 Jeremy Ashkenas + +Permission is hereby granted, free of charge, to any person +obtaining a copy of this software and associated documentation +files (the "Software"), to deal in the Software without +restriction, including without limitation the rights to use, +copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the +Software is furnished to do so, subject to the following +conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR +OTHER DEALINGS IN THE SOFTWARE.
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/README b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/README new file mode 100644 index 00000000..69ee6f43 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/README @@ -0,0 +1,51 @@ + + { + } } { + { { } } + } }{ { + { }{ } } _____ __ __ + ( }{ }{ { ) / ____| / _|/ _| + .- { { } { }} -. | | ___ | |_| |_ ___ ___ + ( ( } { } { } } ) | | / _ \| _| _/ _ \/ _ \ + |`-..________ ..-'| | |___| (_) | | | || __/ __/ + | | \_____\___/|_| |_| \___|\___| + | ;--. + | (__ \ _____ _ _ + | | ) ) / ____| (_) | | + | |/ / | (___ ___ _ __ _ _ __ | |_ + | ( / \___ \ / __| '__| | '_ \| __| + | |/ ____) | (__| | | | |_) | |_ + | | |_____/ \___|_| |_| .__/ \__| + `-.._________..-' | | + |_| + + + CoffeeScript is a little language that compiles into JavaScript. + + Install Node.js, and then the CoffeeScript compiler: + sudo bin/cake install + + Or, if you have the Node Package Manager installed: + npm install -g coffee-script + (Leave off the -g if you don't wish to install globally.) + + Execute a script: + coffee /path/to/script.coffee + + Compile a script: + coffee -c /path/to/script.coffee + + For documentation, usage, and examples, see: + http://coffeescript.org/ + + To suggest a feature, report a bug, or general discussion: + http://github.com/jashkenas/coffee-script/issues/ + + If you'd like to chat, drop by #coffeescript on Freenode IRC, + or on webchat.freenode.net. + + The source repository: + git://github.com/jashkenas/coffee-script.git + + All contributors are listed here: + http://github.com/jashkenas/coffee-script/contributors diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/Rakefile b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/Rakefile new file mode 100644 index 00000000..d90cce36 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/Rakefile @@ -0,0 +1,79 @@ +require 'rubygems' +require 'erb' +require 'fileutils' +require 'rake/testtask' +require 'json' + +desc "Build the documentation page" +task :doc do + source = 'documentation/index.html.erb' + child = fork { exec "bin/coffee -bcw -o documentation/js documentation/coffee/*.coffee" } + at_exit { Process.kill("INT", child) } + Signal.trap("INT") { exit } + loop do + mtime = File.stat(source).mtime + if !@mtime || mtime > @mtime + rendered = ERB.new(File.read(source)).result(binding) + File.open('index.html', 'w+') {|f| f.write(rendered) } + end + @mtime = mtime + sleep 1 + end +end + +desc "Build coffee-script-source gem" +task :gem do + require 'rubygems' + require 'rubygems/package' + + gemspec = Gem::Specification.new do |s| + s.name = 'coffee-script-source' + s.version = JSON.parse(File.read('package.json'))["version"] + s.date = Time.now.strftime("%Y-%m-%d") + + s.homepage = "http://jashkenas.github.com/coffee-script/" + s.summary = "The CoffeeScript Compiler" + s.description = <<-EOS + CoffeeScript is a little language that compiles into JavaScript. + Underneath all of those embarrassing braces and semicolons, + JavaScript has always had a gorgeous object model at its heart. + CoffeeScript is an attempt to expose the good parts of JavaScript + in a simple way. + EOS + + s.files = [ + 'lib/coffee_script/coffee-script.js', + 'lib/coffee_script/source.rb' + ] + + s.authors = ['Jeremy Ashkenas'] + s.email = 'jashkenas@gmail.com' + s.rubyforge_project = 'coffee-script-source' + s.license = "MIT" + end + + file = File.open("coffee-script-source.gem", "w") + Gem::Package.open(file, 'w') do |pkg| + pkg.metadata = gemspec.to_yaml + + path = "lib/coffee_script/source.rb" + contents = <<-ERUBY +module CoffeeScript + module Source + def self.bundled_path + File.expand_path("../coffee-script.js", __FILE__) + end + end +end + ERUBY + pkg.add_file_simple(path, 0644, contents.size) do |tar_io| + tar_io.write(contents) + end + + contents = File.read("extras/coffee-script.js") + path = "lib/coffee_script/coffee-script.js" + pkg.add_file_simple(path, 0644, contents.size) do |tar_io| + tar_io.write(contents) + end + end +end diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/cake b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/cake new file mode 100755 index 00000000..5965f4ee --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/cake @@ -0,0 +1,7 @@ +#!/usr/bin/env node + +var path = require('path'); +var fs = require('fs'); +var lib = path.join(path.dirname(fs.realpathSync(__filename)), '../lib'); + +require(lib + '/coffee-script/cake').run(); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/coffee b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/coffee new file mode 100755 index 00000000..3d1d71c8 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/coffee @@ -0,0 +1,7 @@ +#!/usr/bin/env node + +var path = require('path'); +var fs = require('fs'); +var lib = path.join(path.dirname(fs.realpathSync(__filename)), '../lib'); + +require(lib + '/coffee-script/command').run(); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/extras/jsl.conf b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/extras/jsl.conf new file mode 100644 index 00000000..1190da52 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/extras/jsl.conf @@ -0,0 +1,44 @@ +# JavaScriptLint configuration file for CoffeeScript. + ++no_return_value # function {0} does not always return a value ++duplicate_formal # duplicate formal argument {0} +-equal_as_assign # test for equality (==) mistyped as assignment (=)?{0} ++var_hides_arg # variable {0} hides argument ++redeclared_var # redeclaration of {0} {1} +-anon_no_return_value # anonymous function does not always return a value ++missing_semicolon # missing semicolon ++meaningless_block # meaningless block; curly braces have no impact +-comma_separated_stmts # multiple statements separated by commas (use semicolons?) ++unreachable_code # unreachable code ++missing_break # missing break statement +-missing_break_for_last_case # missing break statement for last case in switch +-comparison_type_conv # comparisons against null, 0, true, false, or an empty string allowing implicit type conversion (use === or !==) +-inc_dec_within_stmt # increment (++) and decrement (--) operators used as part of greater statement +-useless_void # use of the void type may be unnecessary (void is always undefined) ++multiple_plus_minus # unknown order of operations for successive plus (e.g. x+++y) or minus (e.g. x---y) signs ++use_of_label # use of label +-block_without_braces # block statement without curly braces ++leading_decimal_point # leading decimal point may indicate a number or an object member ++trailing_decimal_point # trailing decimal point may indicate a number or an object member ++octal_number # leading zeros make an octal number ++nested_comment # nested comment ++misplaced_regex # regular expressions should be preceded by a left parenthesis, assignment, colon, or comma ++ambiguous_newline # unexpected end of line; it is ambiguous whether these lines are part of the same statement ++empty_statement # empty statement or extra semicolon +-missing_option_explicit # the "option explicit" control comment is missing ++partial_option_explicit # the "option explicit" control comment, if used, must be in the first script tag ++dup_option_explicit # duplicate "option explicit" control comment ++useless_assign # useless assignment ++ambiguous_nested_stmt # block statements containing block statements should use curly braces to resolve ambiguity ++ambiguous_else_stmt # the else statement could be matched with one of multiple if statements (use curly braces to indicate intent) +-missing_default_case # missing default case in switch statement ++duplicate_case_in_switch # duplicate case in switch statements ++default_not_at_end # the default case is not at the end of the switch statement ++legacy_cc_not_understood # couldn't understand control comment using /*@keyword@*/ syntax ++jsl_cc_not_understood # couldn't understand control comment using /*jsl:keyword*/ syntax ++useless_comparison # useless comparison; comparing identical expressions ++with_statement # with statement hides undeclared variables; use temporary variable instead ++trailing_comma_in_array # extra comma is not recommended in array initializers ++assign_to_function_call # assignment to a function call ++parseint_missing_radix # parseInt missing radix parameter ++lambda_assign_requires_semicolon diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/browser.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/browser.js new file mode 100644 index 00000000..fec8e690 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/browser.js @@ -0,0 +1,101 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var CoffeeScript, runScripts, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }; + + CoffeeScript = require('./coffee-script'); + + CoffeeScript.require = require; + + CoffeeScript["eval"] = function(code, options) { + var _ref; + if (options == null) { + options = {}; + } + if ((_ref = options.bare) == null) { + options.bare = true; + } + return eval(CoffeeScript.compile(code, options)); + }; + + CoffeeScript.run = function(code, options) { + if (options == null) { + options = {}; + } + options.bare = true; + return Function(CoffeeScript.compile(code, options))(); + }; + + if (typeof window === "undefined" || window === null) { + return; + } + + CoffeeScript.load = function(url, callback, options) { + var xhr; + if (options == null) { + options = {}; + } + xhr = window.ActiveXObject ? new window.ActiveXObject('Microsoft.XMLHTTP') : new XMLHttpRequest(); + xhr.open('GET', url, true); + if ('overrideMimeType' in xhr) { + xhr.overrideMimeType('text/plain'); + } + xhr.onreadystatechange = function() { + var _ref; + if (xhr.readyState === 4) { + if ((_ref = xhr.status) === 0 || _ref === 200) { + CoffeeScript.run(xhr.responseText, options); + } else { + throw new Error("Could not load " + url); + } + if (callback) { + return callback(); + } + } + }; + return xhr.send(null); + }; + + runScripts = function() { + var coffees, coffeetypes, execute, index, length, s, scripts; + scripts = document.getElementsByTagName('script'); + coffeetypes = ['text/coffeescript', 'text/literate-coffeescript']; + coffees = (function() { + var _i, _len, _ref, _results; + _results = []; + for (_i = 0, _len = scripts.length; _i < _len; _i++) { + s = scripts[_i]; + if (_ref = s.type, __indexOf.call(coffeetypes, _ref) >= 0) { + _results.push(s); + } + } + return _results; + })(); + index = 0; + length = coffees.length; + (execute = function() { + var mediatype, options, script; + script = coffees[index++]; + mediatype = script != null ? script.type : void 0; + if (__indexOf.call(coffeetypes, mediatype) >= 0) { + options = { + literate: mediatype === 'text/literate-coffeescript' + }; + if (script.src) { + return CoffeeScript.load(script.src, execute, options); + } else { + CoffeeScript.run(script.innerHTML, options); + return execute(); + } + } + })(); + return null; + }; + + if (window.addEventListener) { + addEventListener('DOMContentLoaded', runScripts, false); + } else { + attachEvent('onload', runScripts); + } + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/cake.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/cake.js new file mode 100644 index 00000000..a0b643f6 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/cake.js @@ -0,0 +1,113 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var CoffeeScript, cakefileDirectory, existsSync, fatalError, fs, helpers, missingTask, oparse, options, optparse, path, printTasks, switches, tasks; + + fs = require('fs'); + + path = require('path'); + + helpers = require('./helpers'); + + optparse = require('./optparse'); + + CoffeeScript = require('./coffee-script'); + + existsSync = fs.existsSync || path.existsSync; + + tasks = {}; + + options = {}; + + switches = []; + + oparse = null; + + helpers.extend(global, { + task: function(name, description, action) { + var _ref; + if (!action) { + _ref = [description, action], action = _ref[0], description = _ref[1]; + } + return tasks[name] = { + name: name, + description: description, + action: action + }; + }, + option: function(letter, flag, description) { + return switches.push([letter, flag, description]); + }, + invoke: function(name) { + if (!tasks[name]) { + missingTask(name); + } + return tasks[name].action(options); + } + }); + + exports.run = function() { + var arg, args, _i, _len, _ref, _results; + global.__originalDirname = fs.realpathSync('.'); + process.chdir(cakefileDirectory(__originalDirname)); + args = process.argv.slice(2); + CoffeeScript.run(fs.readFileSync('Cakefile').toString(), { + filename: 'Cakefile' + }); + oparse = new optparse.OptionParser(switches); + if (!args.length) { + return printTasks(); + } + try { + options = oparse.parse(args); + } catch (e) { + return fatalError("" + e); + } + _ref = options["arguments"]; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + arg = _ref[_i]; + _results.push(invoke(arg)); + } + return _results; + }; + + printTasks = function() { + var cakefilePath, desc, name, relative, spaces, task; + relative = path.relative || path.resolve; + cakefilePath = path.join(relative(__originalDirname, process.cwd()), 'Cakefile'); + console.log("" + cakefilePath + " defines the following tasks:\n"); + for (name in tasks) { + task = tasks[name]; + spaces = 20 - name.length; + spaces = spaces > 0 ? Array(spaces + 1).join(' ') : ''; + desc = task.description ? "# " + task.description : ''; + console.log("cake " + name + spaces + " " + desc); + } + if (switches.length) { + return console.log(oparse.help()); + } + }; + + fatalError = function(message) { + console.error(message + '\n'); + console.log('To see a list of all tasks/options, run "cake"'); + return process.exit(1); + }; + + missingTask = function(task) { + return fatalError("No such task: " + task); + }; + + cakefileDirectory = function(dir) { + var parent; + if (existsSync(path.join(dir, 'Cakefile'))) { + return dir; + } + parent = path.normalize(path.join(dir, '..')); + if (parent !== dir) { + return cakefileDirectory(parent); + } + throw new Error("Cakefile not found in " + (process.cwd())); + }; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/coffee-script.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/coffee-script.js new file mode 100644 index 00000000..d791035d --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/coffee-script.js @@ -0,0 +1,218 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var Lexer, compile, ext, fs, helpers, lexer, loadFile, parser, path, sourcemap, vm, _i, _len, _ref, + __hasProp = {}.hasOwnProperty; + + fs = require('fs'); + + path = require('path'); + + Lexer = require('./lexer').Lexer; + + parser = require('./parser').parser; + + helpers = require('./helpers'); + + vm = require('vm'); + + sourcemap = require('./sourcemap'); + + loadFile = function(module, filename) { + var raw, stripped; + raw = fs.readFileSync(filename, 'utf8'); + stripped = raw.charCodeAt(0) === 0xFEFF ? raw.substring(1) : raw; + return module._compile(compile(stripped, { + filename: filename, + literate: helpers.isLiterate(filename) + }), filename); + }; + + if (require.extensions) { + _ref = ['.coffee', '.litcoffee', '.md', '.coffee.md']; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + ext = _ref[_i]; + require.extensions[ext] = loadFile; + } + } + + exports.VERSION = '1.6.1'; + + exports.helpers = helpers; + + exports.compile = compile = function(code, options) { + var answer, coffeeFile, currentColumn, currentLine, fragment, fragments, header, js, jsFile, merge, newLines, sourceMap, _j, _len1; + if (options == null) { + options = {}; + } + merge = exports.helpers.merge; + try { + if (options.sourceMap) { + coffeeFile = helpers.baseFileName(options.filename); + jsFile = helpers.baseFileName(options.filename, true) + ".js"; + sourceMap = new sourcemap.SourceMap(); + } + fragments = (parser.parse(lexer.tokenize(code, options))).compileToFragments(options); + currentLine = 0; + if (options.header) { + currentLine += 1; + } + if (options.sourceMap) { + currentLine += 1; + } + currentColumn = 0; + js = ""; + for (_j = 0, _len1 = fragments.length; _j < _len1; _j++) { + fragment = fragments[_j]; + if (sourceMap) { + if (fragment.locationData) { + sourceMap.addMapping([fragment.locationData.first_line, fragment.locationData.first_column], [currentLine, currentColumn], { + noReplace: true + }); + } + newLines = helpers.count(fragment.code, "\n"); + currentLine += newLines; + currentColumn = fragment.code.length - (newLines ? fragment.code.lastIndexOf("\n") : 0); + } + js += fragment.code; + } + } catch (err) { + if (options.filename) { + err.message = "In " + options.filename + ", " + err.message; + } + throw err; + } + if (options.header) { + header = "Generated by CoffeeScript " + this.VERSION; + js = "// " + header + "\n" + js; + } + if (options.sourceMap) { + answer = { + js: js + }; + if (sourceMap) { + answer.sourceMap = sourceMap; + answer.v3SourceMap = sourcemap.generateV3SourceMap(sourceMap, coffeeFile, jsFile); + } + return answer; + } else { + return js; + } + }; + + exports.tokens = function(code, options) { + return lexer.tokenize(code, options); + }; + + exports.nodes = function(source, options) { + if (typeof source === 'string') { + return parser.parse(lexer.tokenize(source, options)); + } else { + return parser.parse(source); + } + }; + + exports.run = function(code, options) { + var mainModule; + if (options == null) { + options = {}; + } + mainModule = require.main; + mainModule.filename = process.argv[1] = options.filename ? fs.realpathSync(options.filename) : '.'; + mainModule.moduleCache && (mainModule.moduleCache = {}); + mainModule.paths = require('module')._nodeModulePaths(path.dirname(fs.realpathSync(options.filename))); + if (!helpers.isCoffee(mainModule.filename) || require.extensions) { + return mainModule._compile(compile(code, options), mainModule.filename); + } else { + return mainModule._compile(code, mainModule.filename); + } + }; + + exports["eval"] = function(code, options) { + var Module, Script, js, k, o, r, sandbox, v, _j, _len1, _module, _ref1, _ref2, _require; + if (options == null) { + options = {}; + } + if (!(code = code.trim())) { + return; + } + Script = vm.Script; + if (Script) { + if (options.sandbox != null) { + if (options.sandbox instanceof Script.createContext().constructor) { + sandbox = options.sandbox; + } else { + sandbox = Script.createContext(); + _ref1 = options.sandbox; + for (k in _ref1) { + if (!__hasProp.call(_ref1, k)) continue; + v = _ref1[k]; + sandbox[k] = v; + } + } + sandbox.global = sandbox.root = sandbox.GLOBAL = sandbox; + } else { + sandbox = global; + } + sandbox.__filename = options.filename || 'eval'; + sandbox.__dirname = path.dirname(sandbox.__filename); + if (!(sandbox !== global || sandbox.module || sandbox.require)) { + Module = require('module'); + sandbox.module = _module = new Module(options.modulename || 'eval'); + sandbox.require = _require = function(path) { + return Module._load(path, _module, true); + }; + _module.filename = sandbox.__filename; + _ref2 = Object.getOwnPropertyNames(require); + for (_j = 0, _len1 = _ref2.length; _j < _len1; _j++) { + r = _ref2[_j]; + if (r !== 'paths') { + _require[r] = require[r]; + } + } + _require.paths = _module.paths = Module._nodeModulePaths(process.cwd()); + _require.resolve = function(request) { + return Module._resolveFilename(request, _module); + }; + } + } + o = {}; + for (k in options) { + if (!__hasProp.call(options, k)) continue; + v = options[k]; + o[k] = v; + } + o.bare = true; + js = compile(code, o); + if (sandbox === global) { + return vm.runInThisContext(js); + } else { + return vm.runInContext(js, sandbox); + } + }; + + lexer = new Lexer; + + parser.lexer = { + lex: function() { + var tag, token; + token = this.tokens[this.pos++]; + if (token) { + tag = token[0], this.yytext = token[1], this.yylloc = token[2]; + this.yylineno = this.yylloc.first_line; + } else { + tag = ''; + } + return tag; + }, + setInput: function(tokens) { + this.tokens = tokens; + return this.pos = 0; + }, + upcomingInput: function() { + return ""; + } + }; + + parser.yy = require('./nodes'); + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/command.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/command.js new file mode 100644 index 00000000..4077577e --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/command.js @@ -0,0 +1,506 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var BANNER, CoffeeScript, EventEmitter, SWITCHES, compileJoin, compileOptions, compilePath, compileScript, compileStdio, exec, exists, forkNode, fs, helpers, hidden, joinTimeout, lint, notSources, optionParser, optparse, opts, outputPath, parseOptions, path, printLine, printTokens, printWarn, removeSource, sourceCode, sources, spawn, timeLog, unwatchDir, usage, version, wait, watch, watchDir, watchers, writeJs, _ref; + + fs = require('fs'); + + path = require('path'); + + helpers = require('./helpers'); + + optparse = require('./optparse'); + + CoffeeScript = require('./coffee-script'); + + _ref = require('child_process'), spawn = _ref.spawn, exec = _ref.exec; + + EventEmitter = require('events').EventEmitter; + + exists = fs.exists || path.exists; + + helpers.extend(CoffeeScript, new EventEmitter); + + printLine = function(line) { + return process.stdout.write(line + '\n'); + }; + + printWarn = function(line) { + return process.stderr.write(line + '\n'); + }; + + hidden = function(file) { + return /^\.|~$/.test(file); + }; + + BANNER = 'Usage: coffee [options] path/to/script.coffee -- [args]\n\nIf called without options, `coffee` will run your script.'; + + SWITCHES = [['-b', '--bare', 'compile without a top-level function wrapper'], ['-c', '--compile', 'compile to JavaScript and save as .js files'], ['-e', '--eval', 'pass a string from the command line as input'], ['-h', '--help', 'display this help message'], ['-i', '--interactive', 'run an interactive CoffeeScript REPL'], ['-j', '--join [FILE]', 'concatenate the source CoffeeScript before compiling'], ['-l', '--lint', 'pipe the compiled JavaScript through JavaScript Lint'], ['-m', '--map', 'generate source map and save as .map files'], ['-n', '--nodes', 'print out the parse tree that the parser produces'], ['--nodejs [ARGS]', 'pass options directly to the "node" binary'], ['-o', '--output [DIR]', 'set the output directory for compiled JavaScript'], ['-p', '--print', 'print out the compiled JavaScript'], ['-s', '--stdio', 'listen for and compile scripts over stdio'], ['-t', '--tokens', 'print out the tokens that the lexer/rewriter produce'], ['-v', '--version', 'display the version number'], ['-w', '--watch', 'watch scripts for changes and rerun commands']]; + + opts = {}; + + sources = []; + + sourceCode = []; + + notSources = {}; + + watchers = {}; + + optionParser = null; + + exports.run = function() { + var literals, source, _i, _len, _results; + parseOptions(); + if (opts.nodejs) { + return forkNode(); + } + if (opts.help) { + return usage(); + } + if (opts.version) { + return version(); + } + if (opts.interactive) { + return require('./repl').start(); + } + if (opts.watch && !fs.watch) { + return printWarn("The --watch feature depends on Node v0.6.0+. You are running " + process.version + "."); + } + if (opts.stdio) { + return compileStdio(); + } + if (opts["eval"]) { + return compileScript(null, sources[0]); + } + if (!sources.length) { + return require('./repl').start(); + } + literals = opts.run ? sources.splice(1) : []; + process.argv = process.argv.slice(0, 2).concat(literals); + process.argv[0] = 'coffee'; + _results = []; + for (_i = 0, _len = sources.length; _i < _len; _i++) { + source = sources[_i]; + _results.push(compilePath(source, true, path.normalize(source))); + } + return _results; + }; + + compilePath = function(source, topLevel, base) { + return fs.stat(source, function(err, stats) { + if (err && err.code !== 'ENOENT') { + throw err; + } + if ((err != null ? err.code : void 0) === 'ENOENT') { + console.error("File not found: " + source); + process.exit(1); + } + if (stats.isDirectory() && path.dirname(source) !== 'node_modules') { + if (opts.watch) { + watchDir(source, base); + } + return fs.readdir(source, function(err, files) { + var file, index, _ref1, _ref2; + if (err && err.code !== 'ENOENT') { + throw err; + } + if ((err != null ? err.code : void 0) === 'ENOENT') { + return; + } + index = sources.indexOf(source); + files = files.filter(function(file) { + return !hidden(file); + }); + [].splice.apply(sources, [index, index - index + 1].concat(_ref1 = (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + _results.push(path.join(source, file)); + } + return _results; + })())), _ref1; + [].splice.apply(sourceCode, [index, index - index + 1].concat(_ref2 = files.map(function() { + return null; + }))), _ref2; + return files.forEach(function(file) { + return compilePath(path.join(source, file), false, base); + }); + }); + } else if (topLevel || helpers.isCoffee(source)) { + if (opts.watch) { + watch(source, base); + } + return fs.readFile(source, function(err, code) { + if (err && err.code !== 'ENOENT') { + throw err; + } + if ((err != null ? err.code : void 0) === 'ENOENT') { + return; + } + return compileScript(source, code.toString(), base); + }); + } else { + notSources[source] = true; + return removeSource(source, base); + } + }); + }; + + compileScript = function(file, input, base) { + var compiled, o, options, t, task; + o = opts; + options = compileOptions(file); + try { + t = task = { + file: file, + input: input, + options: options + }; + CoffeeScript.emit('compile', task); + if (o.tokens) { + return printTokens(CoffeeScript.tokens(t.input, t.options)); + } else if (o.nodes) { + return printLine(CoffeeScript.nodes(t.input, t.options).toString().trim()); + } else if (o.run) { + return CoffeeScript.run(t.input, t.options); + } else if (o.join && t.file !== o.join) { + sourceCode[sources.indexOf(t.file)] = t.input; + return compileJoin(); + } else { + compiled = CoffeeScript.compile(t.input, t.options); + t.output = compiled; + if (o.map) { + t.output = compiled.js; + t.sourceMap = compiled.v3SourceMap; + } + CoffeeScript.emit('success', task); + if (o.print) { + return printLine(t.output.trim()); + } else if (o.compile || o.map) { + return writeJs(base, t.file, t.output, t.sourceMap); + } else if (o.lint) { + return lint(t.file, t.output); + } + } + } catch (err) { + CoffeeScript.emit('failure', err, task); + if (CoffeeScript.listeners('failure').length) { + return; + } + if (o.watch) { + return printLine(err.message + '\x07'); + } + printWarn(err instanceof Error && err.stack || ("ERROR: " + err)); + return process.exit(1); + } + }; + + compileStdio = function() { + var code, stdin; + code = ''; + stdin = process.openStdin(); + stdin.on('data', function(buffer) { + if (buffer) { + return code += buffer.toString(); + } + }); + return stdin.on('end', function() { + return compileScript(null, code); + }); + }; + + joinTimeout = null; + + compileJoin = function() { + if (!opts.join) { + return; + } + if (!sourceCode.some(function(code) { + return code === null; + })) { + clearTimeout(joinTimeout); + return joinTimeout = wait(100, function() { + return compileScript(opts.join, sourceCode.join('\n'), opts.join); + }); + } + }; + + watch = function(source, base) { + var compile, compileTimeout, prevStats, rewatch, watchErr, watcher; + prevStats = null; + compileTimeout = null; + watchErr = function(e) { + if (e.code === 'ENOENT') { + if (sources.indexOf(source) === -1) { + return; + } + try { + rewatch(); + return compile(); + } catch (e) { + removeSource(source, base, true); + return compileJoin(); + } + } else { + throw e; + } + }; + compile = function() { + clearTimeout(compileTimeout); + return compileTimeout = wait(25, function() { + return fs.stat(source, function(err, stats) { + if (err) { + return watchErr(err); + } + if (prevStats && stats.size === prevStats.size && stats.mtime.getTime() === prevStats.mtime.getTime()) { + return rewatch(); + } + prevStats = stats; + return fs.readFile(source, function(err, code) { + if (err) { + return watchErr(err); + } + compileScript(source, code.toString(), base); + return rewatch(); + }); + }); + }); + }; + try { + watcher = fs.watch(source, compile); + } catch (e) { + watchErr(e); + } + return rewatch = function() { + if (watcher != null) { + watcher.close(); + } + return watcher = fs.watch(source, compile); + }; + }; + + watchDir = function(source, base) { + var readdirTimeout, watcher; + readdirTimeout = null; + try { + return watcher = fs.watch(source, function() { + clearTimeout(readdirTimeout); + return readdirTimeout = wait(25, function() { + return fs.readdir(source, function(err, files) { + var file, _i, _len, _results; + if (err) { + if (err.code !== 'ENOENT') { + throw err; + } + watcher.close(); + return unwatchDir(source, base); + } + _results = []; + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + if (!(!hidden(file) && !notSources[file])) { + continue; + } + file = path.join(source, file); + if (sources.some(function(s) { + return s.indexOf(file) >= 0; + })) { + continue; + } + sources.push(file); + sourceCode.push(null); + _results.push(compilePath(file, false, base)); + } + return _results; + }); + }); + }); + } catch (e) { + if (e.code !== 'ENOENT') { + throw e; + } + } + }; + + unwatchDir = function(source, base) { + var file, prevSources, toRemove, _i, _len; + prevSources = sources.slice(0); + toRemove = (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = sources.length; _i < _len; _i++) { + file = sources[_i]; + if (file.indexOf(source) >= 0) { + _results.push(file); + } + } + return _results; + })(); + for (_i = 0, _len = toRemove.length; _i < _len; _i++) { + file = toRemove[_i]; + removeSource(file, base, true); + } + if (!sources.some(function(s, i) { + return prevSources[i] !== s; + })) { + return; + } + return compileJoin(); + }; + + removeSource = function(source, base, removeJs) { + var index, jsPath; + index = sources.indexOf(source); + sources.splice(index, 1); + sourceCode.splice(index, 1); + if (removeJs && !opts.join) { + jsPath = outputPath(source, base); + return exists(jsPath, function(itExists) { + if (itExists) { + return fs.unlink(jsPath, function(err) { + if (err && err.code !== 'ENOENT') { + throw err; + } + return timeLog("removed " + source); + }); + } + }); + } + }; + + outputPath = function(source, base, extension) { + var baseDir, basename, dir, srcDir; + if (extension == null) { + extension = ".js"; + } + basename = helpers.baseFileName(source, true); + srcDir = path.dirname(source); + baseDir = base === '.' ? srcDir : srcDir.substring(base.length); + dir = opts.output ? path.join(opts.output, baseDir) : srcDir; + return path.join(dir, basename + extension); + }; + + writeJs = function(base, sourcePath, js, generatedSourceMap) { + var compile, jsDir, jsPath, sourceMapPath; + if (generatedSourceMap == null) { + generatedSourceMap = null; + } + jsPath = outputPath(sourcePath, base); + sourceMapPath = outputPath(sourcePath, base, ".map"); + jsDir = path.dirname(jsPath); + compile = function() { + if (opts.compile) { + if (js.length <= 0) { + js = ' '; + } + if (generatedSourceMap) { + js = "//@ sourceMappingURL=" + (helpers.baseFileName(sourceMapPath)) + "\n" + js; + } + fs.writeFile(jsPath, js, function(err) { + if (err) { + return printLine(err.message); + } else if (opts.compile && opts.watch) { + return timeLog("compiled " + sourcePath); + } + }); + } + if (generatedSourceMap) { + return fs.writeFile(sourceMapPath, generatedSourceMap, function(err) { + if (err) { + return printLine("Could not write source map: " + err.message); + } + }); + } + }; + return exists(jsDir, function(itExists) { + if (itExists) { + return compile(); + } else { + return exec("mkdir -p " + jsDir, compile); + } + }); + }; + + wait = function(milliseconds, func) { + return setTimeout(func, milliseconds); + }; + + timeLog = function(message) { + return console.log("" + ((new Date).toLocaleTimeString()) + " - " + message); + }; + + lint = function(file, js) { + var conf, jsl, printIt; + printIt = function(buffer) { + return printLine(file + ':\t' + buffer.toString().trim()); + }; + conf = __dirname + '/../../extras/jsl.conf'; + jsl = spawn('jsl', ['-nologo', '-stdin', '-conf', conf]); + jsl.stdout.on('data', printIt); + jsl.stderr.on('data', printIt); + jsl.stdin.write(js); + return jsl.stdin.end(); + }; + + printTokens = function(tokens) { + var strings, tag, token, value; + strings = (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = tokens.length; _i < _len; _i++) { + token = tokens[_i]; + tag = token[0]; + value = token[1].toString().replace(/\n/, '\\n'); + _results.push("[" + tag + " " + value + "]"); + } + return _results; + })(); + return printLine(strings.join(' ')); + }; + + parseOptions = function() { + var i, o, source, _i, _len; + optionParser = new optparse.OptionParser(SWITCHES, BANNER); + o = opts = optionParser.parse(process.argv.slice(2)); + o.compile || (o.compile = !!o.output); + o.run = !(o.compile || o.print || o.lint || o.map); + o.print = !!(o.print || (o["eval"] || o.stdio && o.compile)); + sources = o["arguments"]; + for (i = _i = 0, _len = sources.length; _i < _len; i = ++_i) { + source = sources[i]; + sourceCode[i] = null; + } + }; + + compileOptions = function(filename) { + return { + filename: filename, + literate: helpers.isLiterate(filename), + bare: opts.bare, + header: opts.compile, + sourceMap: opts.map + }; + }; + + forkNode = function() { + var args, nodeArgs; + nodeArgs = opts.nodejs.split(/\s+/); + args = process.argv.slice(1); + args.splice(args.indexOf('--nodejs'), 2); + return spawn(process.execPath, nodeArgs.concat(args), { + cwd: process.cwd(), + env: process.env, + customFds: [0, 1, 2] + }); + }; + + usage = function() { + return printLine((new optparse.OptionParser(SWITCHES, BANNER)).help()); + }; + + version = function() { + return printLine("CoffeeScript version " + CoffeeScript.VERSION); + }; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/grammar.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/grammar.js new file mode 100644 index 00000000..4a767433 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/grammar.js @@ -0,0 +1,623 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var Parser, alt, alternatives, grammar, name, o, operators, token, tokens, unwrap; + + Parser = require('jison').Parser; + + unwrap = /^function\s*\(\)\s*\{\s*return\s*([\s\S]*);\s*\}/; + + o = function(patternString, action, options) { + var addLocationDataFn, match, patternCount; + patternString = patternString.replace(/\s{2,}/g, ' '); + patternCount = patternString.split(' ').length; + if (!action) { + return [patternString, '$$ = $1;', options]; + } + action = (match = unwrap.exec(action)) ? match[1] : "(" + action + "())"; + action = action.replace(/\bnew /g, '$&yy.'); + action = action.replace(/\b(?:Block\.wrap|extend)\b/g, 'yy.$&'); + addLocationDataFn = function(first, last) { + if (!last) { + return "yy.addLocationDataFn(@" + first + ")"; + } else { + return "yy.addLocationDataFn(@" + first + ", @" + last + ")"; + } + }; + action = action.replace(/LOC\(([0-9]*)\)/g, addLocationDataFn('$1')); + action = action.replace(/LOC\(([0-9]*),\s*([0-9]*)\)/g, addLocationDataFn('$1', '$2')); + return [patternString, "$$ = " + (addLocationDataFn(1, patternCount)) + "(" + action + ");", options]; + }; + + grammar = { + Root: [ + o('', function() { + return new Block; + }), o('Body'), o('Block TERMINATOR') + ], + Body: [ + o('Line', function() { + return Block.wrap([$1]); + }), o('Body TERMINATOR Line', function() { + return $1.push($3); + }), o('Body TERMINATOR') + ], + Line: [o('Expression'), o('Statement')], + Statement: [ + o('Return'), o('Comment'), o('STATEMENT', function() { + return new Literal($1); + }) + ], + Expression: [o('Value'), o('Invocation'), o('Code'), o('Operation'), o('Assign'), o('If'), o('Try'), o('While'), o('For'), o('Switch'), o('Class'), o('Throw')], + Block: [ + o('INDENT OUTDENT', function() { + return new Block; + }), o('INDENT Body OUTDENT', function() { + return $2; + }) + ], + Identifier: [ + o('IDENTIFIER', function() { + return new Literal($1); + }) + ], + AlphaNumeric: [ + o('NUMBER', function() { + return new Literal($1); + }), o('STRING', function() { + return new Literal($1); + }) + ], + Literal: [ + o('AlphaNumeric'), o('JS', function() { + return new Literal($1); + }), o('REGEX', function() { + return new Literal($1); + }), o('DEBUGGER', function() { + return new Literal($1); + }), o('UNDEFINED', function() { + return new Undefined; + }), o('NULL', function() { + return new Null; + }), o('BOOL', function() { + return new Bool($1); + }) + ], + Assign: [ + o('Assignable = Expression', function() { + return new Assign($1, $3); + }), o('Assignable = TERMINATOR Expression', function() { + return new Assign($1, $4); + }), o('Assignable = INDENT Expression OUTDENT', function() { + return new Assign($1, $4); + }) + ], + AssignObj: [ + o('ObjAssignable', function() { + return new Value($1); + }), o('ObjAssignable : Expression', function() { + return new Assign(LOC(1)(new Value($1)), $3, 'object'); + }), o('ObjAssignable :\ + INDENT Expression OUTDENT', function() { + return new Assign(LOC(1)(new Value($1)), $4, 'object'); + }), o('Comment') + ], + ObjAssignable: [o('Identifier'), o('AlphaNumeric'), o('ThisProperty')], + Return: [ + o('RETURN Expression', function() { + return new Return($2); + }), o('RETURN', function() { + return new Return; + }) + ], + Comment: [ + o('HERECOMMENT', function() { + return new Comment($1); + }) + ], + Code: [ + o('PARAM_START ParamList PARAM_END FuncGlyph Block', function() { + return new Code($2, $5, $4); + }), o('FuncGlyph Block', function() { + return new Code([], $2, $1); + }) + ], + FuncGlyph: [ + o('->', function() { + return 'func'; + }), o('=>', function() { + return 'boundfunc'; + }) + ], + OptComma: [o(''), o(',')], + ParamList: [ + o('', function() { + return []; + }), o('Param', function() { + return [$1]; + }), o('ParamList , Param', function() { + return $1.concat($3); + }), o('ParamList OptComma TERMINATOR Param', function() { + return $1.concat($4); + }), o('ParamList OptComma INDENT ParamList OptComma OUTDENT', function() { + return $1.concat($4); + }) + ], + Param: [ + o('ParamVar', function() { + return new Param($1); + }), o('ParamVar ...', function() { + return new Param($1, null, true); + }), o('ParamVar = Expression', function() { + return new Param($1, $3); + }) + ], + ParamVar: [o('Identifier'), o('ThisProperty'), o('Array'), o('Object')], + Splat: [ + o('Expression ...', function() { + return new Splat($1); + }) + ], + SimpleAssignable: [ + o('Identifier', function() { + return new Value($1); + }), o('Value Accessor', function() { + return $1.add($2); + }), o('Invocation Accessor', function() { + return new Value($1, [].concat($2)); + }), o('ThisProperty') + ], + Assignable: [ + o('SimpleAssignable'), o('Array', function() { + return new Value($1); + }), o('Object', function() { + return new Value($1); + }) + ], + Value: [ + o('Assignable'), o('Literal', function() { + return new Value($1); + }), o('Parenthetical', function() { + return new Value($1); + }), o('Range', function() { + return new Value($1); + }), o('This') + ], + Accessor: [ + o('. Identifier', function() { + return new Access($2); + }), o('?. Identifier', function() { + return new Access($2, 'soak'); + }), o(':: Identifier', function() { + return [LOC(1)(new Access(new Literal('prototype'))), LOC(2)(new Access($2))]; + }), o('?:: Identifier', function() { + return [LOC(1)(new Access(new Literal('prototype'), 'soak')), LOC(2)(new Access($2))]; + }), o('::', function() { + return new Access(new Literal('prototype')); + }), o('Index') + ], + Index: [ + o('INDEX_START IndexValue INDEX_END', function() { + return $2; + }), o('INDEX_SOAK Index', function() { + return extend($2, { + soak: true + }); + }) + ], + IndexValue: [ + o('Expression', function() { + return new Index($1); + }), o('Slice', function() { + return new Slice($1); + }) + ], + Object: [ + o('{ AssignList OptComma }', function() { + return new Obj($2, $1.generated); + }) + ], + AssignList: [ + o('', function() { + return []; + }), o('AssignObj', function() { + return [$1]; + }), o('AssignList , AssignObj', function() { + return $1.concat($3); + }), o('AssignList OptComma TERMINATOR AssignObj', function() { + return $1.concat($4); + }), o('AssignList OptComma INDENT AssignList OptComma OUTDENT', function() { + return $1.concat($4); + }) + ], + Class: [ + o('CLASS', function() { + return new Class; + }), o('CLASS Block', function() { + return new Class(null, null, $2); + }), o('CLASS EXTENDS Expression', function() { + return new Class(null, $3); + }), o('CLASS EXTENDS Expression Block', function() { + return new Class(null, $3, $4); + }), o('CLASS SimpleAssignable', function() { + return new Class($2); + }), o('CLASS SimpleAssignable Block', function() { + return new Class($2, null, $3); + }), o('CLASS SimpleAssignable EXTENDS Expression', function() { + return new Class($2, $4); + }), o('CLASS SimpleAssignable EXTENDS Expression Block', function() { + return new Class($2, $4, $5); + }) + ], + Invocation: [ + o('Value OptFuncExist Arguments', function() { + return new Call($1, $3, $2); + }), o('Invocation OptFuncExist Arguments', function() { + return new Call($1, $3, $2); + }), o('SUPER', function() { + return new Call('super', [new Splat(new Literal('arguments'))]); + }), o('SUPER Arguments', function() { + return new Call('super', $2); + }) + ], + OptFuncExist: [ + o('', function() { + return false; + }), o('FUNC_EXIST', function() { + return true; + }) + ], + Arguments: [ + o('CALL_START CALL_END', function() { + return []; + }), o('CALL_START ArgList OptComma CALL_END', function() { + return $2; + }) + ], + This: [ + o('THIS', function() { + return new Value(new Literal('this')); + }), o('@', function() { + return new Value(new Literal('this')); + }) + ], + ThisProperty: [ + o('@ Identifier', function() { + return new Value(LOC(1)(new Literal('this')), [LOC(2)(new Access($2))], 'this'); + }) + ], + Array: [ + o('[ ]', function() { + return new Arr([]); + }), o('[ ArgList OptComma ]', function() { + return new Arr($2); + }) + ], + RangeDots: [ + o('..', function() { + return 'inclusive'; + }), o('...', function() { + return 'exclusive'; + }) + ], + Range: [ + o('[ Expression RangeDots Expression ]', function() { + return new Range($2, $4, $3); + }) + ], + Slice: [ + o('Expression RangeDots Expression', function() { + return new Range($1, $3, $2); + }), o('Expression RangeDots', function() { + return new Range($1, null, $2); + }), o('RangeDots Expression', function() { + return new Range(null, $2, $1); + }), o('RangeDots', function() { + return new Range(null, null, $1); + }) + ], + ArgList: [ + o('Arg', function() { + return [$1]; + }), o('ArgList , Arg', function() { + return $1.concat($3); + }), o('ArgList OptComma TERMINATOR Arg', function() { + return $1.concat($4); + }), o('INDENT ArgList OptComma OUTDENT', function() { + return $2; + }), o('ArgList OptComma INDENT ArgList OptComma OUTDENT', function() { + return $1.concat($4); + }) + ], + Arg: [o('Expression'), o('Splat')], + SimpleArgs: [ + o('Expression'), o('SimpleArgs , Expression', function() { + return [].concat($1, $3); + }) + ], + Try: [ + o('TRY Block', function() { + return new Try($2); + }), o('TRY Block Catch', function() { + return new Try($2, $3[0], $3[1]); + }), o('TRY Block FINALLY Block', function() { + return new Try($2, null, null, $4); + }), o('TRY Block Catch FINALLY Block', function() { + return new Try($2, $3[0], $3[1], $5); + }) + ], + Catch: [ + o('CATCH Identifier Block', function() { + return [$2, $3]; + }), o('CATCH Object Block', function() { + return [LOC(2)(new Value($2)), $3]; + }) + ], + Throw: [ + o('THROW Expression', function() { + return new Throw($2); + }) + ], + Parenthetical: [ + o('( Body )', function() { + return new Parens($2); + }), o('( INDENT Body OUTDENT )', function() { + return new Parens($3); + }) + ], + WhileSource: [ + o('WHILE Expression', function() { + return new While($2); + }), o('WHILE Expression WHEN Expression', function() { + return new While($2, { + guard: $4 + }); + }), o('UNTIL Expression', function() { + return new While($2, { + invert: true + }); + }), o('UNTIL Expression WHEN Expression', function() { + return new While($2, { + invert: true, + guard: $4 + }); + }) + ], + While: [ + o('WhileSource Block', function() { + return $1.addBody($2); + }), o('Statement WhileSource', function() { + return $2.addBody(LOC(1)(Block.wrap([$1]))); + }), o('Expression WhileSource', function() { + return $2.addBody(LOC(1)(Block.wrap([$1]))); + }), o('Loop', function() { + return $1; + }) + ], + Loop: [ + o('LOOP Block', function() { + return new While(LOC(1)(new Literal('true'))).addBody($2); + }), o('LOOP Expression', function() { + return new While(LOC(1)(new Literal('true'))).addBody(LOC(2)(Block.wrap([$2]))); + }) + ], + For: [ + o('Statement ForBody', function() { + return new For($1, $2); + }), o('Expression ForBody', function() { + return new For($1, $2); + }), o('ForBody Block', function() { + return new For($2, $1); + }) + ], + ForBody: [ + o('FOR Range', function() { + return { + source: LOC(2)(new Value($2)) + }; + }), o('ForStart ForSource', function() { + $2.own = $1.own; + $2.name = $1[0]; + $2.index = $1[1]; + return $2; + }) + ], + ForStart: [ + o('FOR ForVariables', function() { + return $2; + }), o('FOR OWN ForVariables', function() { + $3.own = true; + return $3; + }) + ], + ForValue: [ + o('Identifier'), o('ThisProperty'), o('Array', function() { + return new Value($1); + }), o('Object', function() { + return new Value($1); + }) + ], + ForVariables: [ + o('ForValue', function() { + return [$1]; + }), o('ForValue , ForValue', function() { + return [$1, $3]; + }) + ], + ForSource: [ + o('FORIN Expression', function() { + return { + source: $2 + }; + }), o('FOROF Expression', function() { + return { + source: $2, + object: true + }; + }), o('FORIN Expression WHEN Expression', function() { + return { + source: $2, + guard: $4 + }; + }), o('FOROF Expression WHEN Expression', function() { + return { + source: $2, + guard: $4, + object: true + }; + }), o('FORIN Expression BY Expression', function() { + return { + source: $2, + step: $4 + }; + }), o('FORIN Expression WHEN Expression BY Expression', function() { + return { + source: $2, + guard: $4, + step: $6 + }; + }), o('FORIN Expression BY Expression WHEN Expression', function() { + return { + source: $2, + step: $4, + guard: $6 + }; + }) + ], + Switch: [ + o('SWITCH Expression INDENT Whens OUTDENT', function() { + return new Switch($2, $4); + }), o('SWITCH Expression INDENT Whens ELSE Block OUTDENT', function() { + return new Switch($2, $4, $6); + }), o('SWITCH INDENT Whens OUTDENT', function() { + return new Switch(null, $3); + }), o('SWITCH INDENT Whens ELSE Block OUTDENT', function() { + return new Switch(null, $3, $5); + }) + ], + Whens: [ + o('When'), o('Whens When', function() { + return $1.concat($2); + }) + ], + When: [ + o('LEADING_WHEN SimpleArgs Block', function() { + return [[$2, $3]]; + }), o('LEADING_WHEN SimpleArgs Block TERMINATOR', function() { + return [[$2, $3]]; + }) + ], + IfBlock: [ + o('IF Expression Block', function() { + return new If($2, $3, { + type: $1 + }); + }), o('IfBlock ELSE IF Expression Block', function() { + return $1.addElse(new If($4, $5, { + type: $3 + })); + }) + ], + If: [ + o('IfBlock'), o('IfBlock ELSE Block', function() { + return $1.addElse($3); + }), o('Statement POST_IF Expression', function() { + return new If($3, LOC(1)(Block.wrap([$1])), { + type: $2, + statement: true + }); + }), o('Expression POST_IF Expression', function() { + return new If($3, LOC(1)(Block.wrap([$1])), { + type: $2, + statement: true + }); + }) + ], + Operation: [ + o('UNARY Expression', function() { + return new Op($1, $2); + }), o('- Expression', (function() { + return new Op('-', $2); + }), { + prec: 'UNARY' + }), o('+ Expression', (function() { + return new Op('+', $2); + }), { + prec: 'UNARY' + }), o('-- SimpleAssignable', function() { + return new Op('--', $2); + }), o('++ SimpleAssignable', function() { + return new Op('++', $2); + }), o('SimpleAssignable --', function() { + return new Op('--', $1, null, true); + }), o('SimpleAssignable ++', function() { + return new Op('++', $1, null, true); + }), o('Expression ?', function() { + return new Existence($1); + }), o('Expression + Expression', function() { + return new Op('+', $1, $3); + }), o('Expression - Expression', function() { + return new Op('-', $1, $3); + }), o('Expression MATH Expression', function() { + return new Op($2, $1, $3); + }), o('Expression SHIFT Expression', function() { + return new Op($2, $1, $3); + }), o('Expression COMPARE Expression', function() { + return new Op($2, $1, $3); + }), o('Expression LOGIC Expression', function() { + return new Op($2, $1, $3); + }), o('Expression RELATION Expression', function() { + if ($2.charAt(0) === '!') { + return new Op($2.slice(1), $1, $3).invert(); + } else { + return new Op($2, $1, $3); + } + }), o('SimpleAssignable COMPOUND_ASSIGN\ + Expression', function() { + return new Assign($1, $3, $2); + }), o('SimpleAssignable COMPOUND_ASSIGN\ + INDENT Expression OUTDENT', function() { + return new Assign($1, $4, $2); + }), o('SimpleAssignable COMPOUND_ASSIGN TERMINATOR\ + Expression', function() { + return new Assign($1, $4, $2); + }), o('SimpleAssignable EXTENDS Expression', function() { + return new Extends($1, $3); + }) + ] + }; + + operators = [['left', '.', '?.', '::', '?::'], ['left', 'CALL_START', 'CALL_END'], ['nonassoc', '++', '--'], ['left', '?'], ['right', 'UNARY'], ['left', 'MATH'], ['left', '+', '-'], ['left', 'SHIFT'], ['left', 'RELATION'], ['left', 'COMPARE'], ['left', 'LOGIC'], ['nonassoc', 'INDENT', 'OUTDENT'], ['right', '=', ':', 'COMPOUND_ASSIGN', 'RETURN', 'THROW', 'EXTENDS'], ['right', 'FORIN', 'FOROF', 'BY', 'WHEN'], ['right', 'IF', 'ELSE', 'FOR', 'WHILE', 'UNTIL', 'LOOP', 'SUPER', 'CLASS'], ['right', 'POST_IF']]; + + tokens = []; + + for (name in grammar) { + alternatives = grammar[name]; + grammar[name] = (function() { + var _i, _j, _len, _len1, _ref, _results; + _results = []; + for (_i = 0, _len = alternatives.length; _i < _len; _i++) { + alt = alternatives[_i]; + _ref = alt[0].split(' '); + for (_j = 0, _len1 = _ref.length; _j < _len1; _j++) { + token = _ref[_j]; + if (!grammar[token]) { + tokens.push(token); + } + } + if (name === 'Root') { + alt[1] = "return " + alt[1]; + } + _results.push(alt); + } + return _results; + })(); + } + + exports.parser = new Parser({ + tokens: tokens.join(' '), + bnf: grammar, + operators: operators.reverse(), + startSymbol: 'Root' + }); + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/helpers.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/helpers.js new file mode 100644 index 00000000..d7bac3b3 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/helpers.js @@ -0,0 +1,150 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var buildLocationData, extend, flatten, _ref; + + exports.starts = function(string, literal, start) { + return literal === string.substr(start, literal.length); + }; + + exports.ends = function(string, literal, back) { + var len; + len = literal.length; + return literal === string.substr(string.length - len - (back || 0), len); + }; + + exports.compact = function(array) { + var item, _i, _len, _results; + _results = []; + for (_i = 0, _len = array.length; _i < _len; _i++) { + item = array[_i]; + if (item) { + _results.push(item); + } + } + return _results; + }; + + exports.count = function(string, substr) { + var num, pos; + num = pos = 0; + if (!substr.length) { + return 1 / 0; + } + while (pos = 1 + string.indexOf(substr, pos)) { + num++; + } + return num; + }; + + exports.merge = function(options, overrides) { + return extend(extend({}, options), overrides); + }; + + extend = exports.extend = function(object, properties) { + var key, val; + for (key in properties) { + val = properties[key]; + object[key] = val; + } + return object; + }; + + exports.flatten = flatten = function(array) { + var element, flattened, _i, _len; + flattened = []; + for (_i = 0, _len = array.length; _i < _len; _i++) { + element = array[_i]; + if (element instanceof Array) { + flattened = flattened.concat(flatten(element)); + } else { + flattened.push(element); + } + } + return flattened; + }; + + exports.del = function(obj, key) { + var val; + val = obj[key]; + delete obj[key]; + return val; + }; + + exports.last = function(array, back) { + return array[array.length - (back || 0) - 1]; + }; + + exports.some = (_ref = Array.prototype.some) != null ? _ref : function(fn) { + var e, _i, _len; + for (_i = 0, _len = this.length; _i < _len; _i++) { + e = this[_i]; + if (fn(e)) { + return true; + } + } + return false; + }; + + buildLocationData = function(first, last) { + if (!last) { + return first; + } else { + return { + first_line: first.first_line, + first_column: first.first_column, + last_line: last.last_line, + last_column: last.last_column + }; + } + }; + + exports.addLocationDataFn = function(first, last) { + return function(obj) { + if (((typeof obj) === 'object') && (!!obj['updateLocationDataIfMissing'])) { + obj.updateLocationDataIfMissing(buildLocationData(first, last)); + } + return obj; + }; + }; + + exports.locationDataToString = function(obj) { + var locationData; + if (("2" in obj) && ("first_line" in obj[2])) { + locationData = obj[2]; + } else if ("first_line" in obj) { + locationData = obj; + } + if (locationData) { + return ("" + (locationData.first_line + 1) + ":" + (locationData.first_column + 1) + "-") + ("" + (locationData.last_line + 1) + ":" + (locationData.last_column + 1)); + } else { + return "No location data"; + } + }; + + exports.baseFileName = function(file, stripExt) { + var parts; + if (stripExt == null) { + stripExt = false; + } + parts = file.split('/'); + file = parts[parts.length - 1]; + if (!stripExt) { + return file; + } + parts = file.split('.'); + parts.pop(); + if (parts[parts.length - 1] === 'coffee') { + parts.pop(); + } + return parts.join('.'); + }; + + exports.isCoffee = function(file) { + return /\.((lit)?coffee|coffee\.md)$/.test(file); + }; + + exports.isLiterate = function(file) { + return /\.(litcoffee|coffee\.md)$/.test(file); + }; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/index.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/index.js new file mode 100644 index 00000000..1452b452 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/index.js @@ -0,0 +1,11 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var key, val, _ref; + + _ref = require('./coffee-script'); + for (key in _ref) { + val = _ref[key]; + exports[key] = val; + } + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/lexer.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/lexer.js new file mode 100644 index 00000000..5261242e --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/lexer.js @@ -0,0 +1,905 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var BOM, BOOL, CALLABLE, CODE, COFFEE_ALIASES, COFFEE_ALIAS_MAP, COFFEE_KEYWORDS, COMMENT, COMPARE, COMPOUND_ASSIGN, HEREDOC, HEREDOC_ILLEGAL, HEREDOC_INDENT, HEREGEX, HEREGEX_OMIT, IDENTIFIER, INDEXABLE, INVERSES, JSTOKEN, JS_FORBIDDEN, JS_KEYWORDS, LINE_BREAK, LINE_CONTINUER, LITERATE, LOGIC, Lexer, MATH, MULTILINER, MULTI_DENT, NOT_REGEX, NOT_SPACED_REGEX, NUMBER, OPERATOR, REGEX, RELATION, RESERVED, Rewriter, SHIFT, SIMPLESTR, STRICT_PROSCRIBED, TRAILING_SPACES, UNARY, WHITESPACE, compact, count, key, last, locationDataToString, starts, _ref, _ref1, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }; + + _ref = require('./rewriter'), Rewriter = _ref.Rewriter, INVERSES = _ref.INVERSES; + + _ref1 = require('./helpers'), count = _ref1.count, starts = _ref1.starts, compact = _ref1.compact, last = _ref1.last, locationDataToString = _ref1.locationDataToString; + + exports.Lexer = Lexer = (function() { + + function Lexer() {} + + Lexer.prototype.tokenize = function(code, opts) { + var consumed, i, tag, _ref2; + if (opts == null) { + opts = {}; + } + this.literate = opts.literate; + this.indent = 0; + this.indebt = 0; + this.outdebt = 0; + this.indents = []; + this.ends = []; + this.tokens = []; + this.chunkLine = opts.line || 0; + this.chunkColumn = opts.column || 0; + code = this.clean(code); + i = 0; + while (this.chunk = code.slice(i)) { + consumed = this.identifierToken() || this.commentToken() || this.whitespaceToken() || this.lineToken() || this.heredocToken() || this.stringToken() || this.numberToken() || this.regexToken() || this.jsToken() || this.literalToken(); + _ref2 = this.getLineAndColumnFromChunk(consumed), this.chunkLine = _ref2[0], this.chunkColumn = _ref2[1]; + i += consumed; + } + this.closeIndentation(); + if (tag = this.ends.pop()) { + this.error("missing " + tag); + } + if (opts.rewrite === false) { + return this.tokens; + } + return (new Rewriter).rewrite(this.tokens); + }; + + Lexer.prototype.clean = function(code) { + var line, lines, match; + if (code.charCodeAt(0) === BOM) { + code = code.slice(1); + } + code = code.replace(/\r/g, '').replace(TRAILING_SPACES, ''); + if (WHITESPACE.test(code)) { + code = "\n" + code; + this.chunkLine--; + } + if (this.literate) { + lines = (function() { + var _i, _len, _ref2, _results; + _ref2 = code.split('\n'); + _results = []; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + line = _ref2[_i]; + if (match = LITERATE.exec(line)) { + _results.push(line.slice(match[0].length)); + } else { + _results.push('# ' + line); + } + } + return _results; + })(); + code = lines.join('\n'); + } + return code; + }; + + Lexer.prototype.identifierToken = function() { + var colon, colonOffset, forcedIdentifier, id, idLength, input, match, poppedToken, prev, tag, tagToken, _ref2, _ref3, _ref4; + if (!(match = IDENTIFIER.exec(this.chunk))) { + return 0; + } + input = match[0], id = match[1], colon = match[2]; + idLength = id.length; + poppedToken = void 0; + if (id === 'own' && this.tag() === 'FOR') { + this.token('OWN', id); + return id.length; + } + forcedIdentifier = colon || (prev = last(this.tokens)) && (((_ref2 = prev[0]) === '.' || _ref2 === '?.' || _ref2 === '::' || _ref2 === '?::') || !prev.spaced && prev[0] === '@'); + tag = 'IDENTIFIER'; + if (!forcedIdentifier && (__indexOf.call(JS_KEYWORDS, id) >= 0 || __indexOf.call(COFFEE_KEYWORDS, id) >= 0)) { + tag = id.toUpperCase(); + if (tag === 'WHEN' && (_ref3 = this.tag(), __indexOf.call(LINE_BREAK, _ref3) >= 0)) { + tag = 'LEADING_WHEN'; + } else if (tag === 'FOR') { + this.seenFor = true; + } else if (tag === 'UNLESS') { + tag = 'IF'; + } else if (__indexOf.call(UNARY, tag) >= 0) { + tag = 'UNARY'; + } else if (__indexOf.call(RELATION, tag) >= 0) { + if (tag !== 'INSTANCEOF' && this.seenFor) { + tag = 'FOR' + tag; + this.seenFor = false; + } else { + tag = 'RELATION'; + if (this.value() === '!') { + poppedToken = this.tokens.pop(); + id = '!' + id; + } + } + } + } + if (__indexOf.call(JS_FORBIDDEN, id) >= 0) { + if (forcedIdentifier) { + tag = 'IDENTIFIER'; + id = new String(id); + id.reserved = true; + } else if (__indexOf.call(RESERVED, id) >= 0) { + this.error("reserved word \"" + id + "\""); + } + } + if (!forcedIdentifier) { + if (__indexOf.call(COFFEE_ALIASES, id) >= 0) { + id = COFFEE_ALIAS_MAP[id]; + } + tag = (function() { + switch (id) { + case '!': + return 'UNARY'; + case '==': + case '!=': + return 'COMPARE'; + case '&&': + case '||': + return 'LOGIC'; + case 'true': + case 'false': + return 'BOOL'; + case 'break': + case 'continue': + return 'STATEMENT'; + default: + return tag; + } + })(); + } + tagToken = this.token(tag, id, 0, idLength); + if (poppedToken) { + _ref4 = [poppedToken[2].first_line, poppedToken[2].first_column], tagToken[2].first_line = _ref4[0], tagToken[2].first_column = _ref4[1]; + } + if (colon) { + colonOffset = input.lastIndexOf(':'); + this.token(':', ':', colonOffset, colon.length); + } + return input.length; + }; + + Lexer.prototype.numberToken = function() { + var binaryLiteral, lexedLength, match, number, octalLiteral; + if (!(match = NUMBER.exec(this.chunk))) { + return 0; + } + number = match[0]; + if (/^0[BOX]/.test(number)) { + this.error("radix prefix '" + number + "' must be lowercase"); + } else if (/E/.test(number) && !/^0x/.test(number)) { + this.error("exponential notation '" + number + "' must be indicated with a lowercase 'e'"); + } else if (/^0\d*[89]/.test(number)) { + this.error("decimal literal '" + number + "' must not be prefixed with '0'"); + } else if (/^0\d+/.test(number)) { + this.error("octal literal '" + number + "' must be prefixed with '0o'"); + } + lexedLength = number.length; + if (octalLiteral = /^0o([0-7]+)/.exec(number)) { + number = '0x' + (parseInt(octalLiteral[1], 8)).toString(16); + } + if (binaryLiteral = /^0b([01]+)/.exec(number)) { + number = '0x' + (parseInt(binaryLiteral[1], 2)).toString(16); + } + this.token('NUMBER', number, 0, lexedLength); + return lexedLength; + }; + + Lexer.prototype.stringToken = function() { + var match, octalEsc, string; + switch (this.chunk.charAt(0)) { + case "'": + if (!(match = SIMPLESTR.exec(this.chunk))) { + return 0; + } + string = match[0]; + this.token('STRING', string.replace(MULTILINER, '\\\n'), 0, string.length); + break; + case '"': + if (!(string = this.balancedString(this.chunk, '"'))) { + return 0; + } + if (0 < string.indexOf('#{', 1)) { + this.interpolateString(string.slice(1, -1), { + strOffset: 1, + lexedLength: string.length + }); + } else { + this.token('STRING', this.escapeLines(string, 0, string.length)); + } + break; + default: + return 0; + } + if (octalEsc = /^(?:\\.|[^\\])*\\(?:0[0-7]|[1-7])/.test(string)) { + this.error("octal escape sequences " + string + " are not allowed"); + } + return string.length; + }; + + Lexer.prototype.heredocToken = function() { + var doc, heredoc, match, quote; + if (!(match = HEREDOC.exec(this.chunk))) { + return 0; + } + heredoc = match[0]; + quote = heredoc.charAt(0); + doc = this.sanitizeHeredoc(match[2], { + quote: quote, + indent: null + }); + if (quote === '"' && 0 <= doc.indexOf('#{')) { + this.interpolateString(doc, { + heredoc: true, + strOffset: 3, + lexedLength: heredoc.length + }); + } else { + this.token('STRING', this.makeString(doc, quote, true), 0, heredoc.length); + } + return heredoc.length; + }; + + Lexer.prototype.commentToken = function() { + var comment, here, match; + if (!(match = this.chunk.match(COMMENT))) { + return 0; + } + comment = match[0], here = match[1]; + if (here) { + this.token('HERECOMMENT', this.sanitizeHeredoc(here, { + herecomment: true, + indent: Array(this.indent + 1).join(' ') + }), 0, comment.length); + } + return comment.length; + }; + + Lexer.prototype.jsToken = function() { + var match, script; + if (!(this.chunk.charAt(0) === '`' && (match = JSTOKEN.exec(this.chunk)))) { + return 0; + } + this.token('JS', (script = match[0]).slice(1, -1), 0, script.length); + return script.length; + }; + + Lexer.prototype.regexToken = function() { + var flags, length, match, prev, regex, _ref2, _ref3; + if (this.chunk.charAt(0) !== '/') { + return 0; + } + if (match = HEREGEX.exec(this.chunk)) { + length = this.heregexToken(match); + return length; + } + prev = last(this.tokens); + if (prev && (_ref2 = prev[0], __indexOf.call((prev.spaced ? NOT_REGEX : NOT_SPACED_REGEX), _ref2) >= 0)) { + return 0; + } + if (!(match = REGEX.exec(this.chunk))) { + return 0; + } + _ref3 = match, match = _ref3[0], regex = _ref3[1], flags = _ref3[2]; + if (regex.slice(0, 2) === '/*') { + this.error('regular expressions cannot begin with `*`'); + } + if (regex === '//') { + regex = '/(?:)/'; + } + this.token('REGEX', "" + regex + flags, 0, match.length); + return match.length; + }; + + Lexer.prototype.heregexToken = function(match) { + var body, flags, flagsOffset, heregex, plusToken, prev, re, tag, token, tokens, value, _i, _len, _ref2, _ref3, _ref4; + heregex = match[0], body = match[1], flags = match[2]; + if (0 > body.indexOf('#{')) { + re = body.replace(HEREGEX_OMIT, '').replace(/\//g, '\\/'); + if (re.match(/^\*/)) { + this.error('regular expressions cannot begin with `*`'); + } + this.token('REGEX', "/" + (re || '(?:)') + "/" + flags, 0, heregex.length); + return heregex.length; + } + this.token('IDENTIFIER', 'RegExp', 0, 0); + this.token('CALL_START', '(', 0, 0); + tokens = []; + _ref2 = this.interpolateString(body, { + regex: true + }); + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + token = _ref2[_i]; + tag = token[0], value = token[1]; + if (tag === 'TOKENS') { + tokens.push.apply(tokens, value); + } else if (tag === 'NEOSTRING') { + if (!(value = value.replace(HEREGEX_OMIT, ''))) { + continue; + } + value = value.replace(/\\/g, '\\\\'); + token[0] = 'STRING'; + token[1] = this.makeString(value, '"', true); + tokens.push(token); + } else { + this.error("Unexpected " + tag); + } + prev = last(this.tokens); + plusToken = ['+', '+']; + plusToken[2] = prev[2]; + tokens.push(plusToken); + } + tokens.pop(); + if (((_ref3 = tokens[0]) != null ? _ref3[0] : void 0) !== 'STRING') { + this.token('STRING', '""', 0, 0); + this.token('+', '+', 0, 0); + } + (_ref4 = this.tokens).push.apply(_ref4, tokens); + if (flags) { + flagsOffset = heregex.lastIndexOf(flags); + this.token(',', ',', flagsOffset, 0); + this.token('STRING', '"' + flags + '"', flagsOffset, flags.length); + } + this.token(')', ')', heregex.length - 1, 0); + return heregex.length; + }; + + Lexer.prototype.lineToken = function() { + var diff, indent, match, noNewlines, size; + if (!(match = MULTI_DENT.exec(this.chunk))) { + return 0; + } + indent = match[0]; + this.seenFor = false; + size = indent.length - 1 - indent.lastIndexOf('\n'); + noNewlines = this.unfinished(); + if (size - this.indebt === this.indent) { + if (noNewlines) { + this.suppressNewlines(); + } else { + this.newlineToken(0); + } + return indent.length; + } + if (size > this.indent) { + if (noNewlines) { + this.indebt = size - this.indent; + this.suppressNewlines(); + return indent.length; + } + diff = size - this.indent + this.outdebt; + this.token('INDENT', diff, 0, indent.length); + this.indents.push(diff); + this.ends.push('OUTDENT'); + this.outdebt = this.indebt = 0; + } else { + this.indebt = 0; + this.outdentToken(this.indent - size, noNewlines, indent.length); + } + this.indent = size; + return indent.length; + }; + + Lexer.prototype.outdentToken = function(moveOut, noNewlines, outdentLength) { + var dent, len; + while (moveOut > 0) { + len = this.indents.length - 1; + if (this.indents[len] === void 0) { + moveOut = 0; + } else if (this.indents[len] === this.outdebt) { + moveOut -= this.outdebt; + this.outdebt = 0; + } else if (this.indents[len] < this.outdebt) { + this.outdebt -= this.indents[len]; + moveOut -= this.indents[len]; + } else { + dent = this.indents.pop() + this.outdebt; + moveOut -= dent; + this.outdebt = 0; + this.pair('OUTDENT'); + this.token('OUTDENT', dent, 0, outdentLength); + } + } + if (dent) { + this.outdebt -= moveOut; + } + while (this.value() === ';') { + this.tokens.pop(); + } + if (!(this.tag() === 'TERMINATOR' || noNewlines)) { + this.token('TERMINATOR', '\n', outdentLength, 0); + } + return this; + }; + + Lexer.prototype.whitespaceToken = function() { + var match, nline, prev; + if (!((match = WHITESPACE.exec(this.chunk)) || (nline = this.chunk.charAt(0) === '\n'))) { + return 0; + } + prev = last(this.tokens); + if (prev) { + prev[match ? 'spaced' : 'newLine'] = true; + } + if (match) { + return match[0].length; + } else { + return 0; + } + }; + + Lexer.prototype.newlineToken = function(offset) { + while (this.value() === ';') { + this.tokens.pop(); + } + if (this.tag() !== 'TERMINATOR') { + this.token('TERMINATOR', '\n', offset, 0); + } + return this; + }; + + Lexer.prototype.suppressNewlines = function() { + if (this.value() === '\\') { + this.tokens.pop(); + } + return this; + }; + + Lexer.prototype.literalToken = function() { + var match, prev, tag, value, _ref2, _ref3, _ref4, _ref5; + if (match = OPERATOR.exec(this.chunk)) { + value = match[0]; + if (CODE.test(value)) { + this.tagParameters(); + } + } else { + value = this.chunk.charAt(0); + } + tag = value; + prev = last(this.tokens); + if (value === '=' && prev) { + if (!prev[1].reserved && (_ref2 = prev[1], __indexOf.call(JS_FORBIDDEN, _ref2) >= 0)) { + this.error("reserved word \"" + (this.value()) + "\" can't be assigned"); + } + if ((_ref3 = prev[1]) === '||' || _ref3 === '&&') { + prev[0] = 'COMPOUND_ASSIGN'; + prev[1] += '='; + return value.length; + } + } + if (value === ';') { + this.seenFor = false; + tag = 'TERMINATOR'; + } else if (__indexOf.call(MATH, value) >= 0) { + tag = 'MATH'; + } else if (__indexOf.call(COMPARE, value) >= 0) { + tag = 'COMPARE'; + } else if (__indexOf.call(COMPOUND_ASSIGN, value) >= 0) { + tag = 'COMPOUND_ASSIGN'; + } else if (__indexOf.call(UNARY, value) >= 0) { + tag = 'UNARY'; + } else if (__indexOf.call(SHIFT, value) >= 0) { + tag = 'SHIFT'; + } else if (__indexOf.call(LOGIC, value) >= 0 || value === '?' && (prev != null ? prev.spaced : void 0)) { + tag = 'LOGIC'; + } else if (prev && !prev.spaced) { + if (value === '(' && (_ref4 = prev[0], __indexOf.call(CALLABLE, _ref4) >= 0)) { + if (prev[0] === '?') { + prev[0] = 'FUNC_EXIST'; + } + tag = 'CALL_START'; + } else if (value === '[' && (_ref5 = prev[0], __indexOf.call(INDEXABLE, _ref5) >= 0)) { + tag = 'INDEX_START'; + switch (prev[0]) { + case '?': + prev[0] = 'INDEX_SOAK'; + } + } + } + switch (value) { + case '(': + case '{': + case '[': + this.ends.push(INVERSES[value]); + break; + case ')': + case '}': + case ']': + this.pair(value); + } + this.token(tag, value); + return value.length; + }; + + Lexer.prototype.sanitizeHeredoc = function(doc, options) { + var attempt, herecomment, indent, match, _ref2; + indent = options.indent, herecomment = options.herecomment; + if (herecomment) { + if (HEREDOC_ILLEGAL.test(doc)) { + this.error("block comment cannot contain \"*/\", starting"); + } + if (doc.indexOf('\n') < 0) { + return doc; + } + } else { + while (match = HEREDOC_INDENT.exec(doc)) { + attempt = match[1]; + if (indent === null || (0 < (_ref2 = attempt.length) && _ref2 < indent.length)) { + indent = attempt; + } + } + } + if (indent) { + doc = doc.replace(RegExp("\\n" + indent, "g"), '\n'); + } + if (this.literate) { + doc = doc.replace(/\n# \n/g, '\n\n'); + } + if (!herecomment) { + doc = doc.replace(/^\n/, ''); + } + return doc; + }; + + Lexer.prototype.tagParameters = function() { + var i, stack, tok, tokens; + if (this.tag() !== ')') { + return this; + } + stack = []; + tokens = this.tokens; + i = tokens.length; + tokens[--i][0] = 'PARAM_END'; + while (tok = tokens[--i]) { + switch (tok[0]) { + case ')': + stack.push(tok); + break; + case '(': + case 'CALL_START': + if (stack.length) { + stack.pop(); + } else if (tok[0] === '(') { + tok[0] = 'PARAM_START'; + return this; + } else { + return this; + } + } + } + return this; + }; + + Lexer.prototype.closeIndentation = function() { + return this.outdentToken(this.indent); + }; + + Lexer.prototype.balancedString = function(str, end) { + var continueCount, i, letter, match, prev, stack, _i, _ref2; + continueCount = 0; + stack = [end]; + for (i = _i = 1, _ref2 = str.length; 1 <= _ref2 ? _i < _ref2 : _i > _ref2; i = 1 <= _ref2 ? ++_i : --_i) { + if (continueCount) { + --continueCount; + continue; + } + switch (letter = str.charAt(i)) { + case '\\': + ++continueCount; + continue; + case end: + stack.pop(); + if (!stack.length) { + return str.slice(0, +i + 1 || 9e9); + } + end = stack[stack.length - 1]; + continue; + } + if (end === '}' && (letter === '"' || letter === "'")) { + stack.push(end = letter); + } else if (end === '}' && letter === '/' && (match = HEREGEX.exec(str.slice(i)) || REGEX.exec(str.slice(i)))) { + continueCount += match[0].length - 1; + } else if (end === '}' && letter === '{') { + stack.push(end = '}'); + } else if (end === '"' && prev === '#' && letter === '{') { + stack.push(end = '}'); + } + prev = letter; + } + return this.error("missing " + (stack.pop()) + ", starting"); + }; + + Lexer.prototype.interpolateString = function(str, options) { + var column, expr, heredoc, i, inner, interpolated, len, letter, lexedLength, line, locationToken, nested, offsetInChunk, pi, plusToken, popped, regex, strOffset, tag, token, tokens, value, _i, _len, _ref2, _ref3, _ref4; + if (options == null) { + options = {}; + } + heredoc = options.heredoc, regex = options.regex, offsetInChunk = options.offsetInChunk, strOffset = options.strOffset, lexedLength = options.lexedLength; + offsetInChunk = offsetInChunk || 0; + strOffset = strOffset || 0; + lexedLength = lexedLength || str.length; + if (heredoc && str.length > 0 && str[0] === '\n') { + str = str.slice(1); + strOffset++; + } + tokens = []; + pi = 0; + i = -1; + while (letter = str.charAt(i += 1)) { + if (letter === '\\') { + i += 1; + continue; + } + if (!(letter === '#' && str.charAt(i + 1) === '{' && (expr = this.balancedString(str.slice(i + 1), '}')))) { + continue; + } + if (pi < i) { + tokens.push(this.makeToken('NEOSTRING', str.slice(pi, i), strOffset + pi)); + } + inner = expr.slice(1, -1); + if (inner.length) { + _ref2 = this.getLineAndColumnFromChunk(strOffset + i + 1), line = _ref2[0], column = _ref2[1]; + nested = new Lexer().tokenize(inner, { + line: line, + column: column, + rewrite: false + }); + popped = nested.pop(); + if (((_ref3 = nested[0]) != null ? _ref3[0] : void 0) === 'TERMINATOR') { + popped = nested.shift(); + } + if (len = nested.length) { + if (len > 1) { + nested.unshift(this.makeToken('(', '(', strOffset + i + 1, 0)); + nested.push(this.makeToken(')', ')', strOffset + i + 1 + inner.length, 0)); + } + tokens.push(['TOKENS', nested]); + } + } + i += expr.length; + pi = i + 1; + } + if ((i > pi && pi < str.length)) { + tokens.push(this.makeToken('NEOSTRING', str.slice(pi), strOffset + pi)); + } + if (regex) { + return tokens; + } + if (!tokens.length) { + return this.token('STRING', '""', offsetInChunk, lexedLength); + } + if (tokens[0][0] !== 'NEOSTRING') { + tokens.unshift(this.makeToken('NEOSTRING', '', offsetInChunk)); + } + if (interpolated = tokens.length > 1) { + this.token('(', '(', offsetInChunk, 0); + } + for (i = _i = 0, _len = tokens.length; _i < _len; i = ++_i) { + token = tokens[i]; + tag = token[0], value = token[1]; + if (i) { + if (i) { + plusToken = this.token('+', '+'); + } + locationToken = tag === 'TOKENS' ? value[0] : token; + plusToken[2] = { + first_line: locationToken[2].first_line, + first_column: locationToken[2].first_column, + last_line: locationToken[2].first_line, + last_column: locationToken[2].first_column + }; + } + if (tag === 'TOKENS') { + (_ref4 = this.tokens).push.apply(_ref4, value); + } else if (tag === 'NEOSTRING') { + token[0] = 'STRING'; + token[1] = this.makeString(value, '"', heredoc); + this.tokens.push(token); + } else { + this.error("Unexpected " + tag); + } + } + if (interpolated) { + this.token(')', ')', offsetInChunk + lexedLength, 0); + } + return tokens; + }; + + Lexer.prototype.pair = function(tag) { + var size, wanted; + if (tag !== (wanted = last(this.ends))) { + if ('OUTDENT' !== wanted) { + this.error("unmatched " + tag); + } + this.indent -= size = last(this.indents); + this.outdentToken(size, true); + return this.pair(tag); + } + return this.ends.pop(); + }; + + Lexer.prototype.getLineAndColumnFromChunk = function(offset) { + var column, lineCount, lines, string; + if (offset === 0) { + return [this.chunkLine, this.chunkColumn]; + } + if (offset >= this.chunk.length) { + string = this.chunk; + } else { + string = this.chunk.slice(0, +(offset - 1) + 1 || 9e9); + } + lineCount = count(string, '\n'); + column = this.chunkColumn; + if (lineCount > 0) { + lines = string.split('\n'); + column = (last(lines)).length; + } else { + column += string.length; + } + return [this.chunkLine + lineCount, column]; + }; + + Lexer.prototype.makeToken = function(tag, value, offsetInChunk, length) { + var lastCharacter, locationData, token, _ref2, _ref3; + if (offsetInChunk == null) { + offsetInChunk = 0; + } + if (length == null) { + length = value.length; + } + locationData = {}; + _ref2 = this.getLineAndColumnFromChunk(offsetInChunk), locationData.first_line = _ref2[0], locationData.first_column = _ref2[1]; + lastCharacter = Math.max(0, length - 1); + _ref3 = this.getLineAndColumnFromChunk(offsetInChunk + (length - 1)), locationData.last_line = _ref3[0], locationData.last_column = _ref3[1]; + token = [tag, value, locationData]; + return token; + }; + + Lexer.prototype.token = function(tag, value, offsetInChunk, length) { + var token; + token = this.makeToken(tag, value, offsetInChunk, length); + this.tokens.push(token); + return token; + }; + + Lexer.prototype.tag = function(index, tag) { + var tok; + return (tok = last(this.tokens, index)) && (tag ? tok[0] = tag : tok[0]); + }; + + Lexer.prototype.value = function(index, val) { + var tok; + return (tok = last(this.tokens, index)) && (val ? tok[1] = val : tok[1]); + }; + + Lexer.prototype.unfinished = function() { + var _ref2; + return LINE_CONTINUER.test(this.chunk) || ((_ref2 = this.tag()) === '\\' || _ref2 === '.' || _ref2 === '?.' || _ref2 === '?::' || _ref2 === 'UNARY' || _ref2 === 'MATH' || _ref2 === '+' || _ref2 === '-' || _ref2 === 'SHIFT' || _ref2 === 'RELATION' || _ref2 === 'COMPARE' || _ref2 === 'LOGIC' || _ref2 === 'THROW' || _ref2 === 'EXTENDS'); + }; + + Lexer.prototype.escapeLines = function(str, heredoc) { + return str.replace(MULTILINER, heredoc ? '\\n' : ''); + }; + + Lexer.prototype.makeString = function(body, quote, heredoc) { + if (!body) { + return quote + quote; + } + body = body.replace(/\\([\s\S])/g, function(match, contents) { + if (contents === '\n' || contents === quote) { + return contents; + } else { + return match; + } + }); + body = body.replace(RegExp("" + quote, "g"), '\\$&'); + return quote + this.escapeLines(body, heredoc) + quote; + }; + + Lexer.prototype.error = function(message) { + throw SyntaxError("" + message + " on line " + (this.chunkLine + 1)); + }; + + return Lexer; + + })(); + + JS_KEYWORDS = ['true', 'false', 'null', 'this', 'new', 'delete', 'typeof', 'in', 'instanceof', 'return', 'throw', 'break', 'continue', 'debugger', 'if', 'else', 'switch', 'for', 'while', 'do', 'try', 'catch', 'finally', 'class', 'extends', 'super']; + + COFFEE_KEYWORDS = ['undefined', 'then', 'unless', 'until', 'loop', 'of', 'by', 'when']; + + COFFEE_ALIAS_MAP = { + and: '&&', + or: '||', + is: '==', + isnt: '!=', + not: '!', + yes: 'true', + no: 'false', + on: 'true', + off: 'false' + }; + + COFFEE_ALIASES = (function() { + var _results; + _results = []; + for (key in COFFEE_ALIAS_MAP) { + _results.push(key); + } + return _results; + })(); + + COFFEE_KEYWORDS = COFFEE_KEYWORDS.concat(COFFEE_ALIASES); + + RESERVED = ['case', 'default', 'function', 'var', 'void', 'with', 'const', 'let', 'enum', 'export', 'import', 'native', '__hasProp', '__extends', '__slice', '__bind', '__indexOf', 'implements', 'interface', 'package', 'private', 'protected', 'public', 'static', 'yield']; + + STRICT_PROSCRIBED = ['arguments', 'eval']; + + JS_FORBIDDEN = JS_KEYWORDS.concat(RESERVED).concat(STRICT_PROSCRIBED); + + exports.RESERVED = RESERVED.concat(JS_KEYWORDS).concat(COFFEE_KEYWORDS).concat(STRICT_PROSCRIBED); + + exports.STRICT_PROSCRIBED = STRICT_PROSCRIBED; + + BOM = 65279; + + IDENTIFIER = /^([$A-Za-z_\x7f-\uffff][$\w\x7f-\uffff]*)([^\n\S]*:(?!:))?/; + + NUMBER = /^0b[01]+|^0o[0-7]+|^0x[\da-f]+|^\d*\.?\d+(?:e[+-]?\d+)?/i; + + HEREDOC = /^("""|''')([\s\S]*?)(?:\n[^\n\S]*)?\1/; + + OPERATOR = /^(?:[-=]>|[-+*\/%<>&|^!?=]=|>>>=?|([-+:])\1|([&|<>])\2=?|\?(\.|::)|\.{2,3})/; + + WHITESPACE = /^[^\n\S]+/; + + COMMENT = /^###([^#][\s\S]*?)(?:###[^\n\S]*|(?:###)$)|^(?:\s*#(?!##[^#]).*)+/; + + LITERATE = /^([ ]{4}|\t)/; + + CODE = /^[-=]>/; + + MULTI_DENT = /^(?:\n[^\n\S]*)+/; + + SIMPLESTR = /^'[^\\']*(?:\\.[^\\']*)*'/; + + JSTOKEN = /^`[^\\`]*(?:\\.[^\\`]*)*`/; + + REGEX = /^(\/(?![\s=])[^[\/\n\\]*(?:(?:\\[\s\S]|\[[^\]\n\\]*(?:\\[\s\S][^\]\n\\]*)*])[^[\/\n\\]*)*\/)([imgy]{0,4})(?!\w)/; + + HEREGEX = /^\/{3}([\s\S]+?)\/{3}([imgy]{0,4})(?!\w)/; + + HEREGEX_OMIT = /\s+(?:#.*)?/g; + + MULTILINER = /\n/g; + + HEREDOC_INDENT = /\n+([^\n\S]*)/g; + + HEREDOC_ILLEGAL = /\*\//; + + LINE_CONTINUER = /^\s*(?:,|\??\.(?![.\d])|::)/; + + TRAILING_SPACES = /\s+$/; + + COMPOUND_ASSIGN = ['-=', '+=', '/=', '*=', '%=', '||=', '&&=', '?=', '<<=', '>>=', '>>>=', '&=', '^=', '|=']; + + UNARY = ['!', '~', 'NEW', 'TYPEOF', 'DELETE', 'DO']; + + LOGIC = ['&&', '||', '&', '|', '^']; + + SHIFT = ['<<', '>>', '>>>']; + + COMPARE = ['==', '!=', '<', '>', '<=', '>=']; + + MATH = ['*', '/', '%']; + + RELATION = ['IN', 'OF', 'INSTANCEOF']; + + BOOL = ['TRUE', 'FALSE']; + + NOT_REGEX = ['NUMBER', 'REGEX', 'BOOL', 'NULL', 'UNDEFINED', '++', '--', ']']; + + NOT_SPACED_REGEX = NOT_REGEX.concat(')', '}', 'THIS', 'IDENTIFIER', 'STRING'); + + CALLABLE = ['IDENTIFIER', 'STRING', 'REGEX', ')', ']', '}', '?', '::', '@', 'THIS', 'SUPER']; + + INDEXABLE = CALLABLE.concat('NUMBER', 'BOOL', 'NULL', 'UNDEFINED'); + + LINE_BREAK = ['INDENT', 'OUTDENT', 'TERMINATOR']; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/nodes.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/nodes.js new file mode 100644 index 00000000..c274724d --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/nodes.js @@ -0,0 +1,3088 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var Access, Arr, Assign, Base, Block, Call, Class, Closure, Code, CodeFragment, Comment, Existence, Extends, For, IDENTIFIER, IDENTIFIER_STR, IS_STRING, If, In, Index, LEVEL_ACCESS, LEVEL_COND, LEVEL_LIST, LEVEL_OP, LEVEL_PAREN, LEVEL_TOP, Literal, METHOD_DEF, NEGATE, NO, Obj, Op, Param, Parens, RESERVED, Range, Return, SIMPLENUM, STRICT_PROSCRIBED, Scope, Slice, Splat, Switch, TAB, THIS, Throw, Try, UTILITIES, Value, While, YES, addLocationDataFn, compact, del, ends, extend, flatten, fragmentsToText, last, locationDataToString, merge, multident, some, starts, unfoldSoak, utility, _ref, _ref1, + __hasProp = {}.hasOwnProperty, + __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor(); child.__super__ = parent.prototype; return child; }, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }, + __slice = [].slice; + + Error.stackTraceLimit = Infinity; + + Scope = require('./scope').Scope; + + _ref = require('./lexer'), RESERVED = _ref.RESERVED, STRICT_PROSCRIBED = _ref.STRICT_PROSCRIBED; + + _ref1 = require('./helpers'), compact = _ref1.compact, flatten = _ref1.flatten, extend = _ref1.extend, merge = _ref1.merge, del = _ref1.del, starts = _ref1.starts, ends = _ref1.ends, last = _ref1.last, some = _ref1.some, addLocationDataFn = _ref1.addLocationDataFn, locationDataToString = _ref1.locationDataToString; + + exports.extend = extend; + + exports.addLocationDataFn = addLocationDataFn; + + YES = function() { + return true; + }; + + NO = function() { + return false; + }; + + THIS = function() { + return this; + }; + + NEGATE = function() { + this.negated = !this.negated; + return this; + }; + + exports.CodeFragment = CodeFragment = (function() { + + function CodeFragment(parent, code) { + var _ref2; + this.code = "" + code; + this.locationData = parent != null ? parent.locationData : void 0; + this.type = (parent != null ? (_ref2 = parent.constructor) != null ? _ref2.name : void 0 : void 0) || 'unknown'; + } + + CodeFragment.prototype.toString = function() { + return "" + this.code + [this.locationData ? ": " + locationDataToString(this.locationData) : void 0]; + }; + + return CodeFragment; + + })(); + + fragmentsToText = function(fragments) { + var fragment; + return ((function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = fragments.length; _i < _len; _i++) { + fragment = fragments[_i]; + _results.push(fragment.code); + } + return _results; + })()).join(''); + }; + + exports.Base = Base = (function() { + + function Base() {} + + Base.prototype.compile = function(o, lvl) { + return fragmentsToText(this.compileToFragments(o, lvl)); + }; + + Base.prototype.compileToFragments = function(o, lvl) { + var node; + o = extend({}, o); + if (lvl) { + o.level = lvl; + } + node = this.unfoldSoak(o) || this; + node.tab = o.indent; + if (o.level === LEVEL_TOP || !node.isStatement(o)) { + return node.compileNode(o); + } else { + return node.compileClosure(o); + } + }; + + Base.prototype.compileClosure = function(o) { + if (this.jumps()) { + throw SyntaxError('cannot use a pure statement in an expression.'); + } + o.sharedScope = true; + return Closure.wrap(this).compileNode(o); + }; + + Base.prototype.cache = function(o, level, reused) { + var ref, sub; + if (!this.isComplex()) { + ref = level ? this.compileToFragments(o, level) : this; + return [ref, ref]; + } else { + ref = new Literal(reused || o.scope.freeVariable('ref')); + sub = new Assign(ref, this); + if (level) { + return [sub.compileToFragments(o, level), [this.makeCode(ref.value)]]; + } else { + return [sub, ref]; + } + } + }; + + Base.prototype.cacheToCodeFragments = function(cacheValues) { + return [fragmentsToText(cacheValues[0]), fragmentsToText(cacheValues[1])]; + }; + + Base.prototype.makeReturn = function(res) { + var me; + me = this.unwrapAll(); + if (res) { + return new Call(new Literal("" + res + ".push"), [me]); + } else { + return new Return(me); + } + }; + + Base.prototype.contains = function(pred) { + var contains; + contains = false; + this.traverseChildren(false, function(node) { + if (pred(node)) { + contains = true; + return false; + } + }); + return contains; + }; + + Base.prototype.containsType = function(type) { + return this instanceof type || this.contains(function(node) { + return node instanceof type; + }); + }; + + Base.prototype.lastNonComment = function(list) { + var i; + i = list.length; + while (i--) { + if (!(list[i] instanceof Comment)) { + return list[i]; + } + } + return null; + }; + + Base.prototype.toString = function(idt, name) { + var location, tree; + if (idt == null) { + idt = ''; + } + if (name == null) { + name = this.constructor.name; + } + location = this.locationData ? locationDataToString(this.locationData) : "??"; + tree = '\n' + idt + location + ": " + name; + if (this.soak) { + tree += '?'; + } + this.eachChild(function(node) { + return tree += node.toString(idt + TAB); + }); + return tree; + }; + + Base.prototype.eachChild = function(func) { + var attr, child, _i, _j, _len, _len1, _ref2, _ref3; + if (!this.children) { + return this; + } + _ref2 = this.children; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + attr = _ref2[_i]; + if (this[attr]) { + _ref3 = flatten([this[attr]]); + for (_j = 0, _len1 = _ref3.length; _j < _len1; _j++) { + child = _ref3[_j]; + if (func(child) === false) { + return this; + } + } + } + } + return this; + }; + + Base.prototype.traverseChildren = function(crossScope, func) { + return this.eachChild(function(child) { + if (func(child) === false) { + return false; + } + return child.traverseChildren(crossScope, func); + }); + }; + + Base.prototype.invert = function() { + return new Op('!', this); + }; + + Base.prototype.unwrapAll = function() { + var node; + node = this; + while (node !== (node = node.unwrap())) { + continue; + } + return node; + }; + + Base.prototype.children = []; + + Base.prototype.isStatement = NO; + + Base.prototype.jumps = NO; + + Base.prototype.isComplex = YES; + + Base.prototype.isChainable = NO; + + Base.prototype.isAssignable = NO; + + Base.prototype.unwrap = THIS; + + Base.prototype.unfoldSoak = NO; + + Base.prototype.assigns = NO; + + Base.prototype.updateLocationDataIfMissing = function(locationData) { + if (!this.locationData) { + this.locationData = {}; + extend(this.locationData, locationData); + } + return this.eachChild(function(child) { + return child.updateLocationDataIfMissing(locationData); + }); + }; + + Base.prototype.makeCode = function(code) { + return new CodeFragment(this, code); + }; + + Base.prototype.wrapInBraces = function(fragments) { + return [].concat(this.makeCode('('), fragments, this.makeCode(')')); + }; + + Base.prototype.joinFragmentArrays = function(fragmentsList, joinStr) { + var answer, fragments, i, _i, _len; + answer = []; + for (i = _i = 0, _len = fragmentsList.length; _i < _len; i = ++_i) { + fragments = fragmentsList[i]; + if (i) { + answer.push(this.makeCode(joinStr)); + } + answer = answer.concat(fragments); + } + return answer; + }; + + return Base; + + })(); + + exports.Block = Block = (function(_super) { + + __extends(Block, _super); + + function Block(nodes) { + this.expressions = compact(flatten(nodes || [])); + } + + Block.prototype.children = ['expressions']; + + Block.prototype.push = function(node) { + this.expressions.push(node); + return this; + }; + + Block.prototype.pop = function() { + return this.expressions.pop(); + }; + + Block.prototype.unshift = function(node) { + this.expressions.unshift(node); + return this; + }; + + Block.prototype.unwrap = function() { + if (this.expressions.length === 1) { + return this.expressions[0]; + } else { + return this; + } + }; + + Block.prototype.isEmpty = function() { + return !this.expressions.length; + }; + + Block.prototype.isStatement = function(o) { + var exp, _i, _len, _ref2; + _ref2 = this.expressions; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + exp = _ref2[_i]; + if (exp.isStatement(o)) { + return true; + } + } + return false; + }; + + Block.prototype.jumps = function(o) { + var exp, _i, _len, _ref2; + _ref2 = this.expressions; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + exp = _ref2[_i]; + if (exp.jumps(o)) { + return exp; + } + } + }; + + Block.prototype.makeReturn = function(res) { + var expr, len; + len = this.expressions.length; + while (len--) { + expr = this.expressions[len]; + if (!(expr instanceof Comment)) { + this.expressions[len] = expr.makeReturn(res); + if (expr instanceof Return && !expr.expression) { + this.expressions.splice(len, 1); + } + break; + } + } + return this; + }; + + Block.prototype.compileToFragments = function(o, level) { + if (o == null) { + o = {}; + } + if (o.scope) { + return Block.__super__.compileToFragments.call(this, o, level); + } else { + return this.compileRoot(o); + } + }; + + Block.prototype.compileNode = function(o) { + var answer, compiledNodes, fragments, index, node, top, _i, _len, _ref2; + this.tab = o.indent; + top = o.level === LEVEL_TOP; + compiledNodes = []; + _ref2 = this.expressions; + for (index = _i = 0, _len = _ref2.length; _i < _len; index = ++_i) { + node = _ref2[index]; + node = node.unwrapAll(); + node = node.unfoldSoak(o) || node; + if (node instanceof Block) { + compiledNodes.push(node.compileNode(o)); + } else if (top) { + node.front = true; + fragments = node.compileToFragments(o); + if (!node.isStatement(o)) { + fragments.unshift(this.makeCode("" + this.tab)); + fragments.push(this.makeCode(";")); + } + compiledNodes.push(fragments); + } else { + compiledNodes.push(node.compileToFragments(o, LEVEL_LIST)); + } + } + if (top) { + if (this.spaced) { + return [].concat(this.makeCode("\n"), this.joinFragmentArrays(compiledNodes, '\n\n'), this.makeCode("\n")); + } else { + return this.joinFragmentArrays(compiledNodes, '\n'); + } + } + if (compiledNodes.length) { + answer = this.joinFragmentArrays(compiledNodes, ', '); + } else { + answer = [this.makeCode("void 0")]; + } + if (compiledNodes.length > 1 && o.level >= LEVEL_LIST) { + return this.wrapInBraces(answer); + } else { + return answer; + } + }; + + Block.prototype.compileRoot = function(o) { + var exp, fragments, i, prelude, preludeExps, rest; + o.indent = o.bare ? '' : TAB; + o.scope = new Scope(null, this, null); + o.level = LEVEL_TOP; + this.spaced = true; + prelude = []; + if (!o.bare) { + preludeExps = (function() { + var _i, _len, _ref2, _results; + _ref2 = this.expressions; + _results = []; + for (i = _i = 0, _len = _ref2.length; _i < _len; i = ++_i) { + exp = _ref2[i]; + if (!(exp.unwrap() instanceof Comment)) { + break; + } + _results.push(exp); + } + return _results; + }).call(this); + rest = this.expressions.slice(preludeExps.length); + this.expressions = preludeExps; + if (preludeExps.length) { + prelude = this.compileNode(merge(o, { + indent: '' + })); + prelude.push(this.makeCode("\n")); + } + this.expressions = rest; + } + fragments = this.compileWithDeclarations(o); + if (o.bare) { + return fragments; + } + return [].concat(prelude, this.makeCode("(function() {\n"), fragments, this.makeCode("\n}).call(this);\n")); + }; + + Block.prototype.compileWithDeclarations = function(o) { + var assigns, declars, exp, fragments, i, post, rest, scope, spaced, _i, _len, _ref2, _ref3, _ref4; + fragments = []; + post = []; + _ref2 = this.expressions; + for (i = _i = 0, _len = _ref2.length; _i < _len; i = ++_i) { + exp = _ref2[i]; + exp = exp.unwrap(); + if (!(exp instanceof Comment || exp instanceof Literal)) { + break; + } + } + o = merge(o, { + level: LEVEL_TOP + }); + if (i) { + rest = this.expressions.splice(i, 9e9); + _ref3 = [this.spaced, false], spaced = _ref3[0], this.spaced = _ref3[1]; + _ref4 = [this.compileNode(o), spaced], fragments = _ref4[0], this.spaced = _ref4[1]; + this.expressions = rest; + } + post = this.compileNode(o); + scope = o.scope; + if (scope.expressions === this) { + declars = o.scope.hasDeclarations(); + assigns = scope.hasAssignments; + if (declars || assigns) { + if (i) { + fragments.push(this.makeCode('\n')); + } + fragments.push(this.makeCode("" + this.tab + "var ")); + if (declars) { + fragments.push(this.makeCode(scope.declaredVariables().join(', '))); + } + if (assigns) { + if (declars) { + fragments.push(this.makeCode(",\n" + (this.tab + TAB))); + } + fragments.push(this.makeCode(scope.assignedVariables().join(",\n" + (this.tab + TAB)))); + } + fragments.push(this.makeCode(';\n')); + } + } + return fragments.concat(post); + }; + + Block.wrap = function(nodes) { + if (nodes.length === 1 && nodes[0] instanceof Block) { + return nodes[0]; + } + return new Block(nodes); + }; + + return Block; + + })(Base); + + exports.Literal = Literal = (function(_super) { + + __extends(Literal, _super); + + function Literal(value) { + this.value = value; + } + + Literal.prototype.makeReturn = function() { + if (this.isStatement()) { + return this; + } else { + return Literal.__super__.makeReturn.apply(this, arguments); + } + }; + + Literal.prototype.isAssignable = function() { + return IDENTIFIER.test(this.value); + }; + + Literal.prototype.isStatement = function() { + var _ref2; + return (_ref2 = this.value) === 'break' || _ref2 === 'continue' || _ref2 === 'debugger'; + }; + + Literal.prototype.isComplex = NO; + + Literal.prototype.assigns = function(name) { + return name === this.value; + }; + + Literal.prototype.jumps = function(o) { + if (this.value === 'break' && !((o != null ? o.loop : void 0) || (o != null ? o.block : void 0))) { + return this; + } + if (this.value === 'continue' && !(o != null ? o.loop : void 0)) { + return this; + } + }; + + Literal.prototype.compileNode = function(o) { + var answer, code, _ref2; + code = this.value === 'this' ? ((_ref2 = o.scope.method) != null ? _ref2.bound : void 0) ? o.scope.method.context : this.value : this.value.reserved ? "\"" + this.value + "\"" : this.value; + answer = this.isStatement() ? "" + this.tab + code + ";" : code; + return [this.makeCode(answer)]; + }; + + Literal.prototype.toString = function() { + return ' "' + this.value + '"'; + }; + + return Literal; + + })(Base); + + exports.Undefined = (function(_super) { + + __extends(Undefined, _super); + + function Undefined() { + return Undefined.__super__.constructor.apply(this, arguments); + } + + Undefined.prototype.isAssignable = NO; + + Undefined.prototype.isComplex = NO; + + Undefined.prototype.compileNode = function(o) { + return [this.makeCode(o.level >= LEVEL_ACCESS ? '(void 0)' : 'void 0')]; + }; + + return Undefined; + + })(Base); + + exports.Null = (function(_super) { + + __extends(Null, _super); + + function Null() { + return Null.__super__.constructor.apply(this, arguments); + } + + Null.prototype.isAssignable = NO; + + Null.prototype.isComplex = NO; + + Null.prototype.compileNode = function() { + return [this.makeCode("null")]; + }; + + return Null; + + })(Base); + + exports.Bool = (function(_super) { + + __extends(Bool, _super); + + Bool.prototype.isAssignable = NO; + + Bool.prototype.isComplex = NO; + + Bool.prototype.compileNode = function() { + return [this.makeCode(this.val)]; + }; + + function Bool(val) { + this.val = val; + } + + return Bool; + + })(Base); + + exports.Return = Return = (function(_super) { + + __extends(Return, _super); + + function Return(expr) { + if (expr && !expr.unwrap().isUndefined) { + this.expression = expr; + } + } + + Return.prototype.children = ['expression']; + + Return.prototype.isStatement = YES; + + Return.prototype.makeReturn = THIS; + + Return.prototype.jumps = THIS; + + Return.prototype.compileToFragments = function(o, level) { + var expr, _ref2; + expr = (_ref2 = this.expression) != null ? _ref2.makeReturn() : void 0; + if (expr && !(expr instanceof Return)) { + return expr.compileToFragments(o, level); + } else { + return Return.__super__.compileToFragments.call(this, o, level); + } + }; + + Return.prototype.compileNode = function(o) { + var answer; + answer = []; + answer.push(this.makeCode(this.tab + ("return" + [this.expression ? " " : void 0]))); + if (this.expression) { + answer = answer.concat(this.expression.compileToFragments(o, LEVEL_PAREN)); + } + answer.push(this.makeCode(";")); + return answer; + }; + + return Return; + + })(Base); + + exports.Value = Value = (function(_super) { + + __extends(Value, _super); + + function Value(base, props, tag) { + if (!props && base instanceof Value) { + return base; + } + this.base = base; + this.properties = props || []; + if (tag) { + this[tag] = true; + } + return this; + } + + Value.prototype.children = ['base', 'properties']; + + Value.prototype.add = function(props) { + this.properties = this.properties.concat(props); + return this; + }; + + Value.prototype.hasProperties = function() { + return !!this.properties.length; + }; + + Value.prototype.isArray = function() { + return !this.properties.length && this.base instanceof Arr; + }; + + Value.prototype.isComplex = function() { + return this.hasProperties() || this.base.isComplex(); + }; + + Value.prototype.isAssignable = function() { + return this.hasProperties() || this.base.isAssignable(); + }; + + Value.prototype.isSimpleNumber = function() { + return this.base instanceof Literal && SIMPLENUM.test(this.base.value); + }; + + Value.prototype.isString = function() { + return this.base instanceof Literal && IS_STRING.test(this.base.value); + }; + + Value.prototype.isAtomic = function() { + var node, _i, _len, _ref2; + _ref2 = this.properties.concat(this.base); + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + node = _ref2[_i]; + if (node.soak || node instanceof Call) { + return false; + } + } + return true; + }; + + Value.prototype.isStatement = function(o) { + return !this.properties.length && this.base.isStatement(o); + }; + + Value.prototype.assigns = function(name) { + return !this.properties.length && this.base.assigns(name); + }; + + Value.prototype.jumps = function(o) { + return !this.properties.length && this.base.jumps(o); + }; + + Value.prototype.isObject = function(onlyGenerated) { + if (this.properties.length) { + return false; + } + return (this.base instanceof Obj) && (!onlyGenerated || this.base.generated); + }; + + Value.prototype.isSplice = function() { + return last(this.properties) instanceof Slice; + }; + + Value.prototype.unwrap = function() { + if (this.properties.length) { + return this; + } else { + return this.base; + } + }; + + Value.prototype.cacheReference = function(o) { + var base, bref, name, nref; + name = last(this.properties); + if (this.properties.length < 2 && !this.base.isComplex() && !(name != null ? name.isComplex() : void 0)) { + return [this, this]; + } + base = new Value(this.base, this.properties.slice(0, -1)); + if (base.isComplex()) { + bref = new Literal(o.scope.freeVariable('base')); + base = new Value(new Parens(new Assign(bref, base))); + } + if (!name) { + return [base, bref]; + } + if (name.isComplex()) { + nref = new Literal(o.scope.freeVariable('name')); + name = new Index(new Assign(nref, name.index)); + nref = new Index(nref); + } + return [base.add(name), new Value(bref || base.base, [nref || name])]; + }; + + Value.prototype.compileNode = function(o) { + var fragments, prop, props, _i, _len; + this.base.front = this.front; + props = this.properties; + fragments = this.base.compileToFragments(o, (props.length ? LEVEL_ACCESS : null)); + if ((this.base instanceof Parens || props.length) && SIMPLENUM.test(fragmentsToText(fragments))) { + fragments.push(this.makeCode('.')); + } + for (_i = 0, _len = props.length; _i < _len; _i++) { + prop = props[_i]; + fragments.push.apply(fragments, prop.compileToFragments(o)); + } + return fragments; + }; + + Value.prototype.unfoldSoak = function(o) { + var _ref2, + _this = this; + return (_ref2 = this.unfoldedSoak) != null ? _ref2 : this.unfoldedSoak = (function() { + var fst, i, ifn, prop, ref, snd, _i, _len, _ref3, _ref4; + if (ifn = _this.base.unfoldSoak(o)) { + (_ref3 = ifn.body.properties).push.apply(_ref3, _this.properties); + return ifn; + } + _ref4 = _this.properties; + for (i = _i = 0, _len = _ref4.length; _i < _len; i = ++_i) { + prop = _ref4[i]; + if (!prop.soak) { + continue; + } + prop.soak = false; + fst = new Value(_this.base, _this.properties.slice(0, i)); + snd = new Value(_this.base, _this.properties.slice(i)); + if (fst.isComplex()) { + ref = new Literal(o.scope.freeVariable('ref')); + fst = new Parens(new Assign(ref, fst)); + snd.base = ref; + } + return new If(new Existence(fst), snd, { + soak: true + }); + } + return false; + })(); + }; + + return Value; + + })(Base); + + exports.Comment = Comment = (function(_super) { + + __extends(Comment, _super); + + function Comment(comment) { + this.comment = comment; + } + + Comment.prototype.isStatement = YES; + + Comment.prototype.makeReturn = THIS; + + Comment.prototype.compileNode = function(o, level) { + var code; + code = '/*' + multident(this.comment, this.tab) + ("\n" + this.tab + "*/\n"); + if ((level || o.level) === LEVEL_TOP) { + code = o.indent + code; + } + return [this.makeCode(code)]; + }; + + return Comment; + + })(Base); + + exports.Call = Call = (function(_super) { + + __extends(Call, _super); + + function Call(variable, args, soak) { + this.args = args != null ? args : []; + this.soak = soak; + this.isNew = false; + this.isSuper = variable === 'super'; + this.variable = this.isSuper ? null : variable; + } + + Call.prototype.children = ['variable', 'args']; + + Call.prototype.newInstance = function() { + var base, _ref2; + base = ((_ref2 = this.variable) != null ? _ref2.base : void 0) || this.variable; + if (base instanceof Call && !base.isNew) { + base.newInstance(); + } else { + this.isNew = true; + } + return this; + }; + + Call.prototype.superReference = function(o) { + var accesses, method; + method = o.scope.namedMethod(); + if (method != null ? method.klass : void 0) { + accesses = [new Access(new Literal('__super__'))]; + if (method["static"]) { + accesses.push(new Access(new Literal('constructor'))); + } + accesses.push(new Access(new Literal(method.name))); + return (new Value(new Literal(method.klass), accesses)).compile(o); + } else if (method != null ? method.ctor : void 0) { + return "" + method.name + ".__super__.constructor"; + } else { + throw SyntaxError('cannot call super outside of an instance method.'); + } + }; + + Call.prototype.superThis = function(o) { + var method; + method = o.scope.method; + return (method && !method.klass && method.context) || "this"; + }; + + Call.prototype.unfoldSoak = function(o) { + var call, ifn, left, list, rite, _i, _len, _ref2, _ref3; + if (this.soak) { + if (this.variable) { + if (ifn = unfoldSoak(o, this, 'variable')) { + return ifn; + } + _ref2 = new Value(this.variable).cacheReference(o), left = _ref2[0], rite = _ref2[1]; + } else { + left = new Literal(this.superReference(o)); + rite = new Value(left); + } + rite = new Call(rite, this.args); + rite.isNew = this.isNew; + left = new Literal("typeof " + (left.compile(o)) + " === \"function\""); + return new If(left, new Value(rite), { + soak: true + }); + } + call = this; + list = []; + while (true) { + if (call.variable instanceof Call) { + list.push(call); + call = call.variable; + continue; + } + if (!(call.variable instanceof Value)) { + break; + } + list.push(call); + if (!((call = call.variable.base) instanceof Call)) { + break; + } + } + _ref3 = list.reverse(); + for (_i = 0, _len = _ref3.length; _i < _len; _i++) { + call = _ref3[_i]; + if (ifn) { + if (call.variable instanceof Call) { + call.variable = ifn; + } else { + call.variable.base = ifn; + } + } + ifn = unfoldSoak(o, call, 'variable'); + } + return ifn; + }; + + Call.prototype.compileNode = function(o) { + var arg, argIndex, compiledArgs, compiledArray, fragments, preface, _i, _len, _ref2, _ref3; + if ((_ref2 = this.variable) != null) { + _ref2.front = this.front; + } + compiledArray = Splat.compileSplattedArray(o, this.args, true); + if (compiledArray.length) { + return this.compileSplat(o, compiledArray); + } + compiledArgs = []; + _ref3 = this.args; + for (argIndex = _i = 0, _len = _ref3.length; _i < _len; argIndex = ++_i) { + arg = _ref3[argIndex]; + if (argIndex) { + compiledArgs.push(this.makeCode(", ")); + } + compiledArgs.push.apply(compiledArgs, arg.compileToFragments(o, LEVEL_LIST)); + } + fragments = []; + if (this.isSuper) { + preface = this.superReference(o) + (".call(" + (this.superThis(o))); + if (compiledArgs.length) { + preface += ", "; + } + fragments.push(this.makeCode(preface)); + } else { + if (this.isNew) { + fragments.push(this.makeCode('new ')); + } + fragments.push.apply(fragments, this.variable.compileToFragments(o, LEVEL_ACCESS)); + fragments.push(this.makeCode("(")); + } + fragments.push.apply(fragments, compiledArgs); + fragments.push(this.makeCode(")")); + return fragments; + }; + + Call.prototype.compileSplat = function(o, splatArgs) { + var answer, base, fun, idt, name, ref; + if (this.isSuper) { + return [].concat(this.makeCode("" + (this.superReference(o)) + ".apply(" + (this.superThis(o)) + ", "), splatArgs, this.makeCode(")")); + } + if (this.isNew) { + idt = this.tab + TAB; + return [].concat(this.makeCode("(function(func, args, ctor) {\n" + idt + "ctor.prototype = func.prototype;\n" + idt + "var child = new ctor, result = func.apply(child, args);\n" + idt + "return Object(result) === result ? result : child;\n" + this.tab + "})("), this.variable.compileToFragments(o, LEVEL_LIST), this.makeCode(", "), splatArgs, this.makeCode(", function(){})")); + } + answer = []; + base = new Value(this.variable); + if ((name = base.properties.pop()) && base.isComplex()) { + ref = o.scope.freeVariable('ref'); + answer = answer.concat(this.makeCode("(" + ref + " = "), base.compileToFragments(o, LEVEL_LIST), this.makeCode(")"), name.compileToFragments(o)); + } else { + fun = base.compileToFragments(o, LEVEL_ACCESS); + if (SIMPLENUM.test(fragmentsToText(fun))) { + fun = this.wrapInBraces(fun); + } + if (name) { + ref = fragmentsToText(fun); + fun.push.apply(fun, name.compileToFragments(o)); + } else { + ref = 'null'; + } + answer = answer.concat(fun); + } + return answer = answer.concat(this.makeCode(".apply(" + ref + ", "), splatArgs, this.makeCode(")")); + }; + + return Call; + + })(Base); + + exports.Extends = Extends = (function(_super) { + + __extends(Extends, _super); + + function Extends(child, parent) { + this.child = child; + this.parent = parent; + } + + Extends.prototype.children = ['child', 'parent']; + + Extends.prototype.compileToFragments = function(o) { + return new Call(new Value(new Literal(utility('extends'))), [this.child, this.parent]).compileToFragments(o); + }; + + return Extends; + + })(Base); + + exports.Access = Access = (function(_super) { + + __extends(Access, _super); + + function Access(name, tag) { + this.name = name; + this.name.asKey = true; + this.soak = tag === 'soak'; + } + + Access.prototype.children = ['name']; + + Access.prototype.compileToFragments = function(o) { + var name; + name = this.name.compileToFragments(o); + if (IDENTIFIER.test(fragmentsToText(name))) { + name.unshift(this.makeCode(".")); + } else { + name.unshift(this.makeCode("[")); + name.push(this.makeCode("]")); + } + return name; + }; + + Access.prototype.isComplex = NO; + + return Access; + + })(Base); + + exports.Index = Index = (function(_super) { + + __extends(Index, _super); + + function Index(index) { + this.index = index; + } + + Index.prototype.children = ['index']; + + Index.prototype.compileToFragments = function(o) { + return [].concat(this.makeCode("["), this.index.compileToFragments(o, LEVEL_PAREN), this.makeCode("]")); + }; + + Index.prototype.isComplex = function() { + return this.index.isComplex(); + }; + + return Index; + + })(Base); + + exports.Range = Range = (function(_super) { + + __extends(Range, _super); + + Range.prototype.children = ['from', 'to']; + + function Range(from, to, tag) { + this.from = from; + this.to = to; + this.exclusive = tag === 'exclusive'; + this.equals = this.exclusive ? '' : '='; + } + + Range.prototype.compileVariables = function(o) { + var step, _ref2, _ref3, _ref4, _ref5; + o = merge(o, { + top: true + }); + _ref2 = this.cacheToCodeFragments(this.from.cache(o, LEVEL_LIST)), this.fromC = _ref2[0], this.fromVar = _ref2[1]; + _ref3 = this.cacheToCodeFragments(this.to.cache(o, LEVEL_LIST)), this.toC = _ref3[0], this.toVar = _ref3[1]; + if (step = del(o, 'step')) { + _ref4 = this.cacheToCodeFragments(step.cache(o, LEVEL_LIST)), this.step = _ref4[0], this.stepVar = _ref4[1]; + } + _ref5 = [this.fromVar.match(SIMPLENUM), this.toVar.match(SIMPLENUM)], this.fromNum = _ref5[0], this.toNum = _ref5[1]; + if (this.stepVar) { + return this.stepNum = this.stepVar.match(SIMPLENUM); + } + }; + + Range.prototype.compileNode = function(o) { + var cond, condPart, from, gt, idx, idxName, known, lt, namedIndex, stepPart, to, varPart, _ref2, _ref3; + if (!this.fromVar) { + this.compileVariables(o); + } + if (!o.index) { + return this.compileArray(o); + } + known = this.fromNum && this.toNum; + idx = del(o, 'index'); + idxName = del(o, 'name'); + namedIndex = idxName && idxName !== idx; + varPart = "" + idx + " = " + this.fromC; + if (this.toC !== this.toVar) { + varPart += ", " + this.toC; + } + if (this.step !== this.stepVar) { + varPart += ", " + this.step; + } + _ref2 = ["" + idx + " <" + this.equals, "" + idx + " >" + this.equals], lt = _ref2[0], gt = _ref2[1]; + condPart = this.stepNum ? +this.stepNum > 0 ? "" + lt + " " + this.toVar : "" + gt + " " + this.toVar : known ? ((_ref3 = [+this.fromNum, +this.toNum], from = _ref3[0], to = _ref3[1], _ref3), from <= to ? "" + lt + " " + to : "" + gt + " " + to) : (cond = this.stepVar ? "" + this.stepVar + " > 0" : "" + this.fromVar + " <= " + this.toVar, "" + cond + " ? " + lt + " " + this.toVar + " : " + gt + " " + this.toVar); + stepPart = this.stepVar ? "" + idx + " += " + this.stepVar : known ? namedIndex ? from <= to ? "++" + idx : "--" + idx : from <= to ? "" + idx + "++" : "" + idx + "--" : namedIndex ? "" + cond + " ? ++" + idx + " : --" + idx : "" + cond + " ? " + idx + "++ : " + idx + "--"; + if (namedIndex) { + varPart = "" + idxName + " = " + varPart; + } + if (namedIndex) { + stepPart = "" + idxName + " = " + stepPart; + } + return [this.makeCode("" + varPart + "; " + condPart + "; " + stepPart)]; + }; + + Range.prototype.compileArray = function(o) { + var args, body, cond, hasArgs, i, idt, post, pre, range, result, vars, _i, _ref2, _ref3, _results; + if (this.fromNum && this.toNum && Math.abs(this.fromNum - this.toNum) <= 20) { + range = (function() { + _results = []; + for (var _i = _ref2 = +this.fromNum, _ref3 = +this.toNum; _ref2 <= _ref3 ? _i <= _ref3 : _i >= _ref3; _ref2 <= _ref3 ? _i++ : _i--){ _results.push(_i); } + return _results; + }).apply(this); + if (this.exclusive) { + range.pop(); + } + return [this.makeCode("[" + (range.join(', ')) + "]")]; + } + idt = this.tab + TAB; + i = o.scope.freeVariable('i'); + result = o.scope.freeVariable('results'); + pre = "\n" + idt + result + " = [];"; + if (this.fromNum && this.toNum) { + o.index = i; + body = fragmentsToText(this.compileNode(o)); + } else { + vars = ("" + i + " = " + this.fromC) + (this.toC !== this.toVar ? ", " + this.toC : ''); + cond = "" + this.fromVar + " <= " + this.toVar; + body = "var " + vars + "; " + cond + " ? " + i + " <" + this.equals + " " + this.toVar + " : " + i + " >" + this.equals + " " + this.toVar + "; " + cond + " ? " + i + "++ : " + i + "--"; + } + post = "{ " + result + ".push(" + i + "); }\n" + idt + "return " + result + ";\n" + o.indent; + hasArgs = function(node) { + return node != null ? node.contains(function(n) { + return n instanceof Literal && n.value === 'arguments' && !n.asKey; + }) : void 0; + }; + if (hasArgs(this.from) || hasArgs(this.to)) { + args = ', arguments'; + } + return [this.makeCode("(function() {" + pre + "\n" + idt + "for (" + body + ")" + post + "}).apply(this" + (args != null ? args : '') + ")")]; + }; + + return Range; + + })(Base); + + exports.Slice = Slice = (function(_super) { + + __extends(Slice, _super); + + Slice.prototype.children = ['range']; + + function Slice(range) { + this.range = range; + Slice.__super__.constructor.call(this); + } + + Slice.prototype.compileNode = function(o) { + var compiled, compiledText, from, fromCompiled, to, toStr, _ref2; + _ref2 = this.range, to = _ref2.to, from = _ref2.from; + fromCompiled = from && from.compileToFragments(o, LEVEL_PAREN) || [this.makeCode('0')]; + if (to) { + compiled = to.compileToFragments(o, LEVEL_PAREN); + compiledText = fragmentsToText(compiled); + if (!(!this.range.exclusive && +compiledText === -1)) { + toStr = ', ' + (this.range.exclusive ? compiledText : SIMPLENUM.test(compiledText) ? "" + (+compiledText + 1) : (compiled = to.compileToFragments(o, LEVEL_ACCESS), "+" + (fragmentsToText(compiled)) + " + 1 || 9e9")); + } + } + return [this.makeCode(".slice(" + (fragmentsToText(fromCompiled)) + (toStr || '') + ")")]; + }; + + return Slice; + + })(Base); + + exports.Obj = Obj = (function(_super) { + + __extends(Obj, _super); + + function Obj(props, generated) { + this.generated = generated != null ? generated : false; + this.objects = this.properties = props || []; + } + + Obj.prototype.children = ['properties']; + + Obj.prototype.compileNode = function(o) { + var answer, i, idt, indent, join, lastNoncom, node, prop, props, _i, _j, _len, _len1; + props = this.properties; + if (!props.length) { + return [this.makeCode(this.front ? '({})' : '{}')]; + } + if (this.generated) { + for (_i = 0, _len = props.length; _i < _len; _i++) { + node = props[_i]; + if (node instanceof Value) { + throw new Error('cannot have an implicit value in an implicit object'); + } + } + } + idt = o.indent += TAB; + lastNoncom = this.lastNonComment(this.properties); + answer = []; + for (i = _j = 0, _len1 = props.length; _j < _len1; i = ++_j) { + prop = props[i]; + join = i === props.length - 1 ? '' : prop === lastNoncom || prop instanceof Comment ? '\n' : ',\n'; + indent = prop instanceof Comment ? '' : idt; + if (prop instanceof Value && prop["this"]) { + prop = new Assign(prop.properties[0].name, prop, 'object'); + } + if (!(prop instanceof Comment)) { + if (!(prop instanceof Assign)) { + prop = new Assign(prop, prop, 'object'); + } + (prop.variable.base || prop.variable).asKey = true; + } + if (indent) { + answer.push(this.makeCode(indent)); + } + answer.push.apply(answer, prop.compileToFragments(o, LEVEL_TOP)); + if (join) { + answer.push(this.makeCode(join)); + } + } + answer.unshift(this.makeCode("{" + (props.length && '\n'))); + answer.push(this.makeCode("" + (props.length && '\n' + this.tab) + "}")); + if (this.front) { + return this.wrapInBraces(answer); + } else { + return answer; + } + }; + + Obj.prototype.assigns = function(name) { + var prop, _i, _len, _ref2; + _ref2 = this.properties; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + prop = _ref2[_i]; + if (prop.assigns(name)) { + return true; + } + } + return false; + }; + + return Obj; + + })(Base); + + exports.Arr = Arr = (function(_super) { + + __extends(Arr, _super); + + function Arr(objs) { + this.objects = objs || []; + } + + Arr.prototype.children = ['objects']; + + Arr.prototype.compileNode = function(o) { + var answer, compiledObjs, fragments, index, obj, _i, _len; + if (!this.objects.length) { + return [this.makeCode('[]')]; + } + o.indent += TAB; + answer = Splat.compileSplattedArray(o, this.objects); + if (answer.length) { + return answer; + } + answer = []; + compiledObjs = (function() { + var _i, _len, _ref2, _results; + _ref2 = this.objects; + _results = []; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + obj = _ref2[_i]; + _results.push(obj.compileToFragments(o, LEVEL_LIST)); + } + return _results; + }).call(this); + for (index = _i = 0, _len = compiledObjs.length; _i < _len; index = ++_i) { + fragments = compiledObjs[index]; + if (index) { + answer.push(this.makeCode(", ")); + } + answer.push.apply(answer, fragments); + } + if ((fragmentsToText(answer)).indexOf('\n') >= 0) { + answer.unshift(this.makeCode("[\n" + o.indent)); + answer.push(this.makeCode("\n" + this.tab + "]")); + } else { + answer.unshift(this.makeCode("[")); + answer.push(this.makeCode("]")); + } + return answer; + }; + + Arr.prototype.assigns = function(name) { + var obj, _i, _len, _ref2; + _ref2 = this.objects; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + obj = _ref2[_i]; + if (obj.assigns(name)) { + return true; + } + } + return false; + }; + + return Arr; + + })(Base); + + exports.Class = Class = (function(_super) { + + __extends(Class, _super); + + function Class(variable, parent, body) { + this.variable = variable; + this.parent = parent; + this.body = body != null ? body : new Block; + this.boundFuncs = []; + this.body.classBody = true; + } + + Class.prototype.children = ['variable', 'parent', 'body']; + + Class.prototype.determineName = function() { + var decl, tail; + if (!this.variable) { + return null; + } + decl = (tail = last(this.variable.properties)) ? tail instanceof Access && tail.name.value : this.variable.base.value; + if (__indexOf.call(STRICT_PROSCRIBED, decl) >= 0) { + throw SyntaxError("variable name may not be " + decl); + } + return decl && (decl = IDENTIFIER.test(decl) && decl); + }; + + Class.prototype.setContext = function(name) { + return this.body.traverseChildren(false, function(node) { + if (node.classBody) { + return false; + } + if (node instanceof Literal && node.value === 'this') { + return node.value = name; + } else if (node instanceof Code) { + node.klass = name; + if (node.bound) { + return node.context = name; + } + } + }); + }; + + Class.prototype.addBoundFunctions = function(o) { + var body, bound, func, lhs, name, rhs, _i, _len, _ref2, _ref3; + if (this.boundFuncs.length) { + o.scope.assign('_this', 'this'); + _ref2 = this.boundFuncs; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + _ref3 = _ref2[_i], name = _ref3[0], func = _ref3[1]; + lhs = new Value(new Literal("this"), [new Access(name)]); + body = new Block([new Return(new Literal("" + this.ctor.name + ".prototype." + name.value + ".apply(_this, arguments)"))]); + rhs = new Code(func.params, body, 'boundfunc'); + bound = new Assign(lhs, rhs); + this.ctor.body.unshift(bound); + } + } + }; + + Class.prototype.addProperties = function(node, name, o) { + var assign, base, exprs, func, props; + props = node.base.properties.slice(0); + exprs = (function() { + var _results; + _results = []; + while (assign = props.shift()) { + if (assign instanceof Assign) { + base = assign.variable.base; + delete assign.context; + func = assign.value; + if (base.value === 'constructor') { + if (this.ctor) { + throw new Error('cannot define more than one constructor in a class'); + } + if (func.bound) { + throw new Error('cannot define a constructor as a bound function'); + } + if (func instanceof Code) { + assign = this.ctor = func; + } else { + this.externalCtor = o.scope.freeVariable('class'); + assign = new Assign(new Literal(this.externalCtor), func); + } + } else { + if (assign.variable["this"]) { + func["static"] = true; + if (func.bound) { + func.context = name; + } + } else { + assign.variable = new Value(new Literal(name), [new Access(new Literal('prototype')), new Access(base)]); + if (func instanceof Code && func.bound) { + this.boundFuncs.push([base, func]); + func.bound = false; + } + } + } + } + _results.push(assign); + } + return _results; + }).call(this); + return compact(exprs); + }; + + Class.prototype.walkBody = function(name, o) { + var _this = this; + return this.traverseChildren(false, function(child) { + var cont, exps, i, node, _i, _len, _ref2; + cont = true; + if (child instanceof Class) { + return false; + } + if (child instanceof Block) { + _ref2 = exps = child.expressions; + for (i = _i = 0, _len = _ref2.length; _i < _len; i = ++_i) { + node = _ref2[i]; + if (node instanceof Value && node.isObject(true)) { + cont = false; + exps[i] = _this.addProperties(node, name, o); + } + } + child.expressions = exps = flatten(exps); + } + return cont && !(child instanceof Class); + }); + }; + + Class.prototype.hoistDirectivePrologue = function() { + var expressions, index, node; + index = 0; + expressions = this.body.expressions; + while ((node = expressions[index]) && node instanceof Comment || node instanceof Value && node.isString()) { + ++index; + } + return this.directives = expressions.splice(0, index); + }; + + Class.prototype.ensureConstructor = function(name) { + if (!this.ctor) { + this.ctor = new Code; + if (this.parent) { + this.ctor.body.push(new Literal("" + name + ".__super__.constructor.apply(this, arguments)")); + } + if (this.externalCtor) { + this.ctor.body.push(new Literal("" + this.externalCtor + ".apply(this, arguments)")); + } + this.ctor.body.makeReturn(); + this.body.expressions.unshift(this.ctor); + } + this.ctor.ctor = this.ctor.name = name; + this.ctor.klass = null; + return this.ctor.noReturn = true; + }; + + Class.prototype.compileNode = function(o) { + var call, decl, klass, lname, name, params, _ref2; + decl = this.determineName(); + name = decl || '_Class'; + if (name.reserved) { + name = "_" + name; + } + lname = new Literal(name); + this.hoistDirectivePrologue(); + this.setContext(name); + this.walkBody(name, o); + this.ensureConstructor(name); + this.body.spaced = true; + if (!(this.ctor instanceof Code)) { + this.body.expressions.unshift(this.ctor); + } + this.body.expressions.push(lname); + (_ref2 = this.body.expressions).unshift.apply(_ref2, this.directives); + this.addBoundFunctions(o); + call = Closure.wrap(this.body); + if (this.parent) { + this.superClass = new Literal(o.scope.freeVariable('super', false)); + this.body.expressions.unshift(new Extends(lname, this.superClass)); + call.args.push(this.parent); + params = call.variable.params || call.variable.base.params; + params.push(new Param(this.superClass)); + } + klass = new Parens(call, true); + if (this.variable) { + klass = new Assign(this.variable, klass); + } + return klass.compileToFragments(o); + }; + + return Class; + + })(Base); + + exports.Assign = Assign = (function(_super) { + + __extends(Assign, _super); + + function Assign(variable, value, context, options) { + var forbidden, name, _ref2; + this.variable = variable; + this.value = value; + this.context = context; + this.param = options && options.param; + this.subpattern = options && options.subpattern; + forbidden = (_ref2 = (name = this.variable.unwrapAll().value), __indexOf.call(STRICT_PROSCRIBED, _ref2) >= 0); + if (forbidden && this.context !== 'object') { + throw SyntaxError("variable name may not be \"" + name + "\""); + } + } + + Assign.prototype.children = ['variable', 'value']; + + Assign.prototype.isStatement = function(o) { + return (o != null ? o.level : void 0) === LEVEL_TOP && (this.context != null) && __indexOf.call(this.context, "?") >= 0; + }; + + Assign.prototype.assigns = function(name) { + return this[this.context === 'object' ? 'value' : 'variable'].assigns(name); + }; + + Assign.prototype.unfoldSoak = function(o) { + return unfoldSoak(o, this, 'variable'); + }; + + Assign.prototype.compileNode = function(o) { + var answer, compiledName, isValue, match, name, val, varBase, _ref2, _ref3, _ref4, _ref5; + if (isValue = this.variable instanceof Value) { + if (this.variable.isArray() || this.variable.isObject()) { + return this.compilePatternMatch(o); + } + if (this.variable.isSplice()) { + return this.compileSplice(o); + } + if ((_ref2 = this.context) === '||=' || _ref2 === '&&=' || _ref2 === '?=') { + return this.compileConditional(o); + } + } + compiledName = this.variable.compileToFragments(o, LEVEL_LIST); + name = fragmentsToText(compiledName); + if (!this.context) { + if (!(varBase = this.variable.unwrapAll()).isAssignable()) { + throw SyntaxError("\"" + (this.variable.compile(o)) + "\" cannot be assigned."); + } + if (!(typeof varBase.hasProperties === "function" ? varBase.hasProperties() : void 0)) { + if (this.param) { + o.scope.add(name, 'var'); + } else { + o.scope.find(name); + } + } + } + if (this.value instanceof Code && (match = METHOD_DEF.exec(name))) { + if (match[1]) { + this.value.klass = match[1]; + } + this.value.name = (_ref3 = (_ref4 = (_ref5 = match[2]) != null ? _ref5 : match[3]) != null ? _ref4 : match[4]) != null ? _ref3 : match[5]; + } + val = this.value.compileToFragments(o, LEVEL_LIST); + if (this.context === 'object') { + return compiledName.concat(this.makeCode(": "), val); + } + answer = compiledName.concat(this.makeCode(" " + (this.context || '=') + " "), val); + if (o.level <= LEVEL_LIST) { + return answer; + } else { + return this.wrapInBraces(answer); + } + }; + + Assign.prototype.compilePatternMatch = function(o) { + var acc, assigns, code, fragments, i, idx, isObject, ivar, name, obj, objects, olen, ref, rest, splat, top, val, value, vvar, vvarText, _i, _len, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7; + top = o.level === LEVEL_TOP; + value = this.value; + objects = this.variable.base.objects; + if (!(olen = objects.length)) { + code = value.compileToFragments(o); + if (o.level >= LEVEL_OP) { + return this.wrapInBraces(code); + } else { + return code; + } + } + isObject = this.variable.isObject(); + if (top && olen === 1 && !((obj = objects[0]) instanceof Splat)) { + if (obj instanceof Assign) { + _ref2 = obj, (_ref3 = _ref2.variable, idx = _ref3.base), obj = _ref2.value; + } else { + idx = isObject ? obj["this"] ? obj.properties[0].name : obj : new Literal(0); + } + acc = IDENTIFIER.test(idx.unwrap().value || 0); + value = new Value(value); + value.properties.push(new (acc ? Access : Index)(idx)); + if (_ref4 = obj.unwrap().value, __indexOf.call(RESERVED, _ref4) >= 0) { + throw new SyntaxError("assignment to a reserved word: " + (obj.compile(o)) + " = " + (value.compile(o))); + } + return new Assign(obj, value, null, { + param: this.param + }).compileToFragments(o, LEVEL_TOP); + } + vvar = value.compileToFragments(o, LEVEL_LIST); + vvarText = fragmentsToText(vvar); + assigns = []; + splat = false; + if (!IDENTIFIER.test(vvarText) || this.variable.assigns(vvarText)) { + assigns.push([this.makeCode("" + (ref = o.scope.freeVariable('ref')) + " = ")].concat(__slice.call(vvar))); + vvar = [this.makeCode(ref)]; + vvarText = ref; + } + for (i = _i = 0, _len = objects.length; _i < _len; i = ++_i) { + obj = objects[i]; + idx = i; + if (isObject) { + if (obj instanceof Assign) { + _ref5 = obj, (_ref6 = _ref5.variable, idx = _ref6.base), obj = _ref5.value; + } else { + if (obj.base instanceof Parens) { + _ref7 = new Value(obj.unwrapAll()).cacheReference(o), obj = _ref7[0], idx = _ref7[1]; + } else { + idx = obj["this"] ? obj.properties[0].name : obj; + } + } + } + if (!splat && obj instanceof Splat) { + name = obj.name.unwrap().value; + obj = obj.unwrap(); + val = "" + olen + " <= " + vvarText + ".length ? " + (utility('slice')) + ".call(" + vvarText + ", " + i; + if (rest = olen - i - 1) { + ivar = o.scope.freeVariable('i'); + val += ", " + ivar + " = " + vvarText + ".length - " + rest + ") : (" + ivar + " = " + i + ", [])"; + } else { + val += ") : []"; + } + val = new Literal(val); + splat = "" + ivar + "++"; + } else { + name = obj.unwrap().value; + if (obj instanceof Splat) { + obj = obj.name.compileToFragments(o); + throw new SyntaxError("multiple splats are disallowed in an assignment: " + obj + "..."); + } + if (typeof idx === 'number') { + idx = new Literal(splat || idx); + acc = false; + } else { + acc = isObject && IDENTIFIER.test(idx.unwrap().value || 0); + } + val = new Value(new Literal(vvarText), [new (acc ? Access : Index)(idx)]); + } + if ((name != null) && __indexOf.call(RESERVED, name) >= 0) { + throw new SyntaxError("assignment to a reserved word: " + (obj.compile(o)) + " = " + (val.compile(o))); + } + assigns.push(new Assign(obj, val, null, { + param: this.param, + subpattern: true + }).compileToFragments(o, LEVEL_LIST)); + } + if (!(top || this.subpattern)) { + assigns.push(vvar); + } + fragments = this.joinFragmentArrays(assigns, ', '); + if (o.level < LEVEL_LIST) { + return fragments; + } else { + return this.wrapInBraces(fragments); + } + }; + + Assign.prototype.compileConditional = function(o) { + var left, right, _ref2; + _ref2 = this.variable.cacheReference(o), left = _ref2[0], right = _ref2[1]; + if (!left.properties.length && left.base instanceof Literal && left.base.value !== "this" && !o.scope.check(left.base.value)) { + throw new Error("the variable \"" + left.base.value + "\" can't be assigned with " + this.context + " because it has not been defined."); + } + if (__indexOf.call(this.context, "?") >= 0) { + o.isExistentialEquals = true; + } + return new Op(this.context.slice(0, -1), left, new Assign(right, this.value, '=')).compileToFragments(o); + }; + + Assign.prototype.compileSplice = function(o) { + var answer, exclusive, from, fromDecl, fromRef, name, to, valDef, valRef, _ref2, _ref3, _ref4; + _ref2 = this.variable.properties.pop().range, from = _ref2.from, to = _ref2.to, exclusive = _ref2.exclusive; + name = this.variable.compile(o); + if (from) { + _ref3 = this.cacheToCodeFragments(from.cache(o, LEVEL_OP)), fromDecl = _ref3[0], fromRef = _ref3[1]; + } else { + fromDecl = fromRef = '0'; + } + if (to) { + if ((from != null ? from.isSimpleNumber() : void 0) && to.isSimpleNumber()) { + to = +to.compile(o) - +fromRef; + if (!exclusive) { + to += 1; + } + } else { + to = to.compile(o, LEVEL_ACCESS) + ' - ' + fromRef; + if (!exclusive) { + to += ' + 1'; + } + } + } else { + to = "9e9"; + } + _ref4 = this.value.cache(o, LEVEL_LIST), valDef = _ref4[0], valRef = _ref4[1]; + answer = [].concat(this.makeCode("[].splice.apply(" + name + ", [" + fromDecl + ", " + to + "].concat("), valDef, this.makeCode(")), "), valRef); + if (o.level > LEVEL_TOP) { + return this.wrapInBraces(answer); + } else { + return answer; + } + }; + + return Assign; + + })(Base); + + exports.Code = Code = (function(_super) { + + __extends(Code, _super); + + function Code(params, body, tag) { + this.params = params || []; + this.body = body || new Block; + this.bound = tag === 'boundfunc'; + if (this.bound) { + this.context = '_this'; + } + } + + Code.prototype.children = ['params', 'body']; + + Code.prototype.isStatement = function() { + return !!this.ctor; + }; + + Code.prototype.jumps = NO; + + Code.prototype.compileNode = function(o) { + var answer, code, exprs, i, idt, lit, name, p, param, params, ref, splats, uniqs, val, wasEmpty, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _len5, _len6, _m, _n, _o, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8; + o.scope = new Scope(o.scope, this.body, this); + o.scope.shared = del(o, 'sharedScope'); + o.indent += TAB; + delete o.bare; + delete o.isExistentialEquals; + params = []; + exprs = []; + _ref2 = this.paramNames(); + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + name = _ref2[_i]; + if (!o.scope.check(name)) { + o.scope.parameter(name); + } + } + _ref3 = this.params; + for (_j = 0, _len1 = _ref3.length; _j < _len1; _j++) { + param = _ref3[_j]; + if (!param.splat) { + continue; + } + _ref4 = this.params; + for (_k = 0, _len2 = _ref4.length; _k < _len2; _k++) { + p = _ref4[_k].name; + if (p["this"]) { + p = p.properties[0].name; + } + if (p.value) { + o.scope.add(p.value, 'var', true); + } + } + splats = new Assign(new Value(new Arr((function() { + var _l, _len3, _ref5, _results; + _ref5 = this.params; + _results = []; + for (_l = 0, _len3 = _ref5.length; _l < _len3; _l++) { + p = _ref5[_l]; + _results.push(p.asReference(o)); + } + return _results; + }).call(this))), new Value(new Literal('arguments'))); + break; + } + _ref5 = this.params; + for (_l = 0, _len3 = _ref5.length; _l < _len3; _l++) { + param = _ref5[_l]; + if (param.isComplex()) { + val = ref = param.asReference(o); + if (param.value) { + val = new Op('?', ref, param.value); + } + exprs.push(new Assign(new Value(param.name), val, '=', { + param: true + })); + } else { + ref = param; + if (param.value) { + lit = new Literal(ref.name.value + ' == null'); + val = new Assign(new Value(param.name), param.value, '='); + exprs.push(new If(lit, val)); + } + } + if (!splats) { + params.push(ref); + } + } + wasEmpty = this.body.isEmpty(); + if (splats) { + exprs.unshift(splats); + } + if (exprs.length) { + (_ref6 = this.body.expressions).unshift.apply(_ref6, exprs); + } + for (i = _m = 0, _len4 = params.length; _m < _len4; i = ++_m) { + p = params[i]; + params[i] = p.compileToFragments(o); + o.scope.parameter(fragmentsToText(params[i])); + } + uniqs = []; + _ref7 = this.paramNames(); + for (_n = 0, _len5 = _ref7.length; _n < _len5; _n++) { + name = _ref7[_n]; + if (__indexOf.call(uniqs, name) >= 0) { + throw SyntaxError("multiple parameters named '" + name + "'"); + } + uniqs.push(name); + } + if (!(wasEmpty || this.noReturn)) { + this.body.makeReturn(); + } + if (this.bound) { + if ((_ref8 = o.scope.parent.method) != null ? _ref8.bound : void 0) { + this.bound = this.context = o.scope.parent.method.context; + } else if (!this["static"]) { + o.scope.parent.assign('_this', 'this'); + } + } + idt = o.indent; + code = 'function'; + if (this.ctor) { + code += ' ' + this.name; + } + code += '('; + answer = [this.makeCode(code)]; + for (i = _o = 0, _len6 = params.length; _o < _len6; i = ++_o) { + p = params[i]; + if (i) { + answer.push(this.makeCode(", ")); + } + answer.push.apply(answer, p); + } + answer.push(this.makeCode(') {')); + if (!this.body.isEmpty()) { + answer = answer.concat(this.makeCode("\n"), this.body.compileWithDeclarations(o), this.makeCode("\n" + this.tab)); + } + answer.push(this.makeCode('}')); + if (this.ctor) { + return [this.makeCode(this.tab)].concat(__slice.call(answer)); + } + if (this.front || (o.level >= LEVEL_ACCESS)) { + return this.wrapInBraces(answer); + } else { + return answer; + } + }; + + Code.prototype.paramNames = function() { + var names, param, _i, _len, _ref2; + names = []; + _ref2 = this.params; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + param = _ref2[_i]; + names.push.apply(names, param.names()); + } + return names; + }; + + Code.prototype.traverseChildren = function(crossScope, func) { + if (crossScope) { + return Code.__super__.traverseChildren.call(this, crossScope, func); + } + }; + + return Code; + + })(Base); + + exports.Param = Param = (function(_super) { + + __extends(Param, _super); + + function Param(name, value, splat) { + var _ref2; + this.name = name; + this.value = value; + this.splat = splat; + if (_ref2 = (name = this.name.unwrapAll().value), __indexOf.call(STRICT_PROSCRIBED, _ref2) >= 0) { + throw SyntaxError("parameter name \"" + name + "\" is not allowed"); + } + } + + Param.prototype.children = ['name', 'value']; + + Param.prototype.compileToFragments = function(o) { + return this.name.compileToFragments(o, LEVEL_LIST); + }; + + Param.prototype.asReference = function(o) { + var node; + if (this.reference) { + return this.reference; + } + node = this.name; + if (node["this"]) { + node = node.properties[0].name; + if (node.value.reserved) { + node = new Literal(o.scope.freeVariable(node.value)); + } + } else if (node.isComplex()) { + node = new Literal(o.scope.freeVariable('arg')); + } + node = new Value(node); + if (this.splat) { + node = new Splat(node); + } + return this.reference = node; + }; + + Param.prototype.isComplex = function() { + return this.name.isComplex(); + }; + + Param.prototype.names = function(name) { + var atParam, names, obj, _i, _len, _ref2; + if (name == null) { + name = this.name; + } + atParam = function(obj) { + var value; + value = obj.properties[0].name.value; + if (value.reserved) { + return []; + } else { + return [value]; + } + }; + if (name instanceof Literal) { + return [name.value]; + } + if (name instanceof Value) { + return atParam(name); + } + names = []; + _ref2 = name.objects; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + obj = _ref2[_i]; + if (obj instanceof Assign) { + names.push.apply(names, this.names(obj.value.unwrap())); + } else if (obj instanceof Splat) { + names.push(obj.name.unwrap().value); + } else if (obj instanceof Value) { + if (obj.isArray() || obj.isObject()) { + names.push.apply(names, this.names(obj.base)); + } else if (obj["this"]) { + names.push.apply(names, atParam(obj)); + } else { + names.push(obj.base.value); + } + } else { + throw SyntaxError("illegal parameter " + (obj.compile())); + } + } + return names; + }; + + return Param; + + })(Base); + + exports.Splat = Splat = (function(_super) { + + __extends(Splat, _super); + + Splat.prototype.children = ['name']; + + Splat.prototype.isAssignable = YES; + + function Splat(name) { + this.name = name.compile ? name : new Literal(name); + } + + Splat.prototype.assigns = function(name) { + return this.name.assigns(name); + }; + + Splat.prototype.compileToFragments = function(o) { + return this.name.compileToFragments(o); + }; + + Splat.prototype.unwrap = function() { + return this.name; + }; + + Splat.compileSplattedArray = function(o, list, apply) { + var args, base, compiledNode, concatPart, fragments, i, index, node, _i, _len; + index = -1; + while ((node = list[++index]) && !(node instanceof Splat)) { + continue; + } + if (index >= list.length) { + return []; + } + if (list.length === 1) { + node = list[0]; + fragments = node.compileToFragments(o, LEVEL_LIST); + if (apply) { + return fragments; + } + return [].concat(node.makeCode("" + (utility('slice')) + ".call("), fragments, node.makeCode(")")); + } + args = list.slice(index); + for (i = _i = 0, _len = args.length; _i < _len; i = ++_i) { + node = args[i]; + compiledNode = node.compileToFragments(o, LEVEL_LIST); + args[i] = node instanceof Splat ? [].concat(node.makeCode("" + (utility('slice')) + ".call("), compiledNode, node.makeCode(")")) : [].concat(node.makeCode("["), compiledNode, node.makeCode("]")); + } + if (index === 0) { + node = list[0]; + concatPart = node.joinFragmentArrays(args.slice(1), ', '); + return args[0].concat(node.makeCode(".concat("), concatPart, node.makeCode(")")); + } + base = (function() { + var _j, _len1, _ref2, _results; + _ref2 = list.slice(0, index); + _results = []; + for (_j = 0, _len1 = _ref2.length; _j < _len1; _j++) { + node = _ref2[_j]; + _results.push(node.compileToFragments(o, LEVEL_LIST)); + } + return _results; + })(); + base = list[0].joinFragmentArrays(base, ', '); + concatPart = list[index].joinFragmentArrays(args, ', '); + return [].concat(list[0].makeCode("["), base, list[index].makeCode("].concat("), concatPart, (last(list)).makeCode(")")); + }; + + return Splat; + + })(Base); + + exports.While = While = (function(_super) { + + __extends(While, _super); + + function While(condition, options) { + this.condition = (options != null ? options.invert : void 0) ? condition.invert() : condition; + this.guard = options != null ? options.guard : void 0; + } + + While.prototype.children = ['condition', 'guard', 'body']; + + While.prototype.isStatement = YES; + + While.prototype.makeReturn = function(res) { + if (res) { + return While.__super__.makeReturn.apply(this, arguments); + } else { + this.returns = !this.jumps({ + loop: true + }); + return this; + } + }; + + While.prototype.addBody = function(body) { + this.body = body; + return this; + }; + + While.prototype.jumps = function() { + var expressions, node, _i, _len; + expressions = this.body.expressions; + if (!expressions.length) { + return false; + } + for (_i = 0, _len = expressions.length; _i < _len; _i++) { + node = expressions[_i]; + if (node.jumps({ + loop: true + })) { + return node; + } + } + return false; + }; + + While.prototype.compileNode = function(o) { + var answer, body, rvar, set; + o.indent += TAB; + set = ''; + body = this.body; + if (body.isEmpty()) { + body = ''; + } else { + if (this.returns) { + body.makeReturn(rvar = o.scope.freeVariable('results')); + set = "" + this.tab + rvar + " = [];\n"; + } + if (this.guard) { + if (body.expressions.length > 1) { + body.expressions.unshift(new If((new Parens(this.guard)).invert(), new Literal("continue"))); + } else { + if (this.guard) { + body = Block.wrap([new If(this.guard, body)]); + } + } + } + body = [].concat(this.makeCode("\n"), body.compileToFragments(o, LEVEL_TOP), this.makeCode("\n" + this.tab)); + } + answer = [].concat(this.makeCode(set + this.tab + "while ("), this.condition.compileToFragments(o, LEVEL_PAREN), this.makeCode(") {"), body, this.makeCode("}")); + if (this.returns) { + answer.push(this.makeCode("\n" + this.tab + "return " + rvar + ";")); + } + return answer; + }; + + return While; + + })(Base); + + exports.Op = Op = (function(_super) { + var CONVERSIONS, INVERSIONS; + + __extends(Op, _super); + + function Op(op, first, second, flip) { + if (op === 'in') { + return new In(first, second); + } + if (op === 'do') { + return this.generateDo(first); + } + if (op === 'new') { + if (first instanceof Call && !first["do"] && !first.isNew) { + return first.newInstance(); + } + if (first instanceof Code && first.bound || first["do"]) { + first = new Parens(first); + } + } + this.operator = CONVERSIONS[op] || op; + this.first = first; + this.second = second; + this.flip = !!flip; + return this; + } + + CONVERSIONS = { + '==': '===', + '!=': '!==', + 'of': 'in' + }; + + INVERSIONS = { + '!==': '===', + '===': '!==' + }; + + Op.prototype.children = ['first', 'second']; + + Op.prototype.isSimpleNumber = NO; + + Op.prototype.isUnary = function() { + return !this.second; + }; + + Op.prototype.isComplex = function() { + var _ref2; + return !(this.isUnary() && ((_ref2 = this.operator) === '+' || _ref2 === '-')) || this.first.isComplex(); + }; + + Op.prototype.isChainable = function() { + var _ref2; + return (_ref2 = this.operator) === '<' || _ref2 === '>' || _ref2 === '>=' || _ref2 === '<=' || _ref2 === '===' || _ref2 === '!=='; + }; + + Op.prototype.invert = function() { + var allInvertable, curr, fst, op, _ref2; + if (this.isChainable() && this.first.isChainable()) { + allInvertable = true; + curr = this; + while (curr && curr.operator) { + allInvertable && (allInvertable = curr.operator in INVERSIONS); + curr = curr.first; + } + if (!allInvertable) { + return new Parens(this).invert(); + } + curr = this; + while (curr && curr.operator) { + curr.invert = !curr.invert; + curr.operator = INVERSIONS[curr.operator]; + curr = curr.first; + } + return this; + } else if (op = INVERSIONS[this.operator]) { + this.operator = op; + if (this.first.unwrap() instanceof Op) { + this.first.invert(); + } + return this; + } else if (this.second) { + return new Parens(this).invert(); + } else if (this.operator === '!' && (fst = this.first.unwrap()) instanceof Op && ((_ref2 = fst.operator) === '!' || _ref2 === 'in' || _ref2 === 'instanceof')) { + return fst; + } else { + return new Op('!', this); + } + }; + + Op.prototype.unfoldSoak = function(o) { + var _ref2; + return ((_ref2 = this.operator) === '++' || _ref2 === '--' || _ref2 === 'delete') && unfoldSoak(o, this, 'first'); + }; + + Op.prototype.generateDo = function(exp) { + var call, func, param, passedParams, ref, _i, _len, _ref2; + passedParams = []; + func = exp instanceof Assign && (ref = exp.value.unwrap()) instanceof Code ? ref : exp; + _ref2 = func.params || []; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + param = _ref2[_i]; + if (param.value) { + passedParams.push(param.value); + delete param.value; + } else { + passedParams.push(param); + } + } + call = new Call(exp, passedParams); + call["do"] = true; + return call; + }; + + Op.prototype.compileNode = function(o) { + var answer, isChain, _ref2, _ref3; + isChain = this.isChainable() && this.first.isChainable(); + if (!isChain) { + this.first.front = this.front; + } + if (this.operator === 'delete' && o.scope.check(this.first.unwrapAll().value)) { + throw SyntaxError('delete operand may not be argument or var'); + } + if (((_ref2 = this.operator) === '--' || _ref2 === '++') && (_ref3 = this.first.unwrapAll().value, __indexOf.call(STRICT_PROSCRIBED, _ref3) >= 0)) { + throw SyntaxError('prefix increment/decrement may not have eval or arguments operand'); + } + if (this.isUnary()) { + return this.compileUnary(o); + } + if (isChain) { + return this.compileChain(o); + } + if (this.operator === '?') { + return this.compileExistence(o); + } + answer = [].concat(this.first.compileToFragments(o, LEVEL_OP), this.makeCode(' ' + this.operator + ' '), this.second.compileToFragments(o, LEVEL_OP)); + if (o.level <= LEVEL_OP) { + return answer; + } else { + return this.wrapInBraces(answer); + } + }; + + Op.prototype.compileChain = function(o) { + var fragments, fst, shared, _ref2; + _ref2 = this.first.second.cache(o), this.first.second = _ref2[0], shared = _ref2[1]; + fst = this.first.compileToFragments(o, LEVEL_OP); + fragments = fst.concat(this.makeCode(" " + (this.invert ? '&&' : '||') + " "), shared.compileToFragments(o), this.makeCode(" " + this.operator + " "), this.second.compileToFragments(o, LEVEL_OP)); + return this.wrapInBraces(fragments); + }; + + Op.prototype.compileExistence = function(o) { + var fst, ref; + if (this.first.isComplex()) { + ref = new Literal(o.scope.freeVariable('ref')); + fst = new Parens(new Assign(ref, this.first)); + } else { + fst = this.first; + ref = fst; + } + return new If(new Existence(fst), ref, { + type: 'if' + }).addElse(this.second).compileToFragments(o); + }; + + Op.prototype.compileUnary = function(o) { + var op, parts, plusMinus; + parts = []; + op = this.operator; + parts.push([this.makeCode(op)]); + if (op === '!' && this.first instanceof Existence) { + this.first.negated = !this.first.negated; + return this.first.compileToFragments(o); + } + if (o.level >= LEVEL_ACCESS) { + return (new Parens(this)).compileToFragments(o); + } + plusMinus = op === '+' || op === '-'; + if ((op === 'new' || op === 'typeof' || op === 'delete') || plusMinus && this.first instanceof Op && this.first.operator === op) { + parts.push([this.makeCode(' ')]); + } + if ((plusMinus && this.first instanceof Op) || (op === 'new' && this.first.isStatement(o))) { + this.first = new Parens(this.first); + } + parts.push(this.first.compileToFragments(o, LEVEL_OP)); + if (this.flip) { + parts.reverse(); + } + return this.joinFragmentArrays(parts, ''); + }; + + Op.prototype.toString = function(idt) { + return Op.__super__.toString.call(this, idt, this.constructor.name + ' ' + this.operator); + }; + + return Op; + + })(Base); + + exports.In = In = (function(_super) { + + __extends(In, _super); + + function In(object, array) { + this.object = object; + this.array = array; + } + + In.prototype.children = ['object', 'array']; + + In.prototype.invert = NEGATE; + + In.prototype.compileNode = function(o) { + var hasSplat, obj, _i, _len, _ref2; + if (this.array instanceof Value && this.array.isArray()) { + _ref2 = this.array.base.objects; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + obj = _ref2[_i]; + if (!(obj instanceof Splat)) { + continue; + } + hasSplat = true; + break; + } + if (!hasSplat) { + return this.compileOrTest(o); + } + } + return this.compileLoopTest(o); + }; + + In.prototype.compileOrTest = function(o) { + var cmp, cnj, i, item, ref, sub, tests, _i, _len, _ref2, _ref3, _ref4; + if (this.array.base.objects.length === 0) { + return [this.makeCode("" + (!!this.negated))]; + } + _ref2 = this.object.cache(o, LEVEL_OP), sub = _ref2[0], ref = _ref2[1]; + _ref3 = this.negated ? [' !== ', ' && '] : [' === ', ' || '], cmp = _ref3[0], cnj = _ref3[1]; + tests = []; + _ref4 = this.array.base.objects; + for (i = _i = 0, _len = _ref4.length; _i < _len; i = ++_i) { + item = _ref4[i]; + if (i) { + tests.push(this.makeCode(cnj)); + } + tests = tests.concat((i ? ref : sub), this.makeCode(cmp), item.compileToFragments(o, LEVEL_ACCESS)); + } + if (o.level < LEVEL_OP) { + return tests; + } else { + return this.wrapInBraces(tests); + } + }; + + In.prototype.compileLoopTest = function(o) { + var fragments, ref, sub, _ref2; + _ref2 = this.object.cache(o, LEVEL_LIST), sub = _ref2[0], ref = _ref2[1]; + fragments = [].concat(this.makeCode(utility('indexOf') + ".call("), this.array.compileToFragments(o, LEVEL_LIST), this.makeCode(", "), ref, this.makeCode(") " + (this.negated ? '< 0' : '>= 0'))); + if ((fragmentsToText(sub)) === (fragmentsToText(ref))) { + return fragments; + } + fragments = sub.concat(this.makeCode(', '), fragments); + if (o.level < LEVEL_LIST) { + return fragments; + } else { + return this.wrapInBraces(fragments); + } + }; + + In.prototype.toString = function(idt) { + return In.__super__.toString.call(this, idt, this.constructor.name + (this.negated ? '!' : '')); + }; + + return In; + + })(Base); + + exports.Try = Try = (function(_super) { + + __extends(Try, _super); + + function Try(attempt, error, recovery, ensure) { + this.attempt = attempt; + this.error = error; + this.recovery = recovery; + this.ensure = ensure; + } + + Try.prototype.children = ['attempt', 'recovery', 'ensure']; + + Try.prototype.isStatement = YES; + + Try.prototype.jumps = function(o) { + var _ref2; + return this.attempt.jumps(o) || ((_ref2 = this.recovery) != null ? _ref2.jumps(o) : void 0); + }; + + Try.prototype.makeReturn = function(res) { + if (this.attempt) { + this.attempt = this.attempt.makeReturn(res); + } + if (this.recovery) { + this.recovery = this.recovery.makeReturn(res); + } + return this; + }; + + Try.prototype.compileNode = function(o) { + var catchPart, ensurePart, placeholder, tryPart; + o.indent += TAB; + tryPart = this.attempt.compileToFragments(o, LEVEL_TOP); + catchPart = (function() { + var _base, _ref2; + if (this.recovery) { + if (typeof (_base = this.error).isObject === "function" ? _base.isObject() : void 0) { + placeholder = new Literal('_error'); + this.recovery.unshift(new Assign(this.error, placeholder)); + this.error = placeholder; + } + if (_ref2 = this.error.value, __indexOf.call(STRICT_PROSCRIBED, _ref2) >= 0) { + throw SyntaxError("catch variable may not be \"" + this.error.value + "\""); + } + if (!o.scope.check(this.error.value)) { + o.scope.add(this.error.value, 'param'); + } + return [].concat(this.makeCode(" catch ("), this.error.compileToFragments(o), this.makeCode(") {\n"), this.recovery.compileToFragments(o, LEVEL_TOP), this.makeCode("\n" + this.tab + "}")); + } else if (!(this.ensure || this.recovery)) { + return [this.makeCode(' catch (_error) {}')]; + } else { + return []; + } + }).call(this); + ensurePart = this.ensure ? [].concat(this.makeCode(" finally {\n"), this.ensure.compileToFragments(o, LEVEL_TOP), this.makeCode("\n" + this.tab + "}")) : []; + return [].concat(this.makeCode("" + this.tab + "try {\n"), tryPart, this.makeCode("\n" + this.tab + "}"), catchPart, ensurePart); + }; + + return Try; + + })(Base); + + exports.Throw = Throw = (function(_super) { + + __extends(Throw, _super); + + function Throw(expression) { + this.expression = expression; + } + + Throw.prototype.children = ['expression']; + + Throw.prototype.isStatement = YES; + + Throw.prototype.jumps = NO; + + Throw.prototype.makeReturn = THIS; + + Throw.prototype.compileNode = function(o) { + return [].concat(this.makeCode(this.tab + "throw "), this.expression.compileToFragments(o), this.makeCode(";")); + }; + + return Throw; + + })(Base); + + exports.Existence = Existence = (function(_super) { + + __extends(Existence, _super); + + function Existence(expression) { + this.expression = expression; + } + + Existence.prototype.children = ['expression']; + + Existence.prototype.invert = NEGATE; + + Existence.prototype.compileNode = function(o) { + var cmp, cnj, code, _ref2; + this.expression.front = this.front; + code = this.expression.compile(o, LEVEL_OP); + if (IDENTIFIER.test(code) && !o.scope.check(code)) { + _ref2 = this.negated ? ['===', '||'] : ['!==', '&&'], cmp = _ref2[0], cnj = _ref2[1]; + code = "typeof " + code + " " + cmp + " \"undefined\" " + cnj + " " + code + " " + cmp + " null"; + } else { + code = "" + code + " " + (this.negated ? '==' : '!=') + " null"; + } + return [this.makeCode(o.level <= LEVEL_COND ? code : "(" + code + ")")]; + }; + + return Existence; + + })(Base); + + exports.Parens = Parens = (function(_super) { + + __extends(Parens, _super); + + function Parens(body) { + this.body = body; + } + + Parens.prototype.children = ['body']; + + Parens.prototype.unwrap = function() { + return this.body; + }; + + Parens.prototype.isComplex = function() { + return this.body.isComplex(); + }; + + Parens.prototype.compileNode = function(o) { + var bare, expr, fragments; + expr = this.body.unwrap(); + if (expr instanceof Value && expr.isAtomic()) { + expr.front = this.front; + return expr.compileToFragments(o); + } + fragments = expr.compileToFragments(o, LEVEL_PAREN); + bare = o.level < LEVEL_OP && (expr instanceof Op || expr instanceof Call || (expr instanceof For && expr.returns)); + if (bare) { + return fragments; + } else { + return this.wrapInBraces(fragments); + } + }; + + return Parens; + + })(Base); + + exports.For = For = (function(_super) { + + __extends(For, _super); + + function For(body, source) { + var _ref2; + this.source = source.source, this.guard = source.guard, this.step = source.step, this.name = source.name, this.index = source.index; + this.body = Block.wrap([body]); + this.own = !!source.own; + this.object = !!source.object; + if (this.object) { + _ref2 = [this.index, this.name], this.name = _ref2[0], this.index = _ref2[1]; + } + if (this.index instanceof Value) { + throw SyntaxError('index cannot be a pattern matching expression'); + } + this.range = this.source instanceof Value && this.source.base instanceof Range && !this.source.properties.length; + this.pattern = this.name instanceof Value; + if (this.range && this.index) { + throw SyntaxError('indexes do not apply to range loops'); + } + if (this.range && this.pattern) { + throw SyntaxError('cannot pattern match over range loops'); + } + this.returns = false; + } + + For.prototype.children = ['body', 'source', 'guard', 'step']; + + For.prototype.compileNode = function(o) { + var body, bodyFragments, compare, compareDown, declare, declareDown, defPart, defPartFragments, down, forPartFragments, guardPart, idt1, increment, index, ivar, kvar, kvarAssign, lastJumps, lvar, name, namePart, ref, resultPart, returnResult, rvar, scope, source, step, stepNum, stepVar, svar, varPart, _ref2, _ref3; + body = Block.wrap([this.body]); + lastJumps = (_ref2 = last(body.expressions)) != null ? _ref2.jumps() : void 0; + if (lastJumps && lastJumps instanceof Return) { + this.returns = false; + } + source = this.range ? this.source.base : this.source; + scope = o.scope; + name = this.name && (this.name.compile(o, LEVEL_LIST)); + index = this.index && (this.index.compile(o, LEVEL_LIST)); + if (name && !this.pattern) { + scope.find(name); + } + if (index) { + scope.find(index); + } + if (this.returns) { + rvar = scope.freeVariable('results'); + } + ivar = (this.object && index) || scope.freeVariable('i'); + kvar = (this.range && name) || index || ivar; + kvarAssign = kvar !== ivar ? "" + kvar + " = " : ""; + if (this.step && !this.range) { + _ref3 = this.cacheToCodeFragments(this.step.cache(o, LEVEL_LIST)), step = _ref3[0], stepVar = _ref3[1]; + stepNum = stepVar.match(SIMPLENUM); + } + if (this.pattern) { + name = ivar; + } + varPart = ''; + guardPart = ''; + defPart = ''; + idt1 = this.tab + TAB; + if (this.range) { + forPartFragments = source.compileToFragments(merge(o, { + index: ivar, + name: name, + step: this.step + })); + } else { + svar = this.source.compile(o, LEVEL_LIST); + if ((name || this.own) && !IDENTIFIER.test(svar)) { + defPart += "" + this.tab + (ref = scope.freeVariable('ref')) + " = " + svar + ";\n"; + svar = ref; + } + if (name && !this.pattern) { + namePart = "" + name + " = " + svar + "[" + kvar + "]"; + } + if (!this.object) { + if (step !== stepVar) { + defPart += "" + this.tab + step + ";\n"; + } + if (!(this.step && stepNum && (down = +stepNum < 0))) { + lvar = scope.freeVariable('len'); + } + declare = "" + kvarAssign + ivar + " = 0, " + lvar + " = " + svar + ".length"; + declareDown = "" + kvarAssign + ivar + " = " + svar + ".length - 1"; + compare = "" + ivar + " < " + lvar; + compareDown = "" + ivar + " >= 0"; + if (this.step) { + if (stepNum) { + if (down) { + compare = compareDown; + declare = declareDown; + } + } else { + compare = "" + stepVar + " > 0 ? " + compare + " : " + compareDown; + declare = "(" + stepVar + " > 0 ? (" + declare + ") : " + declareDown + ")"; + } + increment = "" + ivar + " += " + stepVar; + } else { + increment = "" + (kvar !== ivar ? "++" + ivar : "" + ivar + "++"); + } + forPartFragments = [this.makeCode("" + declare + "; " + compare + "; " + kvarAssign + increment)]; + } + } + if (this.returns) { + resultPart = "" + this.tab + rvar + " = [];\n"; + returnResult = "\n" + this.tab + "return " + rvar + ";"; + body.makeReturn(rvar); + } + if (this.guard) { + if (body.expressions.length > 1) { + body.expressions.unshift(new If((new Parens(this.guard)).invert(), new Literal("continue"))); + } else { + if (this.guard) { + body = Block.wrap([new If(this.guard, body)]); + } + } + } + if (this.pattern) { + body.expressions.unshift(new Assign(this.name, new Literal("" + svar + "[" + kvar + "]"))); + } + defPartFragments = [].concat(this.makeCode(defPart), this.pluckDirectCall(o, body)); + if (namePart) { + varPart = "\n" + idt1 + namePart + ";"; + } + if (this.object) { + forPartFragments = [this.makeCode("" + kvar + " in " + svar)]; + if (this.own) { + guardPart = "\n" + idt1 + "if (!" + (utility('hasProp')) + ".call(" + svar + ", " + kvar + ")) continue;"; + } + } + bodyFragments = body.compileToFragments(merge(o, { + indent: idt1 + }), LEVEL_TOP); + if (bodyFragments && (bodyFragments.length > 0)) { + bodyFragments = [].concat(this.makeCode("\n"), bodyFragments, this.makeCode("\n")); + } + return [].concat(defPartFragments, this.makeCode("" + (resultPart || '') + this.tab + "for ("), forPartFragments, this.makeCode(") {" + guardPart + varPart), bodyFragments, this.makeCode("" + this.tab + "}" + (returnResult || ''))); + }; + + For.prototype.pluckDirectCall = function(o, body) { + var base, defs, expr, fn, idx, ref, val, _i, _len, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7; + defs = []; + _ref2 = body.expressions; + for (idx = _i = 0, _len = _ref2.length; _i < _len; idx = ++_i) { + expr = _ref2[idx]; + expr = expr.unwrapAll(); + if (!(expr instanceof Call)) { + continue; + } + val = expr.variable.unwrapAll(); + if (!((val instanceof Code) || (val instanceof Value && ((_ref3 = val.base) != null ? _ref3.unwrapAll() : void 0) instanceof Code && val.properties.length === 1 && ((_ref4 = (_ref5 = val.properties[0].name) != null ? _ref5.value : void 0) === 'call' || _ref4 === 'apply')))) { + continue; + } + fn = ((_ref6 = val.base) != null ? _ref6.unwrapAll() : void 0) || val; + ref = new Literal(o.scope.freeVariable('fn')); + base = new Value(ref); + if (val.base) { + _ref7 = [base, val], val.base = _ref7[0], base = _ref7[1]; + } + body.expressions[idx] = new Call(base, expr.args); + defs = defs.concat(this.makeCode(this.tab), new Assign(ref, fn).compileToFragments(o, LEVEL_TOP), this.makeCode(';\n')); + } + return defs; + }; + + return For; + + })(While); + + exports.Switch = Switch = (function(_super) { + + __extends(Switch, _super); + + function Switch(subject, cases, otherwise) { + this.subject = subject; + this.cases = cases; + this.otherwise = otherwise; + } + + Switch.prototype.children = ['subject', 'cases', 'otherwise']; + + Switch.prototype.isStatement = YES; + + Switch.prototype.jumps = function(o) { + var block, conds, _i, _len, _ref2, _ref3, _ref4; + if (o == null) { + o = { + block: true + }; + } + _ref2 = this.cases; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + _ref3 = _ref2[_i], conds = _ref3[0], block = _ref3[1]; + if (block.jumps(o)) { + return block; + } + } + return (_ref4 = this.otherwise) != null ? _ref4.jumps(o) : void 0; + }; + + Switch.prototype.makeReturn = function(res) { + var pair, _i, _len, _ref2, _ref3; + _ref2 = this.cases; + for (_i = 0, _len = _ref2.length; _i < _len; _i++) { + pair = _ref2[_i]; + pair[1].makeReturn(res); + } + if (res) { + this.otherwise || (this.otherwise = new Block([new Literal('void 0')])); + } + if ((_ref3 = this.otherwise) != null) { + _ref3.makeReturn(res); + } + return this; + }; + + Switch.prototype.compileNode = function(o) { + var block, body, cond, conditions, expr, fragments, i, idt1, idt2, _i, _j, _len, _len1, _ref2, _ref3, _ref4; + idt1 = o.indent + TAB; + idt2 = o.indent = idt1 + TAB; + fragments = [].concat(this.makeCode(this.tab + "switch ("), (this.subject ? this.subject.compileToFragments(o, LEVEL_PAREN) : this.makeCode("false")), this.makeCode(") {\n")); + _ref2 = this.cases; + for (i = _i = 0, _len = _ref2.length; _i < _len; i = ++_i) { + _ref3 = _ref2[i], conditions = _ref3[0], block = _ref3[1]; + _ref4 = flatten([conditions]); + for (_j = 0, _len1 = _ref4.length; _j < _len1; _j++) { + cond = _ref4[_j]; + if (!this.subject) { + cond = cond.invert(); + } + fragments = fragments.concat(this.makeCode(idt1 + "case "), cond.compileToFragments(o, LEVEL_PAREN), this.makeCode(":\n")); + } + if ((body = block.compileToFragments(o, LEVEL_TOP)).length > 0) { + fragments = fragments.concat(body, this.makeCode('\n')); + } + if (i === this.cases.length - 1 && !this.otherwise) { + break; + } + expr = this.lastNonComment(block.expressions); + if (expr instanceof Return || (expr instanceof Literal && expr.jumps() && expr.value !== 'debugger')) { + continue; + } + fragments.push(cond.makeCode(idt2 + 'break;\n')); + } + if (this.otherwise && this.otherwise.expressions.length) { + fragments.push.apply(fragments, [this.makeCode(idt1 + "default:\n")].concat(__slice.call(this.otherwise.compileToFragments(o, LEVEL_TOP)), [this.makeCode("\n")])); + } + fragments.push(this.makeCode(this.tab + '}')); + return fragments; + }; + + return Switch; + + })(Base); + + exports.If = If = (function(_super) { + + __extends(If, _super); + + function If(condition, body, options) { + this.body = body; + if (options == null) { + options = {}; + } + this.condition = options.type === 'unless' ? condition.invert() : condition; + this.elseBody = null; + this.isChain = false; + this.soak = options.soak; + } + + If.prototype.children = ['condition', 'body', 'elseBody']; + + If.prototype.bodyNode = function() { + var _ref2; + return (_ref2 = this.body) != null ? _ref2.unwrap() : void 0; + }; + + If.prototype.elseBodyNode = function() { + var _ref2; + return (_ref2 = this.elseBody) != null ? _ref2.unwrap() : void 0; + }; + + If.prototype.addElse = function(elseBody) { + if (this.isChain) { + this.elseBodyNode().addElse(elseBody); + } else { + this.isChain = elseBody instanceof If; + this.elseBody = this.ensureBlock(elseBody); + } + return this; + }; + + If.prototype.isStatement = function(o) { + var _ref2; + return (o != null ? o.level : void 0) === LEVEL_TOP || this.bodyNode().isStatement(o) || ((_ref2 = this.elseBodyNode()) != null ? _ref2.isStatement(o) : void 0); + }; + + If.prototype.jumps = function(o) { + var _ref2; + return this.body.jumps(o) || ((_ref2 = this.elseBody) != null ? _ref2.jumps(o) : void 0); + }; + + If.prototype.compileNode = function(o) { + if (this.isStatement(o)) { + return this.compileStatement(o); + } else { + return this.compileExpression(o); + } + }; + + If.prototype.makeReturn = function(res) { + if (res) { + this.elseBody || (this.elseBody = new Block([new Literal('void 0')])); + } + this.body && (this.body = new Block([this.body.makeReturn(res)])); + this.elseBody && (this.elseBody = new Block([this.elseBody.makeReturn(res)])); + return this; + }; + + If.prototype.ensureBlock = function(node) { + if (node instanceof Block) { + return node; + } else { + return new Block([node]); + } + }; + + If.prototype.compileStatement = function(o) { + var answer, body, child, cond, exeq, ifPart, indent; + child = del(o, 'chainChild'); + exeq = del(o, 'isExistentialEquals'); + if (exeq) { + return new If(this.condition.invert(), this.elseBodyNode(), { + type: 'if' + }).compileToFragments(o); + } + indent = o.indent + TAB; + cond = this.condition.compileToFragments(o, LEVEL_PAREN); + body = this.ensureBlock(this.body).compileToFragments(merge(o, { + indent: indent + })); + ifPart = [].concat(this.makeCode("if ("), cond, this.makeCode(") {\n"), body, this.makeCode("\n" + this.tab + "}")); + if (!child) { + ifPart.unshift(this.makeCode(this.tab)); + } + if (!this.elseBody) { + return ifPart; + } + answer = ifPart.concat(this.makeCode(' else ')); + if (this.isChain) { + o.chainChild = true; + answer = answer.concat(this.elseBody.unwrap().compileToFragments(o, LEVEL_TOP)); + } else { + answer = answer.concat(this.makeCode("{\n"), this.elseBody.compileToFragments(merge(o, { + indent: indent + }), LEVEL_TOP), this.makeCode("\n" + this.tab + "}")); + } + return answer; + }; + + If.prototype.compileExpression = function(o) { + var alt, body, cond, fragments; + cond = this.condition.compileToFragments(o, LEVEL_COND); + body = this.bodyNode().compileToFragments(o, LEVEL_LIST); + alt = this.elseBodyNode() ? this.elseBodyNode().compileToFragments(o, LEVEL_LIST) : [this.makeCode('void 0')]; + fragments = cond.concat(this.makeCode(" ? "), body, this.makeCode(" : "), alt); + if (o.level >= LEVEL_COND) { + return this.wrapInBraces(fragments); + } else { + return fragments; + } + }; + + If.prototype.unfoldSoak = function() { + return this.soak && this; + }; + + return If; + + })(Base); + + Closure = { + wrap: function(expressions, statement, noReturn) { + var args, call, func, mentionsArgs, meth; + if (expressions.jumps()) { + return expressions; + } + func = new Code([], Block.wrap([expressions])); + args = []; + if ((mentionsArgs = expressions.contains(this.literalArgs)) || expressions.contains(this.literalThis)) { + if (mentionsArgs && expressions.classBody) { + throw SyntaxError("Class bodies shouldn't reference arguments"); + } + meth = new Literal(mentionsArgs ? 'apply' : 'call'); + args = [new Literal('this')]; + if (mentionsArgs) { + args.push(new Literal('arguments')); + } + func = new Value(func, [new Access(meth)]); + } + func.noReturn = noReturn; + call = new Call(func, args); + if (statement) { + return Block.wrap([call]); + } else { + return call; + } + }, + literalArgs: function(node) { + return node instanceof Literal && node.value === 'arguments' && !node.asKey; + }, + literalThis: function(node) { + return (node instanceof Literal && node.value === 'this' && !node.asKey) || (node instanceof Code && node.bound) || (node instanceof Call && node.isSuper); + } + }; + + unfoldSoak = function(o, parent, name) { + var ifn; + if (!(ifn = parent[name].unfoldSoak(o))) { + return; + } + parent[name] = ifn.body; + ifn.body = new Value(parent); + return ifn; + }; + + UTILITIES = { + "extends": function() { + return "function(child, parent) { for (var key in parent) { if (" + (utility('hasProp')) + ".call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor(); child.__super__ = parent.prototype; return child; }"; + }, + indexOf: function() { + return "[].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }"; + }, + hasProp: function() { + return '{}.hasOwnProperty'; + }, + slice: function() { + return '[].slice'; + } + }; + + LEVEL_TOP = 1; + + LEVEL_PAREN = 2; + + LEVEL_LIST = 3; + + LEVEL_COND = 4; + + LEVEL_OP = 5; + + LEVEL_ACCESS = 6; + + TAB = ' '; + + IDENTIFIER_STR = "[$A-Za-z_\\x7f-\\uffff][$\\w\\x7f-\\uffff]*"; + + IDENTIFIER = RegExp("^" + IDENTIFIER_STR + "$"); + + SIMPLENUM = /^[+-]?\d+$/; + + METHOD_DEF = RegExp("^(?:(" + IDENTIFIER_STR + ")\\.prototype(?:\\.(" + IDENTIFIER_STR + ")|\\[(\"(?:[^\\\\\"\\r\\n]|\\\\.)*\"|'(?:[^\\\\'\\r\\n]|\\\\.)*')\\]|\\[(0x[\\da-fA-F]+|\\d*\\.?\\d+(?:[eE][+-]?\\d+)?)\\]))|(" + IDENTIFIER_STR + ")$"); + + IS_STRING = /^['"]/; + + utility = function(name) { + var ref; + ref = "__" + name; + Scope.root.assign(ref, UTILITIES[name]()); + return ref; + }; + + multident = function(code, tab) { + code = code.replace(/\n/g, '$&' + tab); + return code.replace(/\s+$/, ''); + }; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/optparse.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/optparse.js new file mode 100644 index 00000000..f650fdd1 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/optparse.js @@ -0,0 +1,138 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var LONG_FLAG, MULTI_FLAG, OPTIONAL, OptionParser, SHORT_FLAG, buildRule, buildRules, normalizeArguments; + + exports.OptionParser = OptionParser = (function() { + + function OptionParser(rules, banner) { + this.banner = banner; + this.rules = buildRules(rules); + } + + OptionParser.prototype.parse = function(args) { + var arg, i, isOption, matchedRule, options, originalArgs, pos, rule, seenNonOptionArg, skippingArgument, value, _i, _j, _len, _len1, _ref; + options = { + "arguments": [] + }; + skippingArgument = false; + originalArgs = args; + args = normalizeArguments(args); + for (i = _i = 0, _len = args.length; _i < _len; i = ++_i) { + arg = args[i]; + if (skippingArgument) { + skippingArgument = false; + continue; + } + if (arg === '--') { + pos = originalArgs.indexOf('--'); + options["arguments"] = options["arguments"].concat(originalArgs.slice(pos + 1)); + break; + } + isOption = !!(arg.match(LONG_FLAG) || arg.match(SHORT_FLAG)); + seenNonOptionArg = options["arguments"].length > 0; + if (!seenNonOptionArg) { + matchedRule = false; + _ref = this.rules; + for (_j = 0, _len1 = _ref.length; _j < _len1; _j++) { + rule = _ref[_j]; + if (rule.shortFlag === arg || rule.longFlag === arg) { + value = true; + if (rule.hasArgument) { + skippingArgument = true; + value = args[i + 1]; + } + options[rule.name] = rule.isList ? (options[rule.name] || []).concat(value) : value; + matchedRule = true; + break; + } + } + if (isOption && !matchedRule) { + throw new Error("unrecognized option: " + arg); + } + } + if (seenNonOptionArg || !isOption) { + options["arguments"].push(arg); + } + } + return options; + }; + + OptionParser.prototype.help = function() { + var letPart, lines, rule, spaces, _i, _len, _ref; + lines = []; + if (this.banner) { + lines.unshift("" + this.banner + "\n"); + } + _ref = this.rules; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + rule = _ref[_i]; + spaces = 15 - rule.longFlag.length; + spaces = spaces > 0 ? Array(spaces + 1).join(' ') : ''; + letPart = rule.shortFlag ? rule.shortFlag + ', ' : ' '; + lines.push(' ' + letPart + rule.longFlag + spaces + rule.description); + } + return "\n" + (lines.join('\n')) + "\n"; + }; + + return OptionParser; + + })(); + + LONG_FLAG = /^(--\w[\w\-]*)/; + + SHORT_FLAG = /^(-\w)$/; + + MULTI_FLAG = /^-(\w{2,})/; + + OPTIONAL = /\[(\w+(\*?))\]/; + + buildRules = function(rules) { + var tuple, _i, _len, _results; + _results = []; + for (_i = 0, _len = rules.length; _i < _len; _i++) { + tuple = rules[_i]; + if (tuple.length < 3) { + tuple.unshift(null); + } + _results.push(buildRule.apply(null, tuple)); + } + return _results; + }; + + buildRule = function(shortFlag, longFlag, description, options) { + var match; + if (options == null) { + options = {}; + } + match = longFlag.match(OPTIONAL); + longFlag = longFlag.match(LONG_FLAG)[1]; + return { + name: longFlag.substr(2), + shortFlag: shortFlag, + longFlag: longFlag, + description: description, + hasArgument: !!(match && match[1]), + isList: !!(match && match[2]) + }; + }; + + normalizeArguments = function(args) { + var arg, l, match, result, _i, _j, _len, _len1, _ref; + args = args.slice(0); + result = []; + for (_i = 0, _len = args.length; _i < _len; _i++) { + arg = args[_i]; + if (match = arg.match(MULTI_FLAG)) { + _ref = match[1].split(''); + for (_j = 0, _len1 = _ref.length; _j < _len1; _j++) { + l = _ref[_j]; + result.push('-' + l); + } + } else { + result.push(arg); + } + } + return result; + }; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/parser.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/parser.js new file mode 100755 index 00000000..dde2e61f --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/parser.js @@ -0,0 +1,608 @@ +/* parser generated by jison 0.4.2 */ +var parser = (function(){ +var parser = {trace: function trace() { }, +yy: {}, +symbols_: 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+performAction: function anonymous(yytext,yyleng,yylineno,yy,yystate,$$,_$) { + +var $0 = $$.length - 1; +switch (yystate) { +case 1:return this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Block); +break; +case 2:return this.$ = $$[$0]; +break; +case 3:return this.$ = $$[$0-1]; +break; +case 4:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(yy.Block.wrap([$$[$0]])); +break; +case 5:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].push($$[$0])); +break; +case 6:this.$ = $$[$0-1]; +break; +case 7:this.$ = $$[$0]; +break; +case 8:this.$ = $$[$0]; +break; +case 9:this.$ = $$[$0]; +break; +case 10:this.$ = $$[$0]; +break; +case 11:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Literal($$[$0])); +break; +case 12:this.$ = $$[$0]; +break; +case 13:this.$ = $$[$0]; +break; +case 14:this.$ = $$[$0]; +break; +case 15:this.$ = $$[$0]; +break; +case 16:this.$ = $$[$0]; +break; +case 17:this.$ = $$[$0]; +break; +case 18:this.$ = $$[$0]; +break; +case 19:this.$ = $$[$0]; +break; +case 20:this.$ = $$[$0]; +break; +case 21:this.$ = $$[$0]; +break; +case 22:this.$ = $$[$0]; +break; +case 23:this.$ = $$[$0]; +break; +case 24:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Block); +break; +case 25:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-1]); +break; +case 26:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Literal($$[$0])); +break; +case 27:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Literal($$[$0])); +break; +case 28:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Literal($$[$0])); +break; +case 29:this.$ = $$[$0]; +break; +case 30:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Literal($$[$0])); +break; +case 31:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Literal($$[$0])); +break; +case 32:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Literal($$[$0])); +break; +case 33:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Undefined); +break; +case 34:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Null); +break; +case 35:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Bool($$[$0])); +break; +case 36:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Assign($$[$0-2], $$[$0])); +break; +case 37:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Assign($$[$0-3], $$[$0])); +break; +case 38:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Assign($$[$0-4], $$[$0-1])); +break; +case 39:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 40:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Assign(yy.addLocationDataFn(_$[$0-2])(new yy.Value($$[$0-2])), $$[$0], 'object')); +break; +case 41:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Assign(yy.addLocationDataFn(_$[$0-4])(new yy.Value($$[$0-4])), $$[$0-1], 'object')); +break; +case 42:this.$ = $$[$0]; +break; +case 43:this.$ = $$[$0]; +break; +case 44:this.$ = $$[$0]; +break; +case 45:this.$ = $$[$0]; +break; +case 46:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Return($$[$0])); +break; +case 47:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Return); +break; +case 48:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Comment($$[$0])); +break; +case 49:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Code($$[$0-3], $$[$0], $$[$0-1])); +break; +case 50:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Code([], $$[$0], $$[$0-1])); +break; +case 51:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])('func'); +break; +case 52:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])('boundfunc'); +break; +case 53:this.$ = $$[$0]; +break; +case 54:this.$ = $$[$0]; +break; +case 55:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([]); +break; +case 56:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([$$[$0]]); +break; +case 57:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].concat($$[$0])); +break; +case 58:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-3].concat($$[$0])); +break; +case 59:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])($$[$0-5].concat($$[$0-2])); +break; +case 60:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Param($$[$0])); +break; +case 61:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Param($$[$0-1], null, true)); +break; +case 62:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Param($$[$0-2], $$[$0])); +break; +case 63:this.$ = $$[$0]; +break; +case 64:this.$ = $$[$0]; +break; +case 65:this.$ = $$[$0]; +break; +case 66:this.$ = $$[$0]; +break; +case 67:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Splat($$[$0-1])); +break; +case 68:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 69:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0-1].add($$[$0])); +break; +case 70:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Value($$[$0-1], [].concat($$[$0]))); +break; +case 71:this.$ = $$[$0]; +break; +case 72:this.$ = $$[$0]; +break; +case 73:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 74:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 75:this.$ = $$[$0]; +break; +case 76:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 77:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 78:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 79:this.$ = $$[$0]; +break; +case 80:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Access($$[$0])); +break; +case 81:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Access($$[$0], 'soak')); +break; +case 82:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])([yy.addLocationDataFn(_$[$0-1])(new yy.Access(new yy.Literal('prototype'))), yy.addLocationDataFn(_$[$0])(new yy.Access($$[$0]))]); +break; +case 83:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])([yy.addLocationDataFn(_$[$0-1])(new yy.Access(new yy.Literal('prototype'), 'soak')), yy.addLocationDataFn(_$[$0])(new yy.Access($$[$0]))]); +break; +case 84:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Access(new yy.Literal('prototype'))); +break; +case 85:this.$ = $$[$0]; +break; +case 86:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-1]); +break; +case 87:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(yy.extend($$[$0], { + soak: true + })); +break; +case 88:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Index($$[$0])); +break; +case 89:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Slice($$[$0])); +break; +case 90:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Obj($$[$0-2], $$[$0-3].generated)); +break; +case 91:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([]); +break; +case 92:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([$$[$0]]); +break; +case 93:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].concat($$[$0])); +break; +case 94:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-3].concat($$[$0])); +break; +case 95:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])($$[$0-5].concat($$[$0-2])); +break; +case 96:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Class); +break; +case 97:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Class(null, null, $$[$0])); +break; +case 98:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Class(null, $$[$0])); +break; +case 99:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Class(null, $$[$0-1], $$[$0])); +break; +case 100:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Class($$[$0])); +break; +case 101:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Class($$[$0-1], null, $$[$0])); +break; +case 102:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Class($$[$0-2], $$[$0])); +break; +case 103:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Class($$[$0-3], $$[$0-1], $$[$0])); +break; +case 104:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Call($$[$0-2], $$[$0], $$[$0-1])); +break; +case 105:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Call($$[$0-2], $$[$0], $$[$0-1])); +break; +case 106:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Call('super', [new yy.Splat(new yy.Literal('arguments'))])); +break; +case 107:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Call('super', $$[$0])); +break; +case 108:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(false); +break; +case 109:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(true); +break; +case 110:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])([]); +break; +case 111:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-2]); +break; +case 112:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value(new yy.Literal('this'))); +break; +case 113:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value(new yy.Literal('this'))); +break; +case 114:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Value(yy.addLocationDataFn(_$[$0-1])(new yy.Literal('this')), [yy.addLocationDataFn(_$[$0])(new yy.Access($$[$0]))], 'this')); +break; +case 115:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Arr([])); +break; +case 116:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Arr($$[$0-2])); +break; +case 117:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])('inclusive'); +break; +case 118:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])('exclusive'); +break; +case 119:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Range($$[$0-3], $$[$0-1], $$[$0-2])); +break; +case 120:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Range($$[$0-2], $$[$0], $$[$0-1])); +break; +case 121:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Range($$[$0-1], null, $$[$0])); +break; +case 122:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Range(null, $$[$0], $$[$0-1])); +break; +case 123:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Range(null, null, $$[$0])); +break; +case 124:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([$$[$0]]); +break; +case 125:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].concat($$[$0])); +break; +case 126:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-3].concat($$[$0])); +break; +case 127:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-2]); +break; +case 128:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])($$[$0-5].concat($$[$0-2])); +break; +case 129:this.$ = $$[$0]; +break; +case 130:this.$ = $$[$0]; +break; +case 131:this.$ = $$[$0]; +break; +case 132:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([].concat($$[$0-2], $$[$0])); +break; +case 133:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Try($$[$0])); +break; +case 134:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Try($$[$0-1], $$[$0][0], $$[$0][1])); +break; +case 135:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Try($$[$0-2], null, null, $$[$0])); +break; +case 136:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Try($$[$0-3], $$[$0-2][0], $$[$0-2][1], $$[$0])); +break; +case 137:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([$$[$0-1], $$[$0]]); +break; +case 138:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([yy.addLocationDataFn(_$[$0-1])(new yy.Value($$[$0-1])), $$[$0]]); +break; +case 139:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Throw($$[$0])); +break; +case 140:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Parens($$[$0-1])); +break; +case 141:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Parens($$[$0-2])); +break; +case 142:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.While($$[$0])); +break; +case 143:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.While($$[$0-2], { + guard: $$[$0] + })); +break; +case 144:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.While($$[$0], { + invert: true + })); +break; +case 145:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.While($$[$0-2], { + invert: true, + guard: $$[$0] + })); +break; +case 146:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0-1].addBody($$[$0])); +break; +case 147:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0].addBody(yy.addLocationDataFn(_$[$0-1])(yy.Block.wrap([$$[$0-1]])))); +break; +case 148:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0].addBody(yy.addLocationDataFn(_$[$0-1])(yy.Block.wrap([$$[$0-1]])))); +break; +case 149:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])($$[$0]); +break; +case 150:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.While(yy.addLocationDataFn(_$[$0-1])(new yy.Literal('true'))).addBody($$[$0])); +break; +case 151:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.While(yy.addLocationDataFn(_$[$0-1])(new yy.Literal('true'))).addBody(yy.addLocationDataFn(_$[$0])(yy.Block.wrap([$$[$0]])))); +break; +case 152:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.For($$[$0-1], $$[$0])); +break; +case 153:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.For($$[$0-1], $$[$0])); +break; +case 154:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.For($$[$0], $$[$0-1])); +break; +case 155:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])({ + source: yy.addLocationDataFn(_$[$0])(new yy.Value($$[$0])) + }); +break; +case 156:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])((function () { + $$[$0].own = $$[$0-1].own; + $$[$0].name = $$[$0-1][0]; + $$[$0].index = $$[$0-1][1]; + return $$[$0]; + }())); +break; +case 157:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0]); +break; +case 158:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])((function () { + $$[$0].own = true; + return $$[$0]; + }())); +break; +case 159:this.$ = $$[$0]; +break; +case 160:this.$ = $$[$0]; +break; +case 161:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 162:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0])); +break; +case 163:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([$$[$0]]); +break; +case 164:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([$$[$0-2], $$[$0]]); +break; +case 165:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])({ + source: $$[$0] + }); +break; +case 166:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])({ + source: $$[$0], + object: true + }); +break; +case 167:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])({ + source: $$[$0-2], + guard: $$[$0] + }); +break; +case 168:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])({ + source: $$[$0-2], + guard: $$[$0], + object: true + }); +break; +case 169:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])({ + source: $$[$0-2], + step: $$[$0] + }); +break; +case 170:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])({ + source: $$[$0-4], + guard: $$[$0-2], + step: $$[$0] + }); +break; +case 171:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])({ + source: $$[$0-4], + step: $$[$0-2], + guard: $$[$0] + }); +break; +case 172:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Switch($$[$0-3], $$[$0-1])); +break; +case 173:this.$ = yy.addLocationDataFn(_$[$0-6], _$[$0])(new yy.Switch($$[$0-5], $$[$0-3], $$[$0-1])); +break; +case 174:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Switch(null, $$[$0-1])); +break; +case 175:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])(new yy.Switch(null, $$[$0-3], $$[$0-1])); +break; +case 176:this.$ = $$[$0]; +break; +case 177:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0-1].concat($$[$0])); +break; +case 178:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([[$$[$0-1], $$[$0]]]); +break; +case 179:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])([[$$[$0-2], $$[$0-1]]]); +break; +case 180:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.If($$[$0-1], $$[$0], { + type: $$[$0-2] + })); +break; +case 181:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])($$[$0-4].addElse(new yy.If($$[$0-1], $$[$0], { + type: $$[$0-2] + }))); +break; +case 182:this.$ = $$[$0]; +break; +case 183:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].addElse($$[$0])); +break; +case 184:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.If($$[$0], yy.addLocationDataFn(_$[$0-2])(yy.Block.wrap([$$[$0-2]])), { + type: $$[$0-1], + statement: true + })); +break; +case 185:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.If($$[$0], yy.addLocationDataFn(_$[$0-2])(yy.Block.wrap([$$[$0-2]])), { + type: $$[$0-1], + statement: true + })); +break; +case 186:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op($$[$0-1], $$[$0])); +break; +case 187:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('-', $$[$0])); +break; +case 188:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('+', $$[$0])); +break; +case 189:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('--', $$[$0])); +break; +case 190:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('++', $$[$0])); +break; +case 191:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('--', $$[$0-1], null, true)); +break; +case 192:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('++', $$[$0-1], null, true)); +break; +case 193:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Existence($$[$0-1])); +break; +case 194:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op('+', $$[$0-2], $$[$0])); +break; +case 195:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op('-', $$[$0-2], $$[$0])); +break; +case 196:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op($$[$0-1], $$[$0-2], $$[$0])); +break; +case 197:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op($$[$0-1], $$[$0-2], $$[$0])); +break; +case 198:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op($$[$0-1], $$[$0-2], $$[$0])); +break; +case 199:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op($$[$0-1], $$[$0-2], $$[$0])); +break; +case 200:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])((function () { + if ($$[$0-1].charAt(0) === '!') { + return new yy.Op($$[$0-1].slice(1), $$[$0-2], $$[$0]).invert(); + } else { + return new yy.Op($$[$0-1], $$[$0-2], $$[$0]); + } + }())); +break; +case 201:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Assign($$[$0-2], $$[$0], $$[$0-1])); +break; +case 202:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Assign($$[$0-4], $$[$0-1], $$[$0-3])); +break; +case 203:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Assign($$[$0-3], $$[$0], $$[$0-2])); +break; +case 204:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Extends($$[$0-2], $$[$0])); +break; +} +}, +table: 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+defaultActions: {60:[2,51],61:[2,52],75:[2,3],94:[2,109],191:[2,89]}, +parseError: function parseError(str, hash) { + throw new Error(str); +}, +parse: function parse(input) { + var self = this, stack = [0], vstack = [null], lstack = [], table = this.table, yytext = "", yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1; + this.lexer.setInput(input); + this.lexer.yy = this.yy; + this.yy.lexer = this.lexer; + this.yy.parser = this; + if (typeof this.lexer.yylloc == "undefined") + this.lexer.yylloc = {}; + var yyloc = this.lexer.yylloc; + lstack.push(yyloc); + var ranges = this.lexer.options && this.lexer.options.ranges; + if (typeof this.yy.parseError === "function") + this.parseError = this.yy.parseError; + function popStack(n) { + stack.length = stack.length - 2 * n; + vstack.length = vstack.length - n; + lstack.length = lstack.length - n; + } + function lex() { + var token; + token = self.lexer.lex() || 1; + if (typeof token !== "number") { + token = self.symbols_[token] || token; + } + return token; + } + var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected; + while (true) { + state = stack[stack.length - 1]; + if (this.defaultActions[state]) { + action = this.defaultActions[state]; + } else { + if (symbol === null || typeof symbol == "undefined") { + symbol = lex(); + } + action = table[state] && table[state][symbol]; + } + if (typeof action === "undefined" || !action.length || !action[0]) { + var errStr = ""; + if (!recovering) { + expected = []; + for (p in table[state]) + if (this.terminals_[p] && p > 2) { + expected.push("'" + this.terminals_[p] + "'"); + } + if (this.lexer.showPosition) { + errStr = "Parse error on line " + (yylineno + 1) + ":\n" + this.lexer.showPosition() + "\nExpecting " + expected.join(", ") + ", got '" + (this.terminals_[symbol] || symbol) + "'"; + } else { + errStr = "Parse error on line " + (yylineno + 1) + ": Unexpected " + (symbol == 1?"end of input":"'" + (this.terminals_[symbol] || symbol) + "'"); + } + this.parseError(errStr, {text: this.lexer.match, token: this.terminals_[symbol] || symbol, line: this.lexer.yylineno, loc: yyloc, expected: expected}); + } + } + if (action[0] instanceof Array && action.length > 1) { + throw new Error("Parse Error: multiple actions possible at state: " + state + ", token: " + symbol); + } + switch (action[0]) { + case 1: + stack.push(symbol); + vstack.push(this.lexer.yytext); + lstack.push(this.lexer.yylloc); + stack.push(action[1]); + symbol = null; + if (!preErrorSymbol) { + yyleng = this.lexer.yyleng; + yytext = this.lexer.yytext; + yylineno = this.lexer.yylineno; + yyloc = this.lexer.yylloc; + if (recovering > 0) + recovering--; + } else { + symbol = preErrorSymbol; + preErrorSymbol = null; + } + break; + case 2: + len = this.productions_[action[1]][1]; + yyval.$ = vstack[vstack.length - len]; + yyval._$ = {first_line: lstack[lstack.length - (len || 1)].first_line, last_line: lstack[lstack.length - 1].last_line, first_column: lstack[lstack.length - (len || 1)].first_column, last_column: lstack[lstack.length - 1].last_column}; + if (ranges) { + yyval._$.range = [lstack[lstack.length - (len || 1)].range[0], lstack[lstack.length - 1].range[1]]; + } + r = this.performAction.call(yyval, yytext, yyleng, yylineno, this.yy, action[1], vstack, lstack); + if (typeof r !== "undefined") { + return r; + } + if (len) { + stack = stack.slice(0, -1 * len * 2); + vstack = vstack.slice(0, -1 * len); + lstack = lstack.slice(0, -1 * len); + } + stack.push(this.productions_[action[1]][0]); + vstack.push(yyval.$); + lstack.push(yyval._$); + newState = table[stack[stack.length - 2]][stack[stack.length - 1]]; + stack.push(newState); + break; + case 3: + return true; + } + } + return true; +} +}; +undefined +function Parser () { this.yy = {}; }Parser.prototype = parser;parser.Parser = Parser; +return new Parser; +})(); +if (typeof require !== 'undefined' && typeof exports !== 'undefined') { +exports.parser = parser; +exports.Parser = parser.Parser; +exports.parse = function () { return parser.parse.apply(parser, arguments); }; +exports.main = function commonjsMain(args) { + if (!args[1]) { + console.log('Usage: '+args[0]+' FILE'); + process.exit(1); + } + var source = require('fs').readFileSync(require('path').normalize(args[1]), "utf8"); + return exports.parser.parse(source); +}; +if (typeof module !== 'undefined' && require.main === module) { + exports.main(process.argv.slice(1)); +} +}
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/repl.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/repl.js new file mode 100644 index 00000000..37894a9b --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/repl.js @@ -0,0 +1,104 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var CoffeeScript, addMultilineHandler, merge, nodeREPL, replDefaults, vm; + + vm = require('vm'); + + nodeREPL = require('repl'); + + CoffeeScript = require('./coffee-script'); + + merge = require('./helpers').merge; + + replDefaults = { + prompt: 'coffee> ', + "eval": function(input, context, filename, cb) { + var js; + input = input.replace(/\uFF00/g, '\n'); + input = input.replace(/(^|[\r\n]+)(\s*)##?(?:[^#\r\n][^\r\n]*|)($|[\r\n])/, '$1$2$3'); + if (/^(\s*|\(\s*\))$/.test(input)) { + return cb(null); + } + try { + js = CoffeeScript.compile("_=(" + input + "\n)", { + filename: filename, + bare: true + }); + return cb(null, vm.runInContext(js, context, filename)); + } catch (err) { + return cb(err); + } + } + }; + + addMultilineHandler = function(repl) { + var inputStream, multiline, nodeLineListener, outputStream, rli; + rli = repl.rli, inputStream = repl.inputStream, outputStream = repl.outputStream; + multiline = { + enabled: false, + initialPrompt: repl.prompt.replace(/^[^> ]*/, function(x) { + return x.replace(/./g, '-'); + }), + prompt: repl.prompt.replace(/^[^> ]*>?/, function(x) { + return x.replace(/./g, '.'); + }), + buffer: '' + }; + nodeLineListener = rli.listeners('line')[0]; + rli.removeListener('line', nodeLineListener); + rli.on('line', function(cmd) { + if (multiline.enabled) { + multiline.buffer += "" + cmd + "\n"; + rli.setPrompt(multiline.prompt); + rli.prompt(true); + } else { + nodeLineListener(cmd); + } + }); + return inputStream.on('keypress', function(char, key) { + if (!(key && key.ctrl && !key.meta && !key.shift && key.name === 'v')) { + return; + } + if (multiline.enabled) { + if (!multiline.buffer.match(/\n/)) { + multiline.enabled = !multiline.enabled; + rli.setPrompt(repl.prompt); + rli.prompt(true); + return; + } + if ((rli.line != null) && !rli.line.match(/^\s*$/)) { + return; + } + multiline.enabled = !multiline.enabled; + rli.line = ''; + rli.cursor = 0; + rli.output.cursorTo(0); + rli.output.clearLine(1); + multiline.buffer = multiline.buffer.replace(/\n/g, '\uFF00'); + rli.emit('line', multiline.buffer); + multiline.buffer = ''; + } else { + multiline.enabled = !multiline.enabled; + rli.setPrompt(multiline.initialPrompt); + rli.prompt(true); + } + }); + }; + + module.exports = { + start: function(opts) { + var repl; + if (opts == null) { + opts = {}; + } + opts = merge(replDefaults, opts); + repl = nodeREPL.start(opts); + repl.on('exit', function() { + return repl.outputStream.write('\n'); + }); + addMultilineHandler(repl); + return repl; + } + }; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/rewriter.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/rewriter.js new file mode 100644 index 00000000..b582bb29 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/rewriter.js @@ -0,0 +1,478 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var BALANCED_PAIRS, EXPRESSION_CLOSE, EXPRESSION_END, EXPRESSION_START, IMPLICIT_BLOCK, IMPLICIT_CALL, IMPLICIT_END, IMPLICIT_FUNC, IMPLICIT_UNSPACED_CALL, INVERSES, LINEBREAKS, SINGLE_CLOSERS, SINGLE_LINERS, generate, left, rite, _i, _len, _ref, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }, + __slice = [].slice; + + generate = function(tag, value) { + var tok; + tok = [tag, value]; + tok.generated = true; + return tok; + }; + + exports.Rewriter = (function() { + + function Rewriter() {} + + Rewriter.prototype.rewrite = function(tokens) { + this.tokens = tokens; + this.removeLeadingNewlines(); + this.removeMidExpressionNewlines(); + this.closeOpenCalls(); + this.closeOpenIndexes(); + this.addImplicitIndentation(); + this.tagPostfixConditionals(); + this.addImplicitBracesAndParens(); + this.addLocationDataToGeneratedTokens(); + return this.tokens; + }; + + Rewriter.prototype.scanTokens = function(block) { + var i, token, tokens; + tokens = this.tokens; + i = 0; + while (token = tokens[i]) { + i += block.call(this, token, i, tokens); + } + return true; + }; + + Rewriter.prototype.detectEnd = function(i, condition, action) { + var levels, token, tokens, _ref, _ref1; + tokens = this.tokens; + levels = 0; + while (token = tokens[i]) { + if (levels === 0 && condition.call(this, token, i)) { + return action.call(this, token, i); + } + if (!token || levels < 0) { + return action.call(this, token, i - 1); + } + if (_ref = token[0], __indexOf.call(EXPRESSION_START, _ref) >= 0) { + levels += 1; + } else if (_ref1 = token[0], __indexOf.call(EXPRESSION_END, _ref1) >= 0) { + levels -= 1; + } + i += 1; + } + return i - 1; + }; + + Rewriter.prototype.removeLeadingNewlines = function() { + var i, tag, _i, _len, _ref; + _ref = this.tokens; + for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) { + tag = _ref[i][0]; + if (tag !== 'TERMINATOR') { + break; + } + } + if (i) { + return this.tokens.splice(0, i); + } + }; + + Rewriter.prototype.removeMidExpressionNewlines = function() { + return this.scanTokens(function(token, i, tokens) { + var _ref; + if (!(token[0] === 'TERMINATOR' && (_ref = this.tag(i + 1), __indexOf.call(EXPRESSION_CLOSE, _ref) >= 0))) { + return 1; + } + tokens.splice(i, 1); + return 0; + }); + }; + + Rewriter.prototype.closeOpenCalls = function() { + var action, condition; + condition = function(token, i) { + var _ref; + return ((_ref = token[0]) === ')' || _ref === 'CALL_END') || token[0] === 'OUTDENT' && this.tag(i - 1) === ')'; + }; + action = function(token, i) { + return this.tokens[token[0] === 'OUTDENT' ? i - 1 : i][0] = 'CALL_END'; + }; + return this.scanTokens(function(token, i) { + if (token[0] === 'CALL_START') { + this.detectEnd(i + 1, condition, action); + } + return 1; + }); + }; + + Rewriter.prototype.closeOpenIndexes = function() { + var action, condition; + condition = function(token, i) { + var _ref; + return (_ref = token[0]) === ']' || _ref === 'INDEX_END'; + }; + action = function(token, i) { + return token[0] = 'INDEX_END'; + }; + return this.scanTokens(function(token, i) { + if (token[0] === 'INDEX_START') { + this.detectEnd(i + 1, condition, action); + } + return 1; + }); + }; + + Rewriter.prototype.matchTags = function() { + var fuzz, i, j, pattern, _i, _ref, _ref1; + i = arguments[0], pattern = 2 <= arguments.length ? __slice.call(arguments, 1) : []; + fuzz = 0; + for (j = _i = 0, _ref = pattern.length; 0 <= _ref ? _i < _ref : _i > _ref; j = 0 <= _ref ? ++_i : --_i) { + while (this.tag(i + j + fuzz) === 'HERECOMMENT') { + fuzz += 2; + } + if (pattern[j] == null) { + continue; + } + if (typeof pattern[j] === 'string') { + pattern[j] = [pattern[j]]; + } + if (_ref1 = this.tag(i + j + fuzz), __indexOf.call(pattern[j], _ref1) < 0) { + return false; + } + } + return true; + }; + + Rewriter.prototype.looksObjectish = function(j) { + return this.matchTags(j, '@', null, ':') || this.matchTags(j, null, ':'); + }; + + Rewriter.prototype.findTagsBackwards = function(i, tags) { + var backStack, _ref, _ref1, _ref2, _ref3, _ref4, _ref5; + backStack = []; + while (i >= 0 && (backStack.length || (_ref2 = this.tag(i), __indexOf.call(tags, _ref2) < 0) && ((_ref3 = this.tag(i), __indexOf.call(EXPRESSION_START, _ref3) < 0) || this.tokens[i].generated) && (_ref4 = this.tag(i), __indexOf.call(LINEBREAKS, _ref4) < 0))) { + if (_ref = this.tag(i), __indexOf.call(EXPRESSION_END, _ref) >= 0) { + backStack.push(this.tag(i)); + } + if ((_ref1 = this.tag(i), __indexOf.call(EXPRESSION_START, _ref1) >= 0) && backStack.length) { + backStack.pop(); + } + i -= 1; + } + return _ref5 = this.tag(i), __indexOf.call(tags, _ref5) >= 0; + }; + + Rewriter.prototype.addImplicitBracesAndParens = function() { + var stack; + stack = []; + return this.scanTokens(function(token, i, tokens) { + var endImplicitCall, endImplicitObject, forward, inImplicit, inImplicitCall, inImplicitControl, inImplicitObject, nextTag, offset, prevTag, s, sameLine, stackIdx, stackTag, stackTop, startIdx, startImplicitCall, startImplicitObject, startsLine, tag, _ref, _ref1, _ref2, _ref3, _ref4, _ref5; + tag = token[0]; + prevTag = (i > 0 ? tokens[i - 1] : [])[0]; + nextTag = (i < tokens.length - 1 ? tokens[i + 1] : [])[0]; + stackTop = function() { + return stack[stack.length - 1]; + }; + startIdx = i; + forward = function(n) { + return i - startIdx + n; + }; + inImplicit = function() { + var _ref, _ref1; + return (_ref = stackTop()) != null ? (_ref1 = _ref[2]) != null ? _ref1.ours : void 0 : void 0; + }; + inImplicitCall = function() { + var _ref; + return inImplicit() && ((_ref = stackTop()) != null ? _ref[0] : void 0) === '('; + }; + inImplicitObject = function() { + var _ref; + return inImplicit() && ((_ref = stackTop()) != null ? _ref[0] : void 0) === '{'; + }; + inImplicitControl = function() { + var _ref; + return inImplicit && ((_ref = stackTop()) != null ? _ref[0] : void 0) === 'CONTROL'; + }; + startImplicitCall = function(j) { + var idx; + idx = j != null ? j : i; + stack.push([ + '(', idx, { + ours: true + } + ]); + tokens.splice(idx, 0, generate('CALL_START', '(')); + if (j == null) { + return i += 1; + } + }; + endImplicitCall = function() { + stack.pop(); + tokens.splice(i, 0, generate('CALL_END', ')')); + return i += 1; + }; + startImplicitObject = function(j, startsLine) { + var idx; + if (startsLine == null) { + startsLine = true; + } + idx = j != null ? j : i; + stack.push([ + '{', idx, { + sameLine: true, + startsLine: startsLine, + ours: true + } + ]); + tokens.splice(idx, 0, generate('{', generate(new String('{')))); + if (j == null) { + return i += 1; + } + }; + endImplicitObject = function(j) { + j = j != null ? j : i; + stack.pop(); + tokens.splice(j, 0, generate('}', '}')); + return i += 1; + }; + if (inImplicitCall() && (tag === 'IF' || tag === 'TRY' || tag === 'FINALLY' || tag === 'CATCH' || tag === 'CLASS' || tag === 'SWITCH')) { + stack.push([ + 'CONTROL', i, { + ours: true + } + ]); + return forward(1); + } + if (tag === 'INDENT' && inImplicit()) { + if (prevTag !== '=>' && prevTag !== '->' && prevTag !== '[' && prevTag !== '(' && prevTag !== ',' && prevTag !== '{' && prevTag !== 'TRY' && prevTag !== 'ELSE' && prevTag !== '=') { + while (inImplicitCall()) { + endImplicitCall(); + } + } + if (inImplicitControl()) { + stack.pop(); + } + stack.push([tag, i]); + return forward(1); + } + if (__indexOf.call(EXPRESSION_START, tag) >= 0) { + stack.push([tag, i]); + return forward(1); + } + if (__indexOf.call(EXPRESSION_END, tag) >= 0) { + while (inImplicit()) { + if (inImplicitCall()) { + endImplicitCall(); + } else if (inImplicitObject()) { + endImplicitObject(); + } else { + stack.pop(); + } + } + stack.pop(); + } + if ((__indexOf.call(IMPLICIT_FUNC, tag) >= 0 && token.spaced || tag === '?' && i > 0 && !tokens[i - 1].spaced) && (__indexOf.call(IMPLICIT_CALL, nextTag) >= 0 || __indexOf.call(IMPLICIT_UNSPACED_CALL, nextTag) >= 0 && !((_ref = tokens[i + 1]) != null ? _ref.spaced : void 0) && !((_ref1 = tokens[i + 1]) != null ? _ref1.newLine : void 0))) { + if (tag === '?') { + tag = token[0] = 'FUNC_EXIST'; + } + startImplicitCall(i + 1); + return forward(2); + } + if (this.matchTags(i, IMPLICIT_FUNC, 'INDENT', null, ':') && !this.findTagsBackwards(i, ['CLASS', 'EXTENDS', 'IF', 'CATCH', 'SWITCH', 'LEADING_WHEN', 'FOR', 'WHILE', 'UNTIL'])) { + startImplicitCall(i + 1); + stack.push(['INDENT', i + 2]); + return forward(3); + } + if (tag === ':') { + if (this.tag(i - 2) === '@') { + s = i - 2; + } else { + s = i - 1; + } + while (this.tag(s - 2) === 'HERECOMMENT') { + s -= 2; + } + startsLine = s === 0 || (_ref2 = this.tag(s - 1), __indexOf.call(LINEBREAKS, _ref2) >= 0) || tokens[s - 1].newLine; + if (stackTop()) { + _ref3 = stackTop(), stackTag = _ref3[0], stackIdx = _ref3[1]; + if ((stackTag === '{' || stackTag === 'INDENT' && this.tag(stackIdx - 1) === '{') && (startsLine || this.tag(s - 1) === ',' || this.tag(s - 1) === '{')) { + return forward(1); + } + } + startImplicitObject(s, !!startsLine); + return forward(2); + } + if (prevTag === 'OUTDENT' && inImplicitCall() && (tag === '.' || tag === '?.' || tag === '::' || tag === '?::')) { + endImplicitCall(); + return forward(1); + } + if (inImplicitObject() && __indexOf.call(LINEBREAKS, tag) >= 0) { + stackTop()[2].sameLine = false; + } + if (__indexOf.call(IMPLICIT_END, tag) >= 0) { + while (inImplicit()) { + _ref4 = stackTop(), stackTag = _ref4[0], stackIdx = _ref4[1], (_ref5 = _ref4[2], sameLine = _ref5.sameLine, startsLine = _ref5.startsLine); + if (inImplicitCall() && prevTag !== ',') { + endImplicitCall(); + } else if (inImplicitObject() && sameLine && !startsLine) { + endImplicitObject(); + } else if (inImplicitObject() && tag === 'TERMINATOR' && prevTag !== ',' && !(startsLine && this.looksObjectish(i + 1))) { + endImplicitObject(); + } else { + break; + } + } + } + if (tag === ',' && !this.looksObjectish(i + 1) && inImplicitObject() && (nextTag !== 'TERMINATOR' || !this.looksObjectish(i + 2))) { + offset = nextTag === 'OUTDENT' ? 1 : 0; + while (inImplicitObject()) { + endImplicitObject(i + offset); + } + } + return forward(1); + }); + }; + + Rewriter.prototype.addLocationDataToGeneratedTokens = function() { + return this.scanTokens(function(token, i, tokens) { + var last_column, last_line, _ref, _ref1, _ref2; + if (token[2]) { + return 1; + } + if (!(token.generated || token.explicit)) { + return 1; + } + _ref2 = (_ref = (_ref1 = tokens[i - 1]) != null ? _ref1[2] : void 0) != null ? _ref : { + last_line: 0, + last_column: 0 + }, last_line = _ref2.last_line, last_column = _ref2.last_column; + token[2] = { + first_line: last_line, + first_column: last_column, + last_line: last_line, + last_column: last_column + }; + return 1; + }); + }; + + Rewriter.prototype.addImplicitIndentation = function() { + var action, condition, indent, outdent, starter; + starter = indent = outdent = null; + condition = function(token, i) { + var _ref; + return token[1] !== ';' && (_ref = token[0], __indexOf.call(SINGLE_CLOSERS, _ref) >= 0) && !(token[0] === 'ELSE' && (starter !== 'IF' && starter !== 'THEN')); + }; + action = function(token, i) { + return this.tokens.splice((this.tag(i - 1) === ',' ? i - 1 : i), 0, outdent); + }; + return this.scanTokens(function(token, i, tokens) { + var tag, _ref, _ref1; + tag = token[0]; + if (tag === 'TERMINATOR' && this.tag(i + 1) === 'THEN') { + tokens.splice(i, 1); + return 0; + } + if (tag === 'ELSE' && this.tag(i - 1) !== 'OUTDENT') { + tokens.splice.apply(tokens, [i, 0].concat(__slice.call(this.indentation(token)))); + return 2; + } + if (tag === 'CATCH' && ((_ref = this.tag(i + 2)) === 'OUTDENT' || _ref === 'TERMINATOR' || _ref === 'FINALLY')) { + tokens.splice.apply(tokens, [i + 2, 0].concat(__slice.call(this.indentation(token)))); + return 4; + } + if (__indexOf.call(SINGLE_LINERS, tag) >= 0 && this.tag(i + 1) !== 'INDENT' && !(tag === 'ELSE' && this.tag(i + 1) === 'IF')) { + starter = tag; + _ref1 = this.indentation(token, true), indent = _ref1[0], outdent = _ref1[1]; + if (starter === 'THEN') { + indent.fromThen = true; + } + tokens.splice(i + 1, 0, indent); + this.detectEnd(i + 2, condition, action); + if (tag === 'THEN') { + tokens.splice(i, 1); + } + return 1; + } + return 1; + }); + }; + + Rewriter.prototype.tagPostfixConditionals = function() { + var action, condition, original; + original = null; + condition = function(token, i) { + var _ref; + return (_ref = token[0]) === 'TERMINATOR' || _ref === 'INDENT'; + }; + action = function(token, i) { + if (token[0] !== 'INDENT' || (token.generated && !token.fromThen)) { + return original[0] = 'POST_' + original[0]; + } + }; + return this.scanTokens(function(token, i) { + if (token[0] !== 'IF') { + return 1; + } + original = token; + this.detectEnd(i + 1, condition, action); + return 1; + }); + }; + + Rewriter.prototype.indentation = function(token, implicit) { + var indent, outdent; + if (implicit == null) { + implicit = false; + } + indent = ['INDENT', 2]; + outdent = ['OUTDENT', 2]; + if (implicit) { + indent.generated = outdent.generated = true; + } + if (!implicit) { + indent.explicit = outdent.explicit = true; + } + return [indent, outdent]; + }; + + Rewriter.prototype.generate = generate; + + Rewriter.prototype.tag = function(i) { + var _ref; + return (_ref = this.tokens[i]) != null ? _ref[0] : void 0; + }; + + return Rewriter; + + })(); + + BALANCED_PAIRS = [['(', ')'], ['[', ']'], ['{', '}'], ['INDENT', 'OUTDENT'], ['CALL_START', 'CALL_END'], ['PARAM_START', 'PARAM_END'], ['INDEX_START', 'INDEX_END']]; + + exports.INVERSES = INVERSES = {}; + + EXPRESSION_START = []; + + EXPRESSION_END = []; + + for (_i = 0, _len = BALANCED_PAIRS.length; _i < _len; _i++) { + _ref = BALANCED_PAIRS[_i], left = _ref[0], rite = _ref[1]; + EXPRESSION_START.push(INVERSES[rite] = left); + EXPRESSION_END.push(INVERSES[left] = rite); + } + + EXPRESSION_CLOSE = ['CATCH', 'WHEN', 'ELSE', 'FINALLY'].concat(EXPRESSION_END); + + IMPLICIT_FUNC = ['IDENTIFIER', 'SUPER', ')', 'CALL_END', ']', 'INDEX_END', '@', 'THIS']; + + IMPLICIT_CALL = ['IDENTIFIER', 'NUMBER', 'STRING', 'JS', 'REGEX', 'NEW', 'PARAM_START', 'CLASS', 'IF', 'TRY', 'SWITCH', 'THIS', 'BOOL', 'NULL', 'UNDEFINED', 'UNARY', 'SUPER', '@', '->', '=>', '[', '(', '{', '--', '++']; + + IMPLICIT_UNSPACED_CALL = ['+', '-']; + + IMPLICIT_BLOCK = ['->', '=>', '{', '[', ',']; + + IMPLICIT_END = ['POST_IF', 'FOR', 'WHILE', 'UNTIL', 'WHEN', 'BY', 'LOOP', 'TERMINATOR']; + + SINGLE_LINERS = ['ELSE', '->', '=>', 'TRY', 'FINALLY', 'THEN']; + + SINGLE_CLOSERS = ['TERMINATOR', 'CATCH', 'FINALLY', 'ELSE', 'OUTDENT', 'LEADING_WHEN']; + + LINEBREAKS = ['TERMINATOR', 'INDENT', 'OUTDENT']; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/scope.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/scope.js new file mode 100644 index 00000000..41281734 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/scope.js @@ -0,0 +1,147 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var Scope, extend, last, _ref; + + _ref = require('./helpers'), extend = _ref.extend, last = _ref.last; + + exports.Scope = Scope = (function() { + + Scope.root = null; + + function Scope(parent, expressions, method) { + this.parent = parent; + this.expressions = expressions; + this.method = method; + this.variables = [ + { + name: 'arguments', + type: 'arguments' + } + ]; + this.positions = {}; + if (!this.parent) { + Scope.root = this; + } + } + + Scope.prototype.add = function(name, type, immediate) { + if (this.shared && !immediate) { + return this.parent.add(name, type, immediate); + } + if (Object.prototype.hasOwnProperty.call(this.positions, name)) { + return this.variables[this.positions[name]].type = type; + } else { + return this.positions[name] = this.variables.push({ + name: name, + type: type + }) - 1; + } + }; + + Scope.prototype.namedMethod = function() { + var _ref1; + if (((_ref1 = this.method) != null ? _ref1.name : void 0) || !this.parent) { + return this.method; + } + return this.parent.namedMethod(); + }; + + Scope.prototype.find = function(name) { + if (this.check(name)) { + return true; + } + this.add(name, 'var'); + return false; + }; + + Scope.prototype.parameter = function(name) { + if (this.shared && this.parent.check(name, true)) { + return; + } + return this.add(name, 'param'); + }; + + Scope.prototype.check = function(name) { + var _ref1; + return !!(this.type(name) || ((_ref1 = this.parent) != null ? _ref1.check(name) : void 0)); + }; + + Scope.prototype.temporary = function(name, index) { + if (name.length > 1) { + return '_' + name + (index > 1 ? index - 1 : ''); + } else { + return '_' + (index + parseInt(name, 36)).toString(36).replace(/\d/g, 'a'); + } + }; + + Scope.prototype.type = function(name) { + var v, _i, _len, _ref1; + _ref1 = this.variables; + for (_i = 0, _len = _ref1.length; _i < _len; _i++) { + v = _ref1[_i]; + if (v.name === name) { + return v.type; + } + } + return null; + }; + + Scope.prototype.freeVariable = function(name, reserve) { + var index, temp; + if (reserve == null) { + reserve = true; + } + index = 0; + while (this.check((temp = this.temporary(name, index)))) { + index++; + } + if (reserve) { + this.add(temp, 'var', true); + } + return temp; + }; + + Scope.prototype.assign = function(name, value) { + this.add(name, { + value: value, + assigned: true + }, true); + return this.hasAssignments = true; + }; + + Scope.prototype.hasDeclarations = function() { + return !!this.declaredVariables().length; + }; + + Scope.prototype.declaredVariables = function() { + var realVars, tempVars, v, _i, _len, _ref1; + realVars = []; + tempVars = []; + _ref1 = this.variables; + for (_i = 0, _len = _ref1.length; _i < _len; _i++) { + v = _ref1[_i]; + if (v.type === 'var') { + (v.name.charAt(0) === '_' ? tempVars : realVars).push(v.name); + } + } + return realVars.sort().concat(tempVars.sort()); + }; + + Scope.prototype.assignedVariables = function() { + var v, _i, _len, _ref1, _results; + _ref1 = this.variables; + _results = []; + for (_i = 0, _len = _ref1.length; _i < _len; _i++) { + v = _ref1[_i]; + if (v.type.assigned) { + _results.push("" + v.name + " = " + v.type.value); + } + } + return _results; + }; + + return Scope; + + })(); + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/sourcemap.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/sourcemap.js new file mode 100644 index 00000000..245da945 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/sourcemap.js @@ -0,0 +1,237 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + var BASE64_CHARS, LineMapping, MAX_BASE64_VALUE, VLQ_CONTINUATION_BIT, VLQ_SHIFT, VLQ_VALUE_MASK, decodeBase64Char, encodeBase64Char; + + LineMapping = (function() { + + function LineMapping(generatedLine) { + this.generatedLine = generatedLine; + this.columnMap = {}; + this.columnMappings = []; + } + + LineMapping.prototype.addMapping = function(generatedColumn, _arg, options) { + var sourceColumn, sourceLine; + sourceLine = _arg[0], sourceColumn = _arg[1]; + if (options == null) { + options = {}; + } + if (this.columnMap[generatedColumn] && options.noReplace) { + return; + } + this.columnMap[generatedColumn] = { + generatedLine: this.generatedLine, + generatedColumn: generatedColumn, + sourceLine: sourceLine, + sourceColumn: sourceColumn + }; + this.columnMappings.push(this.columnMap[generatedColumn]); + return this.columnMappings.sort(function(a, b) { + return a.generatedColumn - b.generatedColumn; + }); + }; + + LineMapping.prototype.getSourcePosition = function(generatedColumn) { + var answer, columnMapping, lastColumnMapping, _i, _len, _ref; + answer = null; + lastColumnMapping = null; + _ref = this.columnMappings; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + columnMapping = _ref[_i]; + if (columnMapping.generatedColumn > generatedColumn) { + break; + } else { + lastColumnMapping = columnMapping; + } + } + if (lastColumnMapping) { + return answer = [lastColumnMapping.sourceLine, lastColumnMapping.sourceColumn]; + } + }; + + return LineMapping; + + })(); + + exports.SourceMap = (function() { + + function SourceMap() { + this.generatedLines = []; + } + + SourceMap.prototype.addMapping = function(sourceLocation, generatedLocation, options) { + var generatedColumn, generatedLine, lineMapping; + if (options == null) { + options = {}; + } + generatedLine = generatedLocation[0], generatedColumn = generatedLocation[1]; + lineMapping = this.generatedLines[generatedLine]; + if (!lineMapping) { + lineMapping = this.generatedLines[generatedLine] = new LineMapping(generatedLine); + } + return lineMapping.addMapping(generatedColumn, sourceLocation, options); + }; + + SourceMap.prototype.getSourcePosition = function(_arg) { + var answer, generatedColumn, generatedLine, lineMapping; + generatedLine = _arg[0], generatedColumn = _arg[1]; + answer = null; + lineMapping = this.generatedLines[generatedLine]; + if (!lineMapping) { + + } else { + answer = lineMapping.getSourcePosition(generatedColumn); + } + return answer; + }; + + SourceMap.prototype.forEachMapping = function(fn) { + var columnMapping, generatedLineNumber, lineMapping, _i, _len, _ref, _results; + _ref = this.generatedLines; + _results = []; + for (generatedLineNumber = _i = 0, _len = _ref.length; _i < _len; generatedLineNumber = ++_i) { + lineMapping = _ref[generatedLineNumber]; + if (lineMapping) { + _results.push((function() { + var _j, _len1, _ref1, _results1; + _ref1 = lineMapping.columnMappings; + _results1 = []; + for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { + columnMapping = _ref1[_j]; + _results1.push(fn(columnMapping)); + } + return _results1; + })()); + } else { + _results.push(void 0); + } + } + return _results; + }; + + return SourceMap; + + })(); + + exports.generateV3SourceMap = function(sourceMap, sourceFile, generatedFile) { + var answer, lastGeneratedColumnWritten, lastSourceColumnWritten, lastSourceLineWritten, mappings, needComma, writingGeneratedLine; + if (sourceFile == null) { + sourceFile = null; + } + if (generatedFile == null) { + generatedFile = null; + } + writingGeneratedLine = 0; + lastGeneratedColumnWritten = 0; + lastSourceLineWritten = 0; + lastSourceColumnWritten = 0; + needComma = false; + mappings = ""; + sourceMap.forEachMapping(function(mapping) { + while (writingGeneratedLine < mapping.generatedLine) { + lastGeneratedColumnWritten = 0; + needComma = false; + mappings += ";"; + writingGeneratedLine++; + } + if (needComma) { + mappings += ","; + needComma = false; + } + mappings += exports.vlqEncodeValue(mapping.generatedColumn - lastGeneratedColumnWritten); + lastGeneratedColumnWritten = mapping.generatedColumn; + mappings += exports.vlqEncodeValue(0); + mappings += exports.vlqEncodeValue(mapping.sourceLine - lastSourceLineWritten); + lastSourceLineWritten = mapping.sourceLine; + mappings += exports.vlqEncodeValue(mapping.sourceColumn - lastSourceColumnWritten); + lastSourceColumnWritten = mapping.sourceColumn; + return needComma = true; + }); + answer = { + version: 3, + file: generatedFile, + sourceRoot: "", + sources: sourceFile ? [sourceFile] : [], + names: [], + mappings: mappings + }; + return JSON.stringify(answer, null, 2); + }; + + exports.loadV3SourceMap = function(sourceMap) { + return todo(); + }; + + BASE64_CHARS = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/'; + + MAX_BASE64_VALUE = BASE64_CHARS.length - 1; + + encodeBase64Char = function(value) { + if (value > MAX_BASE64_VALUE) { + throw new Error("Cannot encode value " + value + " > " + MAX_BASE64_VALUE); + } else if (value < 0) { + throw new Error("Cannot encode value " + value + " < 0"); + } + return BASE64_CHARS[value]; + }; + + decodeBase64Char = function(char) { + var value; + value = BASE64_CHARS.indexOf(char); + if (value === -1) { + throw new Error("Invalid Base 64 character: " + char); + } + return value; + }; + + VLQ_SHIFT = 5; + + VLQ_CONTINUATION_BIT = 1 << VLQ_SHIFT; + + VLQ_VALUE_MASK = VLQ_CONTINUATION_BIT - 1; + + exports.vlqEncodeValue = function(value) { + var answer, nextVlqChunk, signBit, valueToEncode; + signBit = value < 0 ? 1 : 0; + valueToEncode = (Math.abs(value) << 1) + signBit; + answer = ""; + while (valueToEncode || !answer) { + nextVlqChunk = valueToEncode & VLQ_VALUE_MASK; + valueToEncode = valueToEncode >> VLQ_SHIFT; + if (valueToEncode) { + nextVlqChunk |= VLQ_CONTINUATION_BIT; + } + answer += encodeBase64Char(nextVlqChunk); + } + return answer; + }; + + exports.vlqDecodeValue = function(str, offset) { + var consumed, continuationShift, done, nextChunkValue, nextVlqChunk, position, signBit, value; + if (offset == null) { + offset = 0; + } + position = offset; + done = false; + value = 0; + continuationShift = 0; + while (!done) { + nextVlqChunk = decodeBase64Char(str[position]); + position += 1; + nextChunkValue = nextVlqChunk & VLQ_VALUE_MASK; + value += nextChunkValue << continuationShift; + if (!(nextVlqChunk & VLQ_CONTINUATION_BIT)) { + done = true; + } + continuationShift += VLQ_SHIFT; + } + consumed = position - offset; + signBit = value & 1; + value = value >> 1; + if (signBit) { + value = -value; + } + return [value, consumed]; + }; + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/package.json b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/package.json new file mode 100644 index 00000000..e1aea0c9 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/package.json @@ -0,0 +1,57 @@ +{ + "name": "coffee-script", + "description": "Unfancy JavaScript", + "keywords": [ + "javascript", + "language", + "coffeescript", + "compiler" + ], + "author": { + "name": "Jeremy Ashkenas" + }, + "version": "1.6.1", + "licenses": [ + { + "type": "MIT", + "url": "https://raw.github.com/jashkenas/coffee-script/master/LICENSE" + } + ], + "engines": { + "node": ">=0.4.0" + }, + "directories": { + "lib": "./lib/coffee-script" + }, + "main": "./lib/coffee-script/coffee-script", + "bin": { + "coffee": "./bin/coffee", + "cake": "./bin/cake" + }, + "scripts": { + "test": "node ./bin/cake test" + }, + "homepage": "http://coffeescript.org", + "bugs": { + "name": "https://github.com/jashkenas/coffee-script/issues" + }, + "repository": { + "type": "git", + "url": "git://github.com/jashkenas/coffee-script.git" + }, + "devDependencies": { + "uglify-js": "~2.2", + "jison": ">=0.2.0" + }, + "_id": "coffee-script@1.6.1", + "dependencies": {}, + "optionalDependencies": {}, + "_engineSupported": true, + "_npmVersion": "1.1.4", + "_nodeVersion": "v0.6.12", + "_defaultsLoaded": true, + "dist": { + "shasum": "05d88f953bcd2e72d53bff583c9318a9572a386d" + }, + "_from": "coffee-script" +} diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index ec93727c..f554267f 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.4.0 +// Generated by CoffeeScript 1.6.1 (function() { var Stat_Table_Rows, is_number, __hasProp = {}.hasOwnProperty, diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 329dcdd9..b309b167 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.4.0 +// Generated by CoffeeScript 1.6.1 (function() { var root; diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js index 4cca0d13..d874995f 100644 --- a/wqflask/wqflask/static/new/javascript/stats.js +++ b/wqflask/wqflask/static/new/javascript/stats.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.4.0 +// Generated by CoffeeScript 1.6.1 (function() { var Stats, bxd_only; diff --git a/wqflask/wqflask/static/new/javascript/thank_you.coffee b/wqflask/wqflask/static/new/javascript/thank_you.coffee new file mode 100644 index 00000000..975f85c6 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/thank_you.coffee @@ -0,0 +1,4 @@ +$ -> + console.log("Starting transform") + $('#login_out').text('Sign out').attr('href', '/logout').removeClass('modalize') + console.log("Transformed to sign out I hope") diff --git a/wqflask/wqflask/static/new/javascript/thank_you.js b/wqflask/wqflask/static/new/javascript/thank_you.js new file mode 100644 index 00000000..bffff179 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/thank_you.js @@ -0,0 +1,10 @@ +// Generated by CoffeeScript 1.6.1 +(function() { + + $(function() { + console.log("Starting transform"); + $('#login_out').text('Sign out').attr('href', '/logout').removeClass('modalize'); + return console.log("Transformed to sign out I hope"); + }); + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/validation.js b/wqflask/wqflask/static/new/javascript/validation.js index 2ac477b5..275bcaa0 100644 --- a/wqflask/wqflask/static/new/javascript/validation.js +++ b/wqflask/wqflask/static/new/javascript/validation.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.4.0 +// Generated by CoffeeScript 1.6.1 (function() { $(function() { @@ -31,7 +31,7 @@ }; validate_remove_samples = function() { /* - Check if input for the remove samples function is valid and notify the user if not + Check if input for the remove samples function is valid and notify the user if not */ var input; diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html new file mode 100644 index 00000000..df3eda33 --- /dev/null +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -0,0 +1,83 @@ +{% extends "base.html" %} +{% block title %}Group Manager{% endblock %} +{% block content %} +<!-- Start of body --> + <header class="jumbotron subhead" id="overview"> + <div class="container"> + <h1>Group Manager</h1> + </div> + </header> + + <div class="container"> + <div class="page-header"> + + </div> + <form> + <div class="control-group"> + <b>Group Name: </b> + <div class="input-append"> + <input type="text" name="group_name"> + <button type="submit" class="btn btn-primary">Save</button> + </div> + </div> + + <table id="dataset_list" class="table table-hover"> + <thead> + <tr> + <th>Read</th> + <th>Type</th> + <th>ID</th> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + {% for dataset in datasets %} + <tr> + <td><input type="checkbox" name="read" value="{{ dataset.type }}:{{ dataset.name }}"></td> + <td>{{ dataset.type }}</td> + <td>{{ dataset.id }}</td> + <td>{{ dataset.name }}</td> + <td>{{ dataset.fullname }}</td> + </tr> + {% endfor %} + </table> + </form> + </div> + +<!-- End of body --> + +{% endblock %} + +{% block js %} + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> + <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + + <script type="text/javascript" charset="utf-8"> + $(document).ready( function () { + console.time("Creating table"); + $('#dataset_list').dataTable( { + "sDom": "Tftipr", + "oTableTools": { + "aButtons": [ + "copy", + "print", + { + "sExtends": "collection", + "sButtonText": 'Save <span class="caret" />', + "aButtons": [ "csv", "xls", "pdf" ] + } + ], + "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf" + }, + "iDisplayLength": 50, + "bLengthChange": true, + "bDeferRender": true, + "bSortClasses": false + } ); + console.timeEnd("Creating table"); + }); + </script> +{% endblock %}
\ No newline at end of file diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 741c5425..cbed5859 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -70,9 +70,9 @@ </li> <li class=""> {% if g.identity.name=="anon" %} - <a id="login" class="modalize" href="/login">Sign in</a> + <a id="login_out" class="modalize" href="/login">Sign in</a> {% else %} - <a href="/logout">Sign out</a> + <a id="login_out" href="/logout">Sign out</a> {% endif %} </li> </ul> @@ -180,7 +180,7 @@ <script src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.9.1/jquery-ui.min.js" type="text/javascript"></script> <script language="javascript" type="text/javascript" src="/static/packages/colorbox/jquery.colorbox.js"></script> -<!-- <script type="text/javascript" src="/static/new/javascript/login.js"></script>--> + <script type="text/javascript" src="/static/new/javascript/login.js"></script> {% block js %} {% endblock %} diff --git a/wqflask/wqflask/templates/security/reset_password.html b/wqflask/wqflask/templates/security/reset_password.html index e6fc3f58..76e978cd 100644 --- a/wqflask/wqflask/templates/security/reset_password.html +++ b/wqflask/wqflask/templates/security/reset_password.html @@ -1,3 +1,7 @@ +{% extends "base.html" %} +{% block title %}Reset Password{% endblock %} + +{% block content %} {% from "security/_macros.html" import render_field_with_errors, render_field %} {% include "security/_messages.html" %} <h1>Reset password</h1> @@ -7,4 +11,5 @@ {{ render_field_with_errors(reset_password_form.password_confirm) }} {{ render_field(reset_password_form.submit) }} </form> -{% include "security/_menu.html" %}
\ No newline at end of file +{% include "security/_menu.html" %} +{% endblock %}
\ No newline at end of file diff --git a/wqflask/wqflask/templates/security/send_confirmation.html b/wqflask/wqflask/templates/security/send_confirmation.html index 29a11257..4552c219 100644 --- a/wqflask/wqflask/templates/security/send_confirmation.html +++ b/wqflask/wqflask/templates/security/send_confirmation.html @@ -1,3 +1,7 @@ +{% extends "base.html" %} +{% block title %}Send Confirmation{% endblock %} +{% block content %} + {% from "security/_macros.html" import render_only_errors %} {% include "security/_messages.html" %} @@ -27,3 +31,4 @@ </fieldset> </form> </div> +{% endblock %}
\ No newline at end of file diff --git a/wqflask/wqflask/templates/security/thank_you.html b/wqflask/wqflask/templates/security/thank_you.html new file mode 100644 index 00000000..1b8de3e5 --- /dev/null +++ b/wqflask/wqflask/templates/security/thank_you.html @@ -0,0 +1,8 @@ +{% from "security/_macros.html" import render_only_errors %} +{% include "security/_messages.html" %} + +<div class="security_box"> + <h4>Thank you for signing in!</h4> +</div> + +<script src="/static/new/javascript/thank_you.js"></script>
\ No newline at end of file diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index b8ebc71f..9e666bbd 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -13,6 +13,8 @@ from flask import Flask, g from pprint import pformat as pf +from base.data_set import create_datasets_list + #from app import db print("globals are:", globals()) @@ -32,6 +34,20 @@ class UserManager(object): #print("user is:", user) self.user = model.User.query.get(self.user_id) print("user is:", self.user) + datasets = create_datasets_list() + for dataset in datasets: + if not dataset.check_confidentiality(): + continue + print("\n Name:", dataset.name) + print(" Type:", dataset.type) + print(" ID:", dataset.id) + print(" Confidential:", dataset.check_confidentiality()) + #print(" ---> self.datasets:", self.datasets) + + +class GroupsManager(object): + def __init__(self, kw): + self.datasets = create_datasets_list() class RolesManager(object): diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index b9aa3acf..d57bbaa7 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -27,6 +27,7 @@ from flask import render_template, request, make_response, Response, Flask, g, c from wqflask import search_results from base.data_set import DataSet # Used by YAML in marker_regression +from base.data_set import create_datasets_list from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data from wqflask.marker_regression import marker_regression @@ -53,6 +54,18 @@ def connect_db(): @app.route("/") def index_page(): print("Sending index_page") + #create_datasets_list() + #key = "all_datasets" + #result = Redis.get(key) + #if result: + # print("Cache hit!!!") + # result = pickle.loads(result) + #else: + # with Bench("Creating DataSets object"): + # ds = DataSets() + # Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) + # Redis.expire(key, 2*60) + #print("[orange] ds:", ds.datasets) return render_template("index_page.html") @app.route("/data_sharing") @@ -83,11 +96,11 @@ def search_page(): else: return render_template("data_sharing.html", **template_vars.__dict__) else: - key = "search_results:v2:" + json.dumps(request.args, sort_keys=True) + key = "search_results:v5:" + json.dumps(request.args, sort_keys=True) print("key is:", pf(key)) with Bench("Loading cache"): result = Redis.get(key) - + if result: print("Cache hit!!!") with Bench("Loading results"): @@ -97,9 +110,9 @@ def search_page(): print("request.args is", request.args) the_search = search_results.SearchResultPage(request.args) result = the_search.__dict__ - + print("result: ", pf(result)) - Redis.set(key, pickle.dumps(result)) + Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) if result['quick']: @@ -219,7 +232,7 @@ def marker_regression_page(): # print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) #causeerror - Redis.set(key, pickle.dumps(result)) + Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) with Bench("Rendering template"): @@ -248,12 +261,16 @@ def sharing_info_page(): template_vars = SharingInfoPage.SharingInfoPage(fd) return template_vars - +# Take this out or secure it before going into production @app.route("/get_temp_data") def get_temp_data(): temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) +@app.route("/thank_you") +def thank_you(): + return render_template("security/thank_you.html") + @app.route("/manage/users") def manage_users(): template_vars = user_manager.UsersManager() @@ -264,6 +281,11 @@ def manage_user(): template_vars = user_manager.UserManager(request.args) return render_template("admin/ind_user_manager.html", **template_vars.__dict__) +@app.route("/manage/groups") +def manage_groups(): + template_vars = user_manager.GroupsManager(request.args) + return render_template("admin/group_manager.html", **template_vars.__dict__) + def json_default_handler(obj): '''Based on http://stackoverflow.com/a/2680060/1175849''' |