diff options
| -rw-r--r-- | doc/database.org | 165 | ||||
| -rw-r--r-- | etc/default_settings.py | 19 | ||||
| -rw-r--r-- | wqflask/runserver.py | 11 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 13 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/biodalliance.js | 72 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee | 37 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/chr_lod_chart.js | 31 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/create_lodchart.coffee | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/create_lodchart.js | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/lod_chart.coffee | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/lod_chart.js | 63 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 210 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 54 |
14 files changed, 556 insertions, 150 deletions
diff --git a/doc/database.org b/doc/database.org index 624174a4..5107b660 100644 --- a/doc/database.org +++ b/doc/database.org @@ -1,9 +1,19 @@ -- github Document reduction issue +* Database Information + +WARNING: This document contains information on the GN databases which +will change over time. The GN database is currently MySQL based and, +while efficient, contains a number of design choices we want to grow +'out' of. Especially with an eye on reproducibility we want to +introduce versioning. + +So do not treat the information in this document as a final way of +accessing data. It is better to use the +[[https://github.com/genenetwork/gn_server/blob/master/doc/API.md][REST API]]. * The small test database (2GB) The default install comes with a smaller database which includes a -number of the BSD's and the Human liver dataset (GSE9588). +number of the BXD's and the Human liver dataset (GSE9588). * GeneNetwork database @@ -750,9 +760,30 @@ show indexes from ProbeSetFreeze; | 1 | 5 | 0.303492 | +--------+----------+----------+ -** Publication and publishdata (all pheno) +** Publication + +Publication: + +| Id | PubMed_ID | Abstract | Title | Pages | Month | Year | + -Phenotype pubs +** Publishdata (all pheno) + +One of three phenotype tables. + +mysql> select * from PublishData limit 5; ++---------+----------+-------+ +| Id | StrainId | value | ++---------+----------+-------+ +| 8966353 | 349 | 29.6 | +| 8966353 | 350 | 27.8 | +| 8966353 | 351 | 26.6 | +| 8966353 | 352 | 28.5 | +| 8966353 | 353 | 24.6 | ++---------+----------+-------+ +5 rows in set (0.25 sec) + +See below for phenotype access. ** QuickSearch @@ -1073,7 +1104,37 @@ select * from ProbeSetXRef limit 5; i.e., for Strain Id 1 (DataId) 1, the locus '10.095.400' has a phenotype value of 5.742. -GeneNetwork1 already has a limited REST interface, if you do +Interestingly ProbeData and PublishData have the same layout as +ProbeSetData. ProbeData is only in use for Affy assays - and not used +for computations. PublishData contains trait values. ProbeSetData.id +matches ProbeSetXRef.DataId while PublishData.id matches +PublishXRef.DataId. + +select * from PublishXRef limit 3; ++-------+-------------+-------------+---------------+---------+----------------+------------------+-----------+----------+-------------------------------------------------------+ +| Id | InbredSetId | PhenotypeId | PublicationId | DataId | Locus | LRS | additive | Sequence | comments | ++-------+-------------+-------------+---------------+---------+----------------+------------------+-----------+----------+-------------------------------------------------------+ +| 10001 | 8 | 1 | 1 | 8966353 | D2Mit5 | 10.18351644706 | -1.20875 | 1 | | +| 10001 | 7 | 2 | 53 | 8966813 | D7Mit25UT | 9.85534330983917 | -2.86875 | 1 | | +| 10001 | 4 | 3 | 81 | 8966947 | CEL-6_57082524 | 11.7119505898121 | -23.28875 | 1 | elissa modified Abstract at Tue Jun 7 11:38:00 2005 | ++-------+-------------+-------------+---------------+---------+----------------+------------------+-----------+----------+-------------------------------------------------------+ +3 rows in set (0.00 sec) + +ties the trait data (PublishData) with the inbredsetid (matching +PublishFreeze.InbredSetId), locus and publication. + +select * from PublishFreeze -> ; ++----+------------+--------------------------+-------------+------------+--------+-------------+-----------------+-----------------+ +| Id | Name | FullName | ShortName | CreateTime | public | InbredSetId | confidentiality | AuthorisedUsers | ++----+------------+--------------------------+-------------+------------+--------+-------------+-----------------+-----------------+ +| 1 | BXDPublish | BXD Published Phenotypes | BXDPublish | 2004-07-17 | 2 | 1 | 0 | NULL | +| 18 | HLCPublish | HLC Published Phenotypes | HLC Publish | 2012-02-20 | 2 | 34 | 0 | NULL | ++----+------------+--------------------------+-------------+------------+--------+-------------+-----------------+-----------------+ +2 rows in set (0.02 sec) + +which gives us the datasets. + +GeneNetwork1 has a limited REST interface, if you do : curl "http://robot.genenetwork.org/webqtl/main.py?cmd=get&probeset=1443823_s_at&db=HC_M2_0606_P" @@ -1082,6 +1143,9 @@ we get : ProbeSetID B6D2F1 C57BL/6J DBA/2J BXD1 BXD2 BXD5 BXD6 BXD8 BXD9 BXD11 BXD12 BXD13 BXD15 BXD16 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24 BXD27 BXD28 BXD29 BXD31 BXD32 BXD33 BXD34 BXD38 BXD39 BXD40 BXD42 BXD67 BXD68 BXD43 BXD44 BXD45 BXD48 BXD50 BXD51 BXD55 BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD69 BXD70 BXD73 BXD74 BXD75 BXD76 BXD77 BXD79 BXD73a BXD83 BXD84 BXD85 BXD86 BXD87 BXD89 BXD90 BXD65b BXD93 BXD94 A/J AKR/J C3H/HeJ C57BL/6ByJ CXB1 CXB2 CXB3 CXB4 CXB5 CXB6 CXB7 CXB8 CXB9 CXB10 CXB11 CXB12 CXB13 BXD48a 129S1/SvImJ BALB/cJ BALB/cByJ LG/J NOD/ShiLtJ PWD/PhJ BXD65a BXD98 BXD99 CAST/EiJ KK/HlJ WSB/EiJ NZO/HlLtJ PWK/PhJ D2B6F1 : 1443823_s_at 15.251 15.626 14.716 15.198 14.918 15.057 15.232 14.968 14.87 15.084 15.192 14.924 15.343 15.226 15.364 15.36 14.792 14.908 15.344 14.948 15.08 15.021 15.176 15.14 14.796 15.443 14.636 14.921 15.22 15.62 14.816 15.39 15.428 14.982 15.05 15.13 14.722 14.636 15.242 15.527 14.825 14.416 15.125 15.362 15.226 15.176 15.328 14.895 15.141 15.634 14.922 14.764 15.122 15.448 15.398 15.089 14.765 15.234 15.302 14.774 14.979 15.212 15.29 15.012 15.041 15.448 14.34 14.338 14.809 15.046 14.816 15.232 14.933 15.255 15.21 14.766 14.8 15.506 15.749 15.274 15.599 15.673 14.651 14.692 14.552 14.563 14.164 14.546 15.044 14.695 15.162 14.772 14.645 15.493 14.75 14.786 15.003 15.148 15.221 +(see https://github.com/genenetwork/gn_server/blob/master/doc/API.md +for the latest REST API). + getTraitData is defined in the file [[https://github.com/genenetwork/genenetwork/blob/master/web/webqtl/textUI/cmdClass.py#L134][web/webqtl/textUI/cmdClass.py]]. probe is None, so the code at line 199 is run @@ -1165,6 +1229,97 @@ select * from ProbeSetData limit 5; 5 rows in set (0.00 sec) linked by ProbeSetXRef.dataid. + +*** For PublishData: + +List datasets for BXD (InbredSetId=1): + +select * from PublishXRef where InbredSetId=1 limit 3; ++-------+-------------+-------------+---------------+---------+-----------+------------------+------------------+----------+--------------------------------------------------------------------------------+ +| Id | InbredSetId | PhenotypeId | PublicationId | DataId | Locus | LRS | additive | Sequence | comments | ++-------+-------------+-------------+---------------+---------+-----------+------------------+------------------+----------+--------------------------------------------------------------------------------+ +| 10001 | 1 | 4 | 116 | 8967043 | rs8253516 | 13.4974914158039 | 2.39444444444444 | 1 | robwilliams modified post_publication_description at Mon Jul 30 14:58:10 2012 + | +| 10002 | 1 | 10 | 116 | 8967044 | rs3666069 | 22.0042692151629 | 2.08178571428572 | 1 | robwilliams modified phenotype at Thu Oct 28 21:43:28 2010 + | +| 10003 | 1 | 15 | 116 | 8967045 | D18Mit4 | 15.5929163293343 | 19.0882352941176 | 1 | robwilliams modified phenotype at Mon May 23 20:52:19 2011 + | ++-------+-------------+-------------+---------------+---------+-----------+------------------+------------------+----------+--------------------------------------------------------------------------------+ + +where ID is the 'record' or, effectively, dataset. + +select distinct(publicationid) from PublishXRef where InbredSetId=1 limit 3; ++---------------+ +| publicationid | ++---------------+ +| 116 | +| 117 | +| 118 | ++---------------+ + +select distinct +PublishXRef.id,publicationid,phenotypeid,Phenotype.post_publication_description +from PublishXRef,Phenotype where InbredSetId=1 and +phenotypeid=Phenotype.id limit 3; ++-------+---------------+-------------+----------------------------------------------------------------------------------------------------------------------------+ +| id | publicationid | phenotypeid | post_publication_description | ++-------+---------------+-------------+----------------------------------------------------------------------------------------------------------------------------+ +| 10001 | 116 | 4 | Central nervous system, morphology: Cerebellum weight [mg] | +| 10002 | 116 | 10 | Central nervous system, morphology: Cerebellum weight after adjustment for covariance with brain size [mg] | +| 10003 | 116 | 15 | Central nervous system, morphology: Brain weight, male and female adult average, unadjusted for body weight, age, sex [mg] | ++-------+---------------+-------------+----------------------------------------------------------------------------------------------------------------------------+ + +The id field is the same that is used in the GN2 web interface and the +PublicationID ties the datasets together. + +To list trait values: + +SELECT Strain.Name, PublishData.id, PublishData.value from +(Strain,PublishData, PublishXRef) Where PublishData.StrainId = +Strain.id limit 3; + ++------+---------+-------+ +| Name | id | value | ++------+---------+-------+ +| CXB1 | 8966353 | 29.6 | +| CXB1 | 8966353 | 29.6 | +| CXB1 | 8966353 | 29.6 | ++------+---------+-------+ + +here id should match dataid again: + +SELECT Strain.Name, PublishData.id, PublishData.value from +(Strain,PublishData, PublishXRef) Where PublishData.StrainId = +Strain.id and PublishXRef.dataid=8967043 and +PublishXRef.dataid=PublishData.id limit 3; ++------+---------+-------+ +| Name | id | value | ++------+---------+-------+ +| BXD1 | 8967043 | 61.4 | +| BXD2 | 8967043 | 49 | +| BXD5 | 8967043 | 62.5 | ++------+---------+-------+ + +*** Datasets + +The REST API aims to present a unified interface for genotype and +phenotype data. Phenotype datasets appear in two major forms in the +database and we want to present them as one resource. + +Dataset names are defined in ProbeSetFreeze.name and Published.id -> +publication (we'll ignore the probe dataset that uses +ProbeFreeze.name). These tables should be meshed. It looks like the +ids are non-overlapping with the publish record IDs starting at 10,001 +(someone has been smart, though it sets the limit of probesets now to +10,000). + +The datasets are organized differently in these tables. All published +BXD data is grouped on BXDpublished with the publications as +'datasets'. So, that is how we list them in the REST API. + +To fetch all the datasets we first list ProbeSetFreeze entries. Then +we list the Published entries. + ** Fetch genotype information *** SNPs diff --git a/etc/default_settings.py b/etc/default_settings.py index 6acea637..08eae024 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -2,18 +2,22 @@ # webserver running in developer mode with limited console # output. Copy this file and run it from ./bin/genenetwork2 configfile # -# Note that these settings are fetched in ./wqflask/utilities/tools.py +# Note: these settings are fetched in ./wqflask/utilities/tools.py # which has support for overriding them through environment variables, # e.g. # # env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2 # env LOG_LEVEL=DEBUG ./bin/genenetwork2 ~/gn2_settings.py # -# Note also that in the near future we will additionally fetch +# Note: in the near future we will additionally fetch # settings from a JSON file # -# Note that values for False and 0 have to be strings here - otherwise +# Note: values for False and 0 have to be strings here - otherwise # Flask won't pick them up +# +# For GNU Guix deployment also check the paths in +# +# ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py import os import sys @@ -22,7 +26,7 @@ GN_VERSION = open("../VERSION","r").read() SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s' SQLALCHEMY_POOL_RECYCLE = 3600 -GN_SERVER_URL = "http://localhost:8880/" +GN_SERVER_URL = "http://test-gn2.genenetwork.org/" # ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True @@ -33,7 +37,7 @@ SECURITY_RECOVERABLE = True SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org" SECURITY_POST_LOGIN_VIEW = "/thank_you" -SERVER_PORT = 5003 +SERVER_PORT = 5003 # running on localhost SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' # ---- Behavioural settings (defaults) note that logger and log levels can @@ -41,6 +45,7 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD) WEBSERVER_BRANDING = None # Set the branding (nyi) WEBSERVER_DEPLOY = None # Deployment specifics (nyi) +WEBSERVER_URL = "http://localhost:"+str(SERVER_PORT)+"/" # external URL LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL) LOG_LEVEL_DEBUG = '0' # logger.debugf log level (0-5, 5 = show all) @@ -53,7 +58,8 @@ USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls # Paths to JS libraries -TWITTER_POST_FETCHER_JS_PATH = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher" +JS_BIODALLIANCE = os.environ['HOME']+"/genenetwork/biodalliance" +JS_TWITTER_POST_FETCHER = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher" # ---- Path overrides for Genenetwork # TMPDIR is normally picked up from the environment @@ -63,6 +69,7 @@ GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files # ---- GN2 Executables +# Paths to invoked binaries PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) PLINK_COMMAND = str.strip(os.popen("which plink2").read()) GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 0342b7ad..adacc712 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -19,11 +19,18 @@ ENDC = '\033[0m' import os app.config['SECRET_KEY'] = os.urandom(24) -from utility.tools import WEBSERVER_MODE,get_setting_int +from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting port = get_setting_int("SERVER_PORT") -logger.info("GN2 is running. Visit %shttp://localhost:%s/%s" % (BLUE,port,ENDC)) +print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]") + +import requests +page = requests.get(get_setting("GN_SERVER_URL")) +if page.status_code != 200: + raise Exception("API server not found!") + +print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))) werkzeug_logger = logging.getLogger('werkzeug') diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index bacb0aa4..128706df 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -72,7 +72,7 @@ LOG_LEVEL_DEBUG (NYI). def warning(self,*args): """Call logging.warning for multiple args""" self.collect(self.logger.warning,*args) - self.logger.warning(self.collect(*args)) + # self.logger.warning(self.collect(*args)) def error(self,*args): """Call logging.error for multiple args""" diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index c28c617a..82ef136f 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -121,9 +121,14 @@ def assert_writable_dir(dir): fh.close() os.remove(fn) except IOError: - raise Exception('Unable to write test.txt to directory ' + dir ) + raise Exception('Unable to write test.txt to directory ' + dir) return dir +def assert_file(fn): + if not valid_file(fn): + raise Exception('Unable to find file '+fn) + return fn + def mk_dir(dir): if not valid_path(dir): os.makedirs(dir) @@ -235,4 +240,8 @@ if os.environ.get('WQFLASK_OVERRIDES'): OVERRIDES[k] = cmd logger.debug(OVERRIDES) -assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH")) +assert_dir(get_setting("JS_BIODALLIANCE")) +assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") +assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") +assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) +assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js") diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js new file mode 100644 index 00000000..3b9e3b7f --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/biodalliance.js @@ -0,0 +1,72 @@ +"use strict"; + + +var BD = {}; +BD.browser = null; +BD.data = {}; +BD.sources = []; + +var getChrLen = function(chr) { + return js_data[chr * 1]; +}; + +BD.createBrowser = function(chr, start, end, speciesName, sources) { + console.log("creating BD browser"); + var b = new Browser({ + chr: chr, + viewStart: start, + viewEnd: end, + + coordSystem: { + speciesName: speciesName + }, + + sources: sources, + + maxHeight: 1400, + setDocumentTitle: false, + prefix: '/dalliance/', + workerPrefix: 'build/', + noPersist: true, + pageName: 'bd_container' + }); + + console.log("created BD browser"); + return b; +}; + +BD.showButton = function() { + $('#open_bd').show(); + $('#close_bd').hide(); +}; + +BD.hideButton = function() { + $('#close_bd').show(); + $('#open_bd').hide(); +}; + + +BD.putData = function(data) { + for (var key in data) { + BD.data[key] = data[key]; + } +}; + +BD.putSource = function(source) { + BD.sources.push(source); +}; + +BD.openBrowser = function() { + console.log("opening browser"); + if (!BD.browser) { + BD.browser = BD.createBrowser(BD.data.chr, + 0, + BD.data.length * 1000000, + BD.data.species, + BD.sources); + } else { + BD.browser.setLocation(BD.data.chr, 0, BD.data.length * 1000000); + } + + BD.browser.maxViewWidth = BD.data.length * 1000000; +}; diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee index e00694be..8a5a3569 100644 --- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee @@ -5,7 +5,7 @@ class Chr_Lod_Chart @qtl_results = js_data.qtl_results console.log("qtl_results are:", @qtl_results) console.log("chr is:", @chr) - + @get_max_chr() @filter_qtl_results() @@ -21,16 +21,16 @@ class Chr_Lod_Chart console.log("@x_coords: ", @x_coords) console.log("@y_coords: ", @y_coords) console.timeEnd('Create coordinates') - + # Buffer to allow for the ticks/labels to be drawn @x_buffer = @plot_width/30 @y_buffer = @plot_height/20 - + @x_max = d3.max(@x_coords) @y_max = d3.max(@y_coords) * 1.2 - + @y_threshold = @get_lod_threshold() - + @svg = @create_svg() @plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names) @@ -43,14 +43,14 @@ class Chr_Lod_Chart console.time('Create graph') @create_graph() console.timeEnd('Create graph') - + get_max_chr: () -> @max_chr = 0 for key of js_data.chromosomes console.log("key is:", key) if parseInt(key) > @max_chr @max_chr = parseInt(key) - + filter_qtl_results: () -> @these_results = [] this_chr = 100 @@ -59,8 +59,8 @@ class Chr_Lod_Chart this_chr = @max_chr else this_chr = result.chr - console.log("this_chr is:", this_chr) - console.log("@chr[0] is:", parseInt(@chr[0])) + # console.log("this_chr is:", this_chr) + # console.log("@chr[0] is:", parseInt(@chr[0])) if this_chr > parseInt(@chr[0]) break if parseInt(this_chr) == parseInt(@chr[0]) @@ -72,7 +72,7 @@ class Chr_Lod_Chart if result.lod_score > 1 high_qtl_count += 1 console.log("high_qtl_count:", high_qtl_count) - + #if high_qtl_count > 10000 @y_axis_filter = 2 #else if high_qtl_count > 1000 @@ -85,7 +85,7 @@ class Chr_Lod_Chart @x_coords.push(parseFloat(result.Mb)) @y_coords.push(result.lod_score) @marker_names.push(result.name) - + create_svg: () -> svg = d3.select("#topchart") .append("svg") @@ -102,7 +102,7 @@ class Chr_Lod_Chart @y_scale = d3.scale.linear() .domain([0, @y_max]) .range([@plot_height, @y_buffer]) - + get_lod_threshold: () -> if @y_max/2 > 2 return @y_max/2 @@ -125,7 +125,7 @@ class Chr_Lod_Chart [@y_buffer, @plot_height, @plot_width, @plot_width], [@y_buffer, @y_buffer, @x_buffer, @plot_width], [@plot_height, @plot_height, @x_buffer, @plot_width]] - + @svg.selectAll("line") .data(border_coords) .enter() @@ -141,7 +141,7 @@ class Chr_Lod_Chart ) .attr("x2", (d) => return d[3] - ) + ) .style("stroke", "#000") add_x_axis: () -> @@ -166,13 +166,13 @@ class Chr_Lod_Chart .attr("transform", (d) => return "translate(-12,0) rotate(-90)" ) - + add_y_axis: () -> @yAxis = d3.svg.axis() .scale(@y_scale) .orient("left") .ticks(5) - + @svg.append("g") .attr("class", "y_axis") .attr("transform", "translate(" + @x_buffer + ",0)") @@ -200,7 +200,7 @@ class Chr_Lod_Chart .x( (d) => return @x_scale(d[0])) .y( (d) => return @y_scale(d[1])) .interpolate("linear") - + line_graph = @svg.append("path") .attr("d", line_function(@plot_coordinates)) .attr("stroke", "blue") @@ -273,6 +273,9 @@ class Chr_Lod_Chart $("#return_to_full_view").hide() $('#topchart').remove() $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>') + BD.hideButton() + $('#close_bd').hide(); + $('#bd_container').hide() create_lod_chart() show_marker_in_table: (marker_info) -> diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js index c6cbd01b..bae4565d 100644 --- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js @@ -1,13 +1,12 @@ -// Generated by CoffeeScript 1.9.2 +// Generated by CoffeeScript 1.10.0 var Chr_Lod_Chart; Chr_Lod_Chart = (function() { - function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) { + function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot) { this.plot_height = plot_height; this.plot_width = plot_width; this.chr = chr; this.manhattanPlot = manhattanPlot; - this.mappingScale = mappingScale; this.qtl_results = js_data.qtl_results; console.log("qtl_results are:", this.qtl_results); console.log("chr is:", this.chr); @@ -95,18 +94,11 @@ Chr_Lod_Chart = (function() { Chr_Lod_Chart.prototype.create_coordinates = function() { var i, len, ref, result, results; ref = this.these_results; - console.log("THESE_RESULTS:", ref) results = []; for (i = 0, len = ref.length; i < len; i++) { result = ref[i]; this.x_coords.push(parseFloat(result.Mb)); - if (js_data.result_score_type == "LOD") { - this.y_coords.push(result.lod_score); - } - else { - console.log("LRS VALUE:", result['lrs_value']) - this.y_coords.push(result['lrs_value']); - } + this.y_coords.push(result.lod_score); results.push(this.marker_names.push(result.name)); } return results; @@ -119,19 +111,7 @@ Chr_Lod_Chart = (function() { }; Chr_Lod_Chart.prototype.create_scales = function() { - if (this.mappingScale == "morgan") { - max_pos = 0 - for (i = 0, len = this.these_results.length; i < len; i++) { - marker = this.these_results[i] - if (parseFloat(marker['Mb']) > max_pos){ - max_pos = parseFloat(marker.Mb) - } - } - this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]); - } - else { - this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); - } + this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]); }; @@ -278,6 +258,9 @@ Chr_Lod_Chart = (function() { $("#return_to_full_view").hide(); $('#topchart').remove(); $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); + BD.hideButton(); + $('#close_bd').hide(); + $('#bd_container').hide(); return create_lod_chart(); }; diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee index 88003f4e..f6dfd7a3 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee @@ -9,9 +9,9 @@ create_lod_chart = -> additive = js_data.additive else additive = false - + console.log("js_data:", js_data) - + # simplest use #d3.json "data.json", (data) -> mychart = lodchart().lodvarname("lod.hk") @@ -21,13 +21,13 @@ create_lod_chart = -> .ylab(js_data.result_score_type + " score") .manhattanPlot(js_data.manhattan_plot) #.additive(additive) - + data = js_data.json_data - + d3.select("div#topchart") .datum(data) .call(mychart) - + # grab chromosome rectangles; color pink on hover chrrect = mychart.chrSelect() chrrect.on "mouseover", -> @@ -36,7 +36,7 @@ create_lod_chart = -> d3.select(this).attr("fill", -> return "#F1F1F9" if i % 2 "#FBFBFF") - + # animate points at markers on click mychart.markerSelect() .on "click", (d) -> @@ -44,7 +44,3 @@ create_lod_chart = -> d3.select(this) .transition().duration(500).attr("r", r*3) .transition().duration(500).attr("r", r) - -$ -> - root.create_lod_chart = create_lod_chart - diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js index 778eed3a..d2c531f9 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.js +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js @@ -1,4 +1,5 @@ -//var create_lod_chart; +// Generated by CoffeeScript 1.10.0 +var create_lod_chart; create_lod_chart = function() { var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w; @@ -40,11 +41,3 @@ create_lod_chart = function() { return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r); }); }; - -create_lod_chart() - -/* -$(function() { - return root.create_lod_chart = create_lod_chart; -}); -*/ \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee index 55ffdce0..a65df84f 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee @@ -123,6 +123,8 @@ lodchart = () -> .on("click", (d) -> console.log("d is:", d) redraw_plot(d) + BD.putData({chr: d[0], length: d[1]}); + BD.showButton() ) # x-axis labels diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js index 014bf59b..f1df6bd8 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/lod_chart.js @@ -1,8 +1,8 @@ -// Generated by CoffeeScript 1.9.2 +// Generated by CoffeeScript 1.10.0 var lodchart; lodchart = function() { - var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; + var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; width = 800; height = 500; margin = { @@ -20,6 +20,7 @@ lodchart = function() { }; titlepos = 20; manhattanPlot = false; + additive = false; ylim = null; additive_ylim = null; nyticks = 5; @@ -29,8 +30,7 @@ lodchart = function() { darkrect = "#F1F1F9"; lightrect = "#FBFBFF"; lodlinecolor = "darkslateblue"; - additivelinecolor_plus = "red"; - additivelinecolor_negative = "green"; + additivelinecolor = "red"; linewidth = 2; suggestivecolor = "gainsboro"; significantcolor = "#EBC7C7"; @@ -70,15 +70,14 @@ lodchart = function() { return results; })(); ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])]; - - if ('additive' in data) { + if (additive) { data['additive'] = (function() { var j, len, ref, results; ref = data['additive']; results = []; for (j = 0, len = ref.length; j < len; j++) { x = ref[j]; - results.push(x); + results.push(Math.abs(x)); } return results; })(); @@ -92,12 +91,12 @@ lodchart = function() { g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none"); yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]); yticks = yticks != null ? yticks : yscale.ticks(nyticks); - if ('additive' in data) { + if (additive) { additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]); additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks); } reorgLodData(data, lodvarname); - data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale); + data = chrscales(data, width, chrGap, margin.left, pad4heatmap); xscale = data.xscale; chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { return "chrrect" + d[0]; @@ -118,7 +117,12 @@ lodchart = function() { return lightrect; }).attr("stroke", "none").on("click", function(d) { console.log("d is:", d); - return redraw_plot(d); + redraw_plot(d); + BD.putData({ + chr: d[0], + length: d[1] + }); + return BD.showButton(); }); xaxis = g.append("g").attr("class", "x axis"); xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) { @@ -133,7 +137,7 @@ lodchart = function() { var chr_plot; $('#topchart').remove(); $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); - return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale); + return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot); }; rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; yaxis = g.append("g").attr("class", "y axis"); @@ -148,7 +152,7 @@ lodchart = function() { return formatAxis(yticks)(d); }); yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue"); - if ('additive' in data) { + if (additive) { rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1; additive_yaxis = g.append("g").attr("class", "y axis"); additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) { @@ -187,19 +191,13 @@ lodchart = function() { return yscale(data.lodByChr[chr][i][lodcolumn]); }); }; - if ('additive' in data) { + if (additive) { additivecurve = function(chr, lodcolumn) { - if (data.additiveByChr[chr][0] < 0) { - pos_neg = "negative" - } - else { - pos_neg = "positive" - } - return [pos_neg, d3.svg.line().x(function(d) { + return d3.svg.line().x(function(d) { return xscale[chr](d); }).y(function(d, i) { - return additive_yscale(Math.abs(data.additiveByChr[chr][i])); - })]; + return additive_yscale(data.additiveByChr[chr][i][lodcolumn]); + }); }; } curves = g.append("g").attr("id", "curves"); @@ -210,17 +208,12 @@ lodchart = function() { curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none"); } } - if ('additive' in data) { + if (additive) { ref1 = data.chrnames; for (k = 0, len1 = ref1.length; k < len1; k++) { chr = ref1[k]; if (chr.indexOf(data['chr'])) { - if (additivecurve(chr[0], lodvarnum)[0] == "negative") { - curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_negative).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); - } - else { - curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_plus).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); - } + curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); } } } @@ -305,13 +298,6 @@ lodchart = function() { manhattanPlot = value; return chart; }; - chart.mappingScale = function(value) { - if (!arguments.length) { - return mappingScale; - } - mappingScale = value; - return chart; - }; chart.ylim = function(value) { if (!arguments.length) { return ylim; @@ -449,6 +435,9 @@ lodchart = function() { chart.yscale = function() { return yscale; }; + chart.additive = function() { + return additive; + }; chart.additive_yscale = function() { return additive_yscale; }; @@ -470,4 +459,4 @@ lodchart = function() { return chrSelect; }; return chart; -}; \ No newline at end of file +}; diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 6d3f9326..31b8c595 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -32,7 +32,7 @@ <input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}"> <input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}"> <input type="hidden" name="pair_scan" value="{{ pair_scan }}"> - + <div class="container"> <div class="col-xs-5"> <h2>Map Viewer: Whole Genome</h2><br> @@ -81,7 +81,7 @@ <tr> <td></td> <td style="padding: 5px;"> - <input type="text" name="lrsMax" value="{{ '%0.1f' | format(lrsMax|float) }}" size="3"> <span style="font-size: 12px;">units on the y-axis (0 for default)</span> + <input type="text" name="lrsMax" value="{{ '%0.1f' | format(lrsMax|float) }}" size="3"> <span style="font-size: 12px;">units on the y-axis (0 for default)</span> </td> </tr> <tr> @@ -94,14 +94,14 @@ </div> <div class="col-xs-4" style="padding: 0px;"> {% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %} - <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test + <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test <a href="http://genenetwork.org/glossary.html#Permutation" target="_blank"> <sup style="color:#f00"> ?</sup> </a> <br> {% endif %} {% if mapping_method == "reaper" and nboot > 0 %} - <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test + <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test <a href="http://genenetwork.org/glossary.html#bootstrap" target="_blank"> <sup style="color:#f00"> ?</sup> </a> @@ -131,7 +131,7 @@ </div> </div> </div> - + <div class="tabbable" style="margin: 10px;"> <ul class="nav nav-tabs"> <li id="gn1_map_tab"> @@ -163,8 +163,23 @@ </div> {% if mapping_method != "gemma" %} <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map"> - <div id="chart_container"> - <div class="qtlcharts" id="topchart"></div> + <div id="chart_container"> + <ul class="nav nav-tabs"> + <li id="return_to_full_view" class="btn btn-default buttons-html5" style="display:none"> + Return to full view + </li> + <li id="open_bd" class="btn btn-default buttons-html5" style="display:none"> + Open BioDalliance view + </li> + <li id="close_bd" class="btn btn-default buttons-html5" style="display:none"> + Return to vector map + </li> + </ul> + + <div class="qtlcharts" id="topchart"></div> + + <div id="bd_container" class="qtlcharts"> + </div> </div> </div> {% endif %} @@ -265,7 +280,37 @@ {% endblock %} -{% block js %} +{% block js %} + + <script> + /* This section checks for paths to JS libraries by + checking the headers */ + list = [ + /* check for static path */ + "/static/new/javascript/biodalliance.js", + "/static/new/js_external/underscore-min.js", + /* check for dalliance JS (see ./etc/default_settings.py) */ + "/dalliance/build/dalliance-all.js", + /* D3 path (FIXME) */ + "http://d3js.org/d3.v3.min.js", + /* datatables path (FIXME) */ + "https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js" + ]; + for (var i = 0; i < list.length; i++) { + url = list[i]; + $.ajax({ + type: 'HEAD', + url: url, + success: function() { + // page exists + }, + error: function() { + // page does not exist + console.log("Failed to load "+this.url); + alert("Failed to load Javascript for "+this.url); + } + })}; + </script> <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script> <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script> @@ -277,19 +322,19 @@ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> - <script> - js_data = {{ js_data | safe }} - </script> {% if mapping_method != "gemma" %} <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script> + + <script language="javascript" type="text/javascript" src="/dalliance/build/dalliance-all.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/biodalliance.js"></script> {% endif %} - <script type="text/javascript" charset="utf-8"> - $(document).ready( function () { + <script> + createTable = function() { console.time("Creating table"); $('#qtl_results').DataTable( { {% if mapping_method != "reaper" %} @@ -353,15 +398,145 @@ "scrollCollapse": false, "paging": false } ); + }; + + filename = "{{json_filename}}"; + js_data = null; + $.ajax("/generated_text/{{json_filename}}", + {success: + function(data) { + js_data = data; + create_lod_chart(); + createTable(); + } + }); + + BD.putSource({name: 'Genome', + twoBitURI: 'http://www.biodalliance.org/datasets/GRCm38/mm10.2bit', + desc: 'Mouse reference genome build GRCm38', + tier_type: 'sequence', + provides_entrypoints: true + }); + BD.putSource({name: 'Genotype', + controlURI: "{{gn_server_url}}/api_pre1/genotype/mouse/BXD.json", + URIBase: "{{gn_server_url}}/api_pre1/genotype/mouse/", + tier_type: 'rqtl-genotype', + vOffset: 8, + pinned: true, + transposed: true, + hideSubpixelGlyphs: true, + style: [ + { type: "default", + method: "U", + style: { glyph: "BOX", + LINE: "0.5", + FGCOLOR: "black", + BGCOLOR: "white", + BGITEM: "true", + HEIGHT: "2", + BUMP: "true", + }}, + { type: "default", + method: "B", + style: { glyph: "BOX", + LINE: "0.5", + FGCOLOR: "blue", + BGCOLOR: "blue", + BGITEM: "true", + HEIGHT: "2", + BUMP: "true", + }}, + { type: "default", + method: "H", + style: { glyph: "BOX", + LINE: "0.5", + FGCOLOR: "green", + BGCOLOR: "green", + BGITEM: "true", + HEIGHT: "2", + BUMP: "true", + }}, + { type: "default", + method: "D", + style: { glyph: "BOX", + LINE: "0.5", + FGCOLOR: "red", + BGCOLOR: "red", + BGITEM: "true", + HEIGHT: "2", + BUMP: "true", + }}, + ] + }); + BD.putSource({name: 'QTL', + tier_type: 'qtl', + uri: '/generated_text/{{csv_filename}}', + style: [{ + type: 'default', + style: { + glyph: "LINEPLOT", + AUTOMAX: "true", + MIN: 0, + MAX: 3, + HEIGHT: 200, + STEPS: 500, + COLOR1: "blue", + } + }], + }); + BD.putSource({name: 'SNP density', + jbURI: "{{gn_server_url}}/api_pre1/snp", + jbQuery: "", + refetchOnZoom: true, + style: [{ + type: 'default', + style: { + glyph: "HISTOGRAM", + MIN: 0, + MAX: 5000, + AUTOMAX: "true", + HEIGHT: 60, + STEPS: 100, + COLOR1: "red", + COLOR2: "red", + COLOR3: "red", + AXISCENTER: "true", + } + }] + }); + </script> + + <script type="text/javascript" charset="utf-8"> + $(document).ready( function () { + BD.putData({species: "{{ dataset.group.species }}" }); + $('#vector_map_tab').click(function(){ $('div#gn1_map_options').hide(); }); $('#gn1_map_tab').click(function(){ - $('div#gn1_map_options').show(); + $('#gn1_map_options').show(); + $('div#bd_container').hide(); }); + $('#close_bd').click(function() { + $('#open_bd').show(); + $('#close_bd').hide(); + + $('#bd_container').hide(); + $('#topchart').show(); + }); + + $('#open_bd').click(function() { + $('#close_bd').show(); + $('#open_bd').hide() + + $('#topchart').hide(); + $('#bd_container').show(); + + BD.openBrowser(); + }) }); chrView = function(this_chr, chr_mb_list) { @@ -380,9 +555,9 @@ return $('#marker_regression_form').submit(); }; - remap = function() { + remap = function() { $('input[name=selected_chr]').val($('select[name=chromosomes]').val()); - return $('#marker_regression_form').submit(); + return $('#marker_regression_form').submit(); }; export_perm_data = function() { @@ -398,4 +573,3 @@ </script> {% endblock %} - diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index ab6c433d..c3b91c6e 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -21,6 +21,7 @@ import uuid import simplejson as json import yaml +import csv #Switching from Redis to StrictRedis; might cause some issues import redis @@ -52,12 +53,13 @@ from wqflask.wgcna import wgcna_analysis from wqflask.ctl import ctl_analysis #from wqflask.trait_submission import submit_trait +from utility import webqtlUtil from utility import temp_data from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION from utility.helper_functions import get_species_groups from base import webqtlFormData -from base.webqtlConfig import GENERATED_IMAGE_DIR +from base.webqtlConfig import GENERATED_IMAGE_DIR, GENERATED_TEXT_DIR from utility.benchmark import Bench from pprint import pformat as pf @@ -147,10 +149,16 @@ def tmp_page(img_path): img_base64 = bytesarray ) @app.route("/twitter/<path:filename>") -def bd_files(filename): - bd_path = app.config['TWITTER_POST_FETCHER_JS_PATH'] +def twitter_js(filename): + bd_path = app.config['JS_TWITTER_POST_FETCHER'] + return send_from_directory(bd_path, filename) + +@app.route("/dalliance/<path:filename>") +def biodalliance_js(filename): + bd_path = app.config['JS_BIODALLIANCE'] return send_from_directory(bd_path, filename) + #@app.route("/data_sharing") #def data_sharing_page(): # logger.info("In data_sharing") @@ -235,6 +243,10 @@ def docedit(): def generated_file(filename): return send_from_directory(GENERATED_IMAGE_DIR,filename) +@app.route('/generated_text/<filename>') +def generated_text(filename): + return send_from_directory(GENERATED_TEXT_DIR, filename) + @app.route("/help") def help(): doc = docs.Docs("help") @@ -575,10 +587,27 @@ def marker_regression_page(): with Bench("Total time in MarkerRegression"): template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid) + + qtl_results = template_vars.js_data['qtl_results'] + template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") + + json_filename = webqtlUtil.genRandStr("") + ".json" + with open(GENERATED_TEXT_DIR + "/" + json_filename, "wb") as json_file: + json_file.write(template_vars.js_data) + + csv_filename = webqtlUtil.genRandStr("") + ".csv" + with open(GENERATED_TEXT_DIR + "/" + csv_filename, "wb") as csv_file: + writer = csv.writer(csv_file) + writer.writerow(("Locus", "Chr", "Mb", "LOD")) + for (row) in qtl_results: + score = row["lod_score"] if "lod_score" in row else row["lrs_value"] + writer.writerow((row["name"], row["chr"], row["Mb"], score)) + + result = template_vars.__dict__ if result['pair_scan']: @@ -598,6 +627,9 @@ def marker_regression_page(): # logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__ + gn1_template_vars['json_filename'] = json_filename; + gn1_template_vars['csv_filename'] = csv_filename; + gn1_template_vars['gn_server_url'] = GN_SERVER_URL; pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) logger.info("pickled result length:", len(pickled_result)) @@ -607,22 +639,6 @@ def marker_regression_page(): with Bench("Rendering template"): rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars) - # with Bench("Rendering template"): - # if result['pair_scan'] == True: - # img_path = result['pair_scan_filename'] - # logger.info("img_path:", img_path) - # initial_start_vars = request.form - # logger.info("initial_start_vars:", initial_start_vars) - # imgfile = open(TEMPDIR + '/' + img_path, 'rb') - # imgdata = imgfile.read() - # imgB64 = imgdata.encode("base64") - # bytesarray = array.array('B', imgB64) - # result['pair_scan_array'] = bytesarray - # rendered_template = render_template("pair_scan_results.html", **result) - # else: - # rendered_template = render_template("marker_regression.html", **result) - # rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars) - return rendered_template |