diff options
1188 files changed, 1593 insertions, 957 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index bbb2a19f..d3bf3299 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -33,7 +33,7 @@ if [ -z $TEMPDIR ]; then TEMPDIR="/tmp" fi -# Start the redis server +echo "Starting the redis server:" echo -n "dir $TEMPDIR dbfilename gn2.rdb " | redis-server - & diff --git a/doc/Architecture.org b/doc/Architecture.org index c263d3b9..b9e8e355 100644 --- a/doc/Architecture.org +++ b/doc/Architecture.org @@ -1,5 +1,13 @@ * GeneNetwork Architecture +#+TITLE: Installing GeneNetwork services + +* Table of Contents :TOC: + - [[#genenetwork-architecture][GeneNetwork Architecture]] + - [[#introduction][Introduction]] + - [[#webserver][Webserver]] + - [[#gnserver-rest][GnServer (REST)]] + ** Introduction This document describes the architecture of GN2. Because GN2 is @@ -7,9 +15,33 @@ evolving, only a high-level overview is given here. ** Webserver -The webserver is built on [[http://flask.pocoo.org/][Python flask]] and this GN2 source code can be -found on [[https://github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask][github]] in the wqflask directory. The routing tables are -defined in [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/views.py][views.py]]. For example the main page is loaded from a -template named [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/index_page.htm][index_page.html]] in the [[https://github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask/templates][templates]] directory. In the -template you can find get the form gets filled by a Javascript -routine defined in [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/static/new/javascript/dataset_select_menu.js][data_select_menu.js]]. +The main [[https://github.com/genenetwork/genenetwork2][GN2 webserver]] is built on [[http://flask.pocoo.org/][Python flask]] and this GN2 source +code can be found on [[https://github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask][github]] in the wqflask directory. The routing +tables are defined in [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/views.py][views.py]]. For example the main page is loaded +from a template named [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/index_page.htm][index_page.html]] in the [[https://github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask/templates][templates]] directory. In +the template you can find get the form gets filled by a Javascript +routine defined in [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/static/new/javascript/dataset_select_menu.js][data_select_menu.js]] which picks up a static JSON +file for the menu. This static file is generated with +[[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/maintenance/gen_select_dataset.py][gen_select_dataset.py]]. Note that this JSON data is served by +gn_server in the latest version, see [[#gnserver-rest][GnServer (REST)]]. + +When you hit a search with, for example, +'http://localhost:5003/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29+&FormID=searchResult' +it has the menu items as parameters. According to the routing table, +the search is executed and Redis caching is used (we'll probably +change that to the level of the gn_server). The logic is in +search_result.py which invokes database functions in +wqflask/dbFunction/webqtlDatabaseFunction.py, for example. The +receiving template lives at [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/search_result_page.html][search_result_page.html]]. + +For what happens at the database level see [[database.org]]. + +** GnServer (REST) + +The [[https://github.com/genenetwork/gn_server][GnServer REST API]] is built on high performance [[http://elixir-lang.org/][Elixir]] with [[https://github.com/falood/maru][Maru]]. +Mainly the GnServer serves JSON requests, for example to fetch data +from the database. To get the menu data in YAML you can do something like + +: curl localhost:8880/int/menu/main.json|ruby extra/json2yaml.rb + +(json2yaml.rb is in the gn_server repo). diff --git a/doc/README.org b/doc/README.org index 3754dbbd..b3c78f29 100644 --- a/doc/README.org +++ b/doc/README.org @@ -1,4 +1,3 @@ - #+TITLE: Installing GeneNetwork services * Table of Contents :TOC: diff --git a/doc/database.org b/doc/database.org index 2221c4fb..c20e4564 100644 --- a/doc/database.org +++ b/doc/database.org @@ -7,7 +7,7 @@ number of the BSD's and the Human liver dataset (GSE9588). * GeneNetwork database -** Estimated table sizes +** Estimated table sizes select table_name,round(((data_length + index_length) / 1024 / 1024), 2) `Size in MB` from information_schema.TABLES where table_schema = "db_webqtl" order by data_length; @@ -172,24 +172,24 @@ This table is being used by both GN1 and GN2 from the trait pages! gn1/web/webqtl/showTrait/ShowTraitPage.py: query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \ gn1/web/webqtl/showTrait/ShowTraitPage.py: self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)" ,user_ip) gn1/web/webqtl/textUI/cmdClass.py: query = """SELECT count(id) FROM AccessLog WHERE ip_address = %s AND UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400""" -gn1/web/webqtl/textUI/cmdClass.py: query = """INSERT INTO AccessLog(accesstime,ip_address) values(Now(),%s)""" +gn1/web/webqtl/textUI/cmdClass.py: query = """INSERT INTO AccessLog(accesstime,ip_address) values(Now(),%s)""" gn2/wqflask/wqflask/show_trait/show_trait_page.py: query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \ gn2/wqflask/wqflask/show_trait/show_trait_page.py: self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip) When looking at the code in GN1 and GN2 it restricts the daily use of the trait data page (set to 1,000 - whoever reaches that?). Unlike mentioned in the schema description, this table does *not* keep track -of cookies. +of cookies. From the code it looks like GN2 uses a mixture of Redis and sqlalchemy to keep track of logged in sessions (see -gn2/wqflask/wqflask/user_manager.py) and cookies through a user_uuid in +gn2/wqflask/wqflask/user_manager.py) and cookies through a user_uuid in model.py. In gn2/wqflask/wqflask/templates/collections/view_anonymous.html it show_trait_page appears to be loaded (need to check). -** AvgMethod +** AvgMethod Probesetfreeze refers to AvgMethod @@ -235,7 +235,7 @@ Hooked in API (URL encoding) GN2 only (see menu bar) -** Ensembl* +** Ensembl* Probe information @@ -321,15 +321,15 @@ Indel Snp browser (variant browser Gn1) ** Info* -Infra system PhP +Infra system PhP -Data Info button +Data Info button Infosystem users has separate entries -Also Investigators, User, Organizations, +Also Investigators, User, Organizations, -** LCorrRamin3 +** LCorrRamin3 Lit. Correlations Prof. Ramin @@ -376,7 +376,7 @@ This table contains names, full descriptions, and short symbols for traits and phenotype used primarily in the Published Phenotypes databases. -Contains 10k rows, March 2016, of which 5000 are for the BXDs). +Contains 10k rows, March 2016, of which 5000 are for the BXDs). | Id | Pre_publication_description | Post_publication_description | Original_description | Units | Pre_publication_abbreviation | Post_publication_abbreviation | Lab_code | Submitter | Owner | Authorized_Users | +----+-----------------------------+----------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------+------------------------------+-------------------------------+----------+-------------+-------+------------------+ @@ -493,7 +493,7 @@ select count(*) from ProbeSet limit 5; ** ProbeSetData -Probedata - main molecular data. Probesets, metabolome, +Probedata - main molecular data. Probesets, metabolome, Almost all important molecular assay data is in this table including probe set data, RNA-seq data, proteomic data, and metabolomic @@ -599,7 +599,7 @@ select * from ProbeSetFreeze limit 5; Note that the following unlimited search is very slow: -select max(value) from ProbeSetData; +select max(value) from ProbeSetData; +------------+ | max(value) | @@ -617,12 +617,12 @@ Suggestions on the schema page: "StrainId" should be "CaseId" or "SampleId". -"ProbeSetData" should probably be "AssayData" or something more neutral. +"ProbeSetData" should probably be "AssayData" or something more neutral. *** Comments I think the ProbeSetData table should be generalized to a 'phenotypes' -table with an 'sample_id' column and a 'value' column. +table with an 'sample_id' column and a 'value' column. A new table 'samples' will link each sample against an 'experiment', an 'individual' and which in turn can link to a 'strain'. @@ -697,7 +697,7 @@ select * from Species; +----+-----------+----------------------+----------------+----------------------+-------------------------+------------+---------+ -** InbredSet +** InbredSet Menu @@ -723,10 +723,128 @@ User selection - retained ** UserPrivilege -** Vlookup +** Vlookup * Fetching Data +** Search + +What happens at the main search menu can be emulated with curl. + +*** Search Mouse mRNA from HC_M2_0606_P dataset + +: curl "http://localhost:5003/search?species=mouse&group=BXD&ppocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29+&FormID=searchResult" + +the first SQL query checks whether a dataset is confidential or not: + +INFO:base.data_set:.sql: geno_mrna_confidentiality: u'SELECT Id, Name, +FullName, confidentiality,AuthorisedUsers FROM ProbeSetFreeze WHERE +Name = "HC_M2_0606_P"' + +The following is executed once per search: + +INFO:db.call:.sql: retrieve_other_names: + SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name + FROM ProbeSetFreeze, ProbeFreeze, Tissue + WHERE ProbeSetFreeze.public > 0 AND + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND + ProbeFreeze.TissueId = Tissue.Id AND + (ProbeSetFreeze.Name = 'HC_M2_0606_P' OR ProbeSetFreeze.FullName = 'HC_M2_0606_P' OR ProbeSetFreeze.ShortName = 'HC_M2_0606_P') + +INFO:db.call:.sql: (112, 'HC_M2_0606_P', 'Hippocampus Consortium M430v2 (Jun06) PDNN', 'Hippocampus M430v2 BXD 06/06 PDNN', 'log2', 'Hippocampus mRNA') + +INFO:db.call:.sql: __init__: + SELECT + InbredSet.Name, InbredSet.Id + FROM + InbredSet, ProbeSetFreeze, ProbeFreeze + WHERE + ProbeFreeze.InbredSetId = InbredSet.Id AND + ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND + ProbeSetFreeze.Name = "HC_M2_0606_P" + +INFO:db.call:.sql: ('BXD', 1) + +INFO:base.species:.sql: __init__: + Select + Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet + where + Chr_Length.SpeciesId = InbredSet.SpeciesId AND + InbredSet.Name = 'BXD' + Order by OrderId + +And the following are executed for every trait: + +INFO:wqflask.do_search:.sql: execute: SELECT distinct ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, ProbeSetXRef.PVALUE as TPVALUE, ProbeSet.Chr_num as TCHR_NUM, ProbeSet.Mb as TMB, ProbeSet.Symbol as TSYMBOL, ProbeSet.name_num as TNAME_NUM FROM ProbeSetXRef, ProbeSet WHERE (( ProbeSetXRef.mean > 15.0 and ProbeSetXRef.mean < 16.0 )AND( ProbeSetXRef.LRS > 23.0 and ProbeSetXRef.LRS < 46.0 )) and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = 112 ORDER BY ProbeSet.symbol ASC + +INFO:base.trait:.sql: retrieve_info: SELECT ProbeSet.name, + ProbeSet.symbol, ProbeSet.description, + ProbeSet.probe_target_description, ProbeSet.chr, + ProbeSet.mb, ProbeSet.alias, ProbeSet.geneid, + ProbeSet.genbankid, ProbeSet.unigeneid, + ProbeSet.omim, ProbeSet.refseq_transcriptid, + ProbeSet.blatseq, ProbeSet.targetseq, + ProbeSet.chipid, ProbeSet.comments, + ProbeSet.strand_probe, ProbeSet.strand_gene, + ProbeSet.probe_set_target_region, + ProbeSet.probe_set_specificity, + ProbeSet.probe_set_blat_score, + ProbeSet.probe_set_blat_mb_start, + ProbeSet.probe_set_blat_mb_end, + ProbeSet.probe_set_strand, + ProbeSet.probe_set_note_by_rw, ProbeSet.flag + + FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetFreeze.Name = 'HC_M2_0606_P' AND + ProbeSet.Name = '1443823_s_at' + +INFO:base.trait:.sql: retrieve_info: + SELECT + HomologeneId + FROM + Homologene, Species, InbredSet + WHERE + Homologene.GeneId =98660 AND + InbredSet.Name = 'BXD' AND + InbredSet.SpeciesId = Species.Id AND + Species.TaxonomyId = Homologene.TaxonomyId + +INFO:base.trait:.sql: retrieve_info: + SELECT + ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive + FROM + ProbeSetXRef, ProbeSet + WHERE + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSet.Name = "1443823_s_at" AND + ProbeSetXRef.ProbeSetFreezeId =112 + +INFO:base.trait:.sql: retrieve_info: + select Geno.Chr, Geno.Mb from Geno, Species + where Species.Name = 'mouse' and + Geno.Name = 'NES13033186' and + Geno.SpeciesId = Species.Id + + +and finally mean and chromosome positions are fetched a second time +for every trait with + +INFO:base.data_set:.sql: get_trait_info: select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet + where ProbeSetXRef.ProbeSetFreezeId = 112 and + ProbeSet.Id = ProbeSetXRef.ProbeSetId and + ProbeSet.Name = '1443823_s_at' + +INFO:base.data_set:.sql: get_trait_info: + select Geno.Chr, Geno.Mb from Geno, Species + where Species.Name = 'mouse' and + Geno.Name = 'NES13033186' and + Geno.SpeciesId = Species.Id + +(that is a bug!). + ** Fetch phenotypes To get at phenotype data ProbeSetData is the main table (almost all diff --git a/etc/default_settings.py b/etc/default_settings.py index 0cf40265..df734f7c 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -1,29 +1,58 @@ +# Default settings file defines a single Flask process for the Python +# 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 +# which has support for overriding them through environment variables, +# e.g. +# +# env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2 +# +# Note also that 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 +# Flask won't pick them up + import os import sys -LOGFILE = "/tmp/genenetwork2.log" - -# This is needed because Flask turns key errors into a -# 400 bad request response with no exception/log -TRAP_BAD_REQUEST_ERRORS = True - -DB_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" +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/" -# http://pythonhosted.org/Flask-Security/configuration.html +# Flask configuration (see website) +TRAP_BAD_REQUEST_ERRORS = True SECURITY_CONFIRMABLE = True SECURITY_TRACKABLE = True SECURITY_REGISTERABLE = True SECURITY_RECOVERABLE = True SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org" SECURITY_POST_LOGIN_VIEW = "/thank_you" -SQLALCHEMY_POOL_RECYCLE = 3600 SERVER_PORT = 5003 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 +# be overridden at the module level and with enviroment settings +WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD) +WEBSERVER_BRANDING = None # Set the branding (nyi) +WEBSERVER_DEPLOY = None # Deployment specifics (nyi) + +LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL) +LOG_LEVEL_DEBUG = '0' # Debug log level (0-5, 0 = show all) +LOG_SQL = 'False' # Log SQL/backend and GN_SERVER calls +LOG_SQLALCHEMY = 'False' +LOG_BENCH = True # Log bench marks + +USE_REDIS = True # REDIS caching (note that redis will be phased out) +USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls + # Path overrides for Genenetwork -GENENETWORK_FILES = os.environ['HOME']+"/gn2_data" +HOME=os.environ['HOME'] +LOGFILE = HOME+"/genenetwork2.log" +GENENETWORK_FILES = HOME+"/gn2_data" 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/genotype_files/genotype/AD-cases-controls-Myers.geno b/genotype_files/genotype/AD-cases-controls-Myers.geno index 5429cfb0..5429cfb0 100755..100644 --- a/genotype_files/genotype/AD-cases-controls-Myers.geno +++ b/genotype_files/genotype/AD-cases-controls-Myers.geno diff --git a/genotype_files/genotype/AD-cases-controls.geno b/genotype_files/genotype/AD-cases-controls.geno index 07aa0896..07aa0896 100755..100644 --- a/genotype_files/genotype/AD-cases-controls.geno +++ b/genotype_files/genotype/AD-cases-controls.geno diff --git a/genotype_files/genotype/AKXD.geno b/genotype_files/genotype/AKXD.geno index 623e4ed1..623e4ed1 100755..100644 --- a/genotype_files/genotype/AKXD.geno +++ b/genotype_files/genotype/AKXD.geno diff --git a/genotype_files/genotype/AKXD.geno.update b/genotype_files/genotype/AKXD.geno.update index 5f490334..5f490334 100755..100644 --- a/genotype_files/genotype/AKXD.geno.update +++ b/genotype_files/genotype/AKXD.geno.update diff --git a/genotype_files/genotype/AKXD.geno.update.csv b/genotype_files/genotype/AKXD.geno.update.csv index fea7ec25..fea7ec25 100755..100644 --- a/genotype_files/genotype/AKXD.geno.update.csv +++ b/genotype_files/genotype/AKXD.geno.update.csv diff --git a/genotype_files/genotype/AKXD.geno.update.recal b/genotype_files/genotype/AKXD.geno.update.recal index 0a152e01..0a152e01 100755..100644 --- a/genotype_files/genotype/AKXD.geno.update.recal +++ 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b/genotype_files/genotype/AKXDforQTL index 0a652b86..0a652b86 100755..100644 --- a/genotype_files/genotype/AKXDforQTL +++ b/genotype_files/genotype/AKXDforQTL diff --git a/genotype_files/genotype/AXB.geno b/genotype_files/genotype/AXB.geno index 4a8dea60..4a8dea60 100755..100644 --- a/genotype_files/genotype/AXB.geno +++ b/genotype_files/genotype/AXB.geno diff --git a/genotype_files/genotype/AXB.geno.update b/genotype_files/genotype/AXB.geno.update index 4a8dea60..4a8dea60 100755..100644 --- a/genotype_files/genotype/AXB.geno.update +++ b/genotype_files/genotype/AXB.geno.update diff --git a/genotype_files/genotype/AXB.geno.update.csv b/genotype_files/genotype/AXB.geno.update.csv index e69de29b..e69de29b 100755..100644 --- a/genotype_files/genotype/AXB.geno.update.csv +++ b/genotype_files/genotype/AXB.geno.update.csv diff --git a/genotype_files/genotype/AXB.geno.update.recal b/genotype_files/genotype/AXB.geno.update.recal index 4a8dea60..4a8dea60 100755..100644 --- 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b/genotype_files/genotype/MDP.geno diff --git a/genotype_files/genotype/MDP.geno.update b/genotype_files/genotype/MDP.geno.update index b3f56835..b3f56835 100755..100644 --- a/genotype_files/genotype/MDP.geno.update +++ b/genotype_files/genotype/MDP.geno.update diff --git a/genotype_files/genotype/MDP.geno.update.csv b/genotype_files/genotype/MDP.geno.update.csv index 54c5e5fa..54c5e5fa 100755..100644 --- a/genotype_files/genotype/MDP.geno.update.csv +++ b/genotype_files/genotype/MDP.geno.update.csv diff --git a/genotype_files/genotype/MDP.geno.update.recal b/genotype_files/genotype/MDP.geno.update.recal index 592933d5..592933d5 100755..100644 --- a/genotype_files/genotype/MDP.geno.update.recal +++ b/genotype_files/genotype/MDP.geno.update.recal diff --git a/genotype_files/genotype/MDP.geno.update.reorder b/genotype_files/genotype/MDP.geno.update.reorder index b35f43dc..b35f43dc 100755..100644 --- a/genotype_files/genotype/MDP.geno.update.reorder +++ b/genotype_files/genotype/MDP.geno.update.reorder diff --git a/genotype_files/genotype/MDPBK.geno b/genotype_files/genotype/MDPBK.geno index 713777d5..713777d5 100755..100644 --- a/genotype_files/genotype/MDPBK.geno +++ b/genotype_files/genotype/MDPBK.geno diff --git a/genotype_files/genotype/MDP_mm8.geno b/genotype_files/genotype/MDP_mm8.geno index a3ceaa02..a3ceaa02 100755..100644 --- a/genotype_files/genotype/MDP_mm8.geno +++ b/genotype_files/genotype/MDP_mm8.geno diff --git a/genotype_files/genotype/Macaca-fasicularis.geno b/genotype_files/genotype/Macaca-fasicularis.geno index ca950770..ca950770 100755..100644 --- a/genotype_files/genotype/Macaca-fasicularis.geno +++ b/genotype_files/genotype/Macaca-fasicularis.geno diff --git a/genotype_files/genotype/NZBXFVB-N2.geno b/genotype_files/genotype/NZBXFVB-N2.geno index 4401c13c..4401c13c 100755..100644 --- a/genotype_files/genotype/NZBXFVB-N2.geno +++ b/genotype_files/genotype/NZBXFVB-N2.geno diff --git a/genotype_files/genotype/Oregon-R_x_2b3.geno b/genotype_files/genotype/Oregon-R_x_2b3.geno index 149966c2..149966c2 100755..100644 --- a/genotype_files/genotype/Oregon-R_x_2b3.geno +++ b/genotype_files/genotype/Oregon-R_x_2b3.geno diff --git a/genotype_files/genotype/QSM.geno b/genotype_files/genotype/QSM.geno index 685ee2ff..685ee2ff 100755..100644 --- a/genotype_files/genotype/QSM.geno +++ b/genotype_files/genotype/QSM.geno diff --git a/genotype_files/genotype/SOTNOT-OHSU.geno b/genotype_files/genotype/SOTNOT-OHSU.geno index 50892c8a..50892c8a 100755..100644 --- a/genotype_files/genotype/SOTNOT-OHSU.geno +++ b/genotype_files/genotype/SOTNOT-OHSU.geno diff --git a/genotype_files/genotype/SRxSHRSPF2.geno b/genotype_files/genotype/SRxSHRSPF2.geno index 6ec478f8..6ec478f8 100755..100644 --- a/genotype_files/genotype/SRxSHRSPF2.geno +++ b/genotype_files/genotype/SRxSHRSPF2.geno diff --git a/genotype_files/genotype/SRxSHRSPF2_original.geno b/genotype_files/genotype/SRxSHRSPF2_original.geno index 7530bb89..7530bb89 100755..100644 --- a/genotype_files/genotype/SRxSHRSPF2_original.geno +++ b/genotype_files/genotype/SRxSHRSPF2_original.geno diff --git a/genotype_files/genotype/SXM.geno b/genotype_files/genotype/SXM.geno index 3d45b7a6..3d45b7a6 100755..100644 --- a/genotype_files/genotype/SXM.geno +++ b/genotype_files/genotype/SXM.geno diff --git a/genotype_files/genotype/SXM.geno.update b/genotype_files/genotype/SXM.geno.update index 571325f7..571325f7 100755..100644 --- a/genotype_files/genotype/SXM.geno.update +++ b/genotype_files/genotype/SXM.geno.update diff --git a/genotype_files/genotype/SXM.geno.update.csv b/genotype_files/genotype/SXM.geno.update.csv index e69de29b..e69de29b 100755..100644 --- a/genotype_files/genotype/SXM.geno.update.csv +++ b/genotype_files/genotype/SXM.geno.update.csv diff --git a/genotype_files/genotype/SXM.geno.update.recal b/genotype_files/genotype/SXM.geno.update.recal index 571325f7..571325f7 100755..100644 --- a/genotype_files/genotype/SXM.geno.update.recal +++ b/genotype_files/genotype/SXM.geno.update.recal diff --git a/genotype_files/genotype/SXM.geno.update.reorder b/genotype_files/genotype/SXM.geno.update.reorder index 571325f7..571325f7 100755..100644 --- a/genotype_files/genotype/SXM.geno.update.reorder +++ b/genotype_files/genotype/SXM.geno.update.reorder diff --git a/genotype_files/genotype/Scripps-2013.geno b/genotype_files/genotype/Scripps-2013.geno index 7c220f92..7c220f92 100755..100644 --- a/genotype_files/genotype/Scripps-2013.geno +++ b/genotype_files/genotype/Scripps-2013.geno diff --git a/genotype_files/genotype/mouseChromInfo.txt b/genotype_files/genotype/mouseChromInfo.txt index 54930e79..54930e79 100755..100644 --- a/genotype_files/genotype/mouseChromInfo.txt +++ b/genotype_files/genotype/mouseChromInfo.txt diff --git a/genotype_files/genotype/mouseChromInfo_mm5.txt b/genotype_files/genotype/mouseChromInfo_mm5.txt index d6e71e0b..d6e71e0b 100755..100644 --- a/genotype_files/genotype/mouseChromInfo_mm5.txt +++ b/genotype_files/genotype/mouseChromInfo_mm5.txt diff --git a/genotype_files/genotype/output.geno b/genotype_files/genotype/output.geno index 7e9aaccc..7e9aaccc 100755..100644 --- a/genotype_files/genotype/output.geno +++ b/genotype_files/genotype/output.geno diff --git a/genotype_files/genotype/process.py b/genotype_files/genotype/process.py index 96cbc9b4..112dd83a 100755..100644 --- a/genotype_files/genotype/process.py +++ b/genotype_files/genotype/process.py @@ -108,6 +108,7 @@ mysql> select * from Strain order by Id desc limit 5; try: #import getpass #passwd = getpass.getpass('Please enter mysql password here : ') + logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)") con = MySQLdb.Connect(db='db_webqtl',user='webqtlupd',passwd='webqtl', host="opteron") cursor = con.cursor() print "You have successfully connected to mysql.\n" diff --git a/webtests/chromedriver b/webtests/chromedriver Binary files differindex 754eb668..754eb668 100755..100644 --- a/webtests/chromedriver +++ b/webtests/chromedriver diff --git a/wqflask/__init__.py b/wqflask/__init__.py index 4aa081d3..315b709e 100644 --- a/wqflask/__init__.py +++ b/wqflask/__init__.py @@ -1,2 +1 @@ -import logging from wqflask import app diff --git a/wqflask/base/__init__.py b/wqflask/base/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/base/__init__.py +++ b/wqflask/base/__init__.py diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py index 8ee73296..8ee73296 100755..100644 --- a/wqflask/base/anon_collection.py +++ b/wqflask/base/anon_collection.py diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4953e728..c70738f7 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -40,7 +40,7 @@ import reaper from base import webqtlConfig from base import species -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks @@ -50,6 +50,12 @@ from maintenance import get_group_samplelists from MySQLdb import escape_string as escape from pprint import pformat as pf +from db.gn_server import menu_main +from db.call import fetchall,fetchone,fetch1 + +from utility.tools import USE_GN_SERVER, USE_REDIS +from utility.logger import getLogger +logger = getLogger(__name__ ) # Used by create_database to instantiate objects # Each subclass will add to this @@ -58,8 +64,7 @@ DS_NAME_MAP = {} def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): if not dataset_type: dataset_type = Dataset_Getter(dataset_name) - - print("dataset_type is:", dataset_type) + logger.debug("dataset_type", dataset_type) dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] @@ -68,12 +73,28 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): class Dataset_Types(object): def __init__(self): + """Create a dictionary of samples where the value is set to Geno, +Publish or ProbeSet. E.g. + + {'AD-cases-controls-MyersGeno': 'Geno', + 'AD-cases-controls-MyersPublish': 'Publish', + 'AKXDGeno': 'Geno', + 'AXBXAGeno': 'Geno', + 'AXBXAPublish': 'Publish', + 'Aging-Brain-UCIPublish': 'Publish', + 'All Phenotypes': 'Publish', + 'B139_K_1206_M': 'ProbeSet', + 'B139_K_1206_R': 'ProbeSet' ... + + """ self.datasets = {} - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" - with open(file_name, 'r') as fh: - data = json.load(fh) + if USE_GN_SERVER: + data = menu_main() + else: + 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]: @@ -85,7 +106,8 @@ class Dataset_Types(object): new_type = "Geno" else: new_type = "ProbeSet" - self.datasets[short_dataset_name] = new_type + self.datasets[short_dataset_name] = new_type + logger.info("datasets",self.datasets) def __call__(self, name): return self.datasets[name] @@ -94,14 +116,15 @@ class Dataset_Types(object): Dataset_Getter = Dataset_Types() def create_datasets_list(): - key = "all_datasets" - result = Redis.get(key) + if USE_REDIS: + key = "all_datasets" + result = Redis.get(key) - if result: - print("Cache hit!!!") - datasets = pickle.loads(result) + if result: + logger.debug("Redis cache hit") + datasets = pickle.loads(result) - else: + if result is None: datasets = list() with Bench("Creating DataSets object"): type_dict = {'Publish': 'PublishFreeze', @@ -110,15 +133,17 @@ def create_datasets_list(): 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)) + for result in fetchall(query): + #The query at the beginning of this function isn't + #necessary here, but still would rather just reuse + #it logger.debug("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) + if USE_REDIS: + Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*60) return datasets @@ -133,7 +158,7 @@ def create_in_clause(items): def mescape(*items): """Multiple escape""" escaped = [escape(str(item)) for item in items] - #print("escaped is:", escaped) + #logger.debug("escaped is:", escaped) return escaped @@ -152,12 +177,12 @@ class Markers(object): marker['Mb'] = float(marker['Mb']) self.markers = markers - #print("self.markers:", self.markers) + #logger.debug("self.markers:", self.markers) def add_pvalues(self, p_values): - print("length of self.markers:", len(self.markers)) - print("length of p_values:", len(p_values)) + logger.debug("length of self.markers:", len(self.markers)) + logger.debug("length of p_values:", len(p_values)) if type(p_values) is list: # THIS IS only needed for the case when we are limiting the number of p-values calculated @@ -178,10 +203,10 @@ class Markers(object): elif type(p_values) is dict: filtered_markers = [] for marker in self.markers: - #print("marker[name]", marker['name']) - #print("p_values:", p_values) + #logger.debug("marker[name]", marker['name']) + #logger.debug("p_values:", p_values) if marker['name'] in p_values: - #print("marker {} IS in p_values".format(i)) + #logger.debug("marker {} IS in p_values".format(i)) marker['p_value'] = p_values[marker['name']] if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 @@ -192,7 +217,7 @@ class Markers(object): marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 filtered_markers.append(marker) #else: - #print("marker {} NOT in p_values".format(i)) + #logger.debug("marker {} NOT in p_values".format(i)) #self.markers.remove(marker) #del self.markers[i] self.markers = filtered_markers @@ -204,7 +229,7 @@ class HumanMarkers(Markers): self.markers = [] for line in marker_data_fh: splat = line.strip().split() - #print("splat:", splat) + #logger.debug("splat:", splat) if len(specified_markers) > 0: if splat[1] in specified_markers: marker = {} @@ -220,7 +245,7 @@ class HumanMarkers(Markers): marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) - #print("markers is: ", pf(self.markers)) + #logger.debug("markers is: ", pf(self.markers)) def add_pvalues(self, p_values): @@ -237,15 +262,15 @@ class DatasetGroup(object): """ def __init__(self, dataset): """This sets self.group and self.group_id""" - #print("DATASET NAME2:", dataset.name) - self.name, self.id = g.db.execute(dataset.query_for_group).fetchone() + #logger.debug("DATASET NAME2:", dataset.name) + self.name, self.id = fetchone(dataset.query_for_group) if self.name == 'BXD300': self.name = "BXD" self.f1list = None self.parlist = None self.get_f1_parent_strains() - #print("parents/f1s: {}:{}".format(self.parlist, self.f1list)) + #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list)) self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -257,7 +282,7 @@ class DatasetGroup(object): self.markers = HumanMarkers(self.name, markers) def get_markers(self): - #print("self.species is:", self.species) + #logger.debug("self.species is:", self.species) if self.species == "human": marker_class = HumanMarkers else: @@ -267,21 +292,21 @@ class DatasetGroup(object): def datasets(self): key = "group_dataset_menu:v2:" + self.name - print("key is2:", key) + logger.debug("key is2:", key) dataset_menu = [] - print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) - print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) - results = g.db.execute(''' + logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) + logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) + the_results = fetchall(''' (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name FROM PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id - and InbredSet.Name = %s + and InbredSet.Name = '%s' and PublishFreeze.public > %s) UNION (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze, InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id - and InbredSet.Name = %s + and InbredSet.Name = '%s' and GenoFreeze.public > %s) UNION (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name @@ -292,11 +317,9 @@ class DatasetGroup(object): and InbredSet.Name like %s and ProbeSetFreeze.public > %s ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId) - ''', (self.name, webqtlConfig.PUBLICTHRESH, + ''' % (self.name, webqtlConfig.PUBLICTHRESH, self.name, webqtlConfig.PUBLICTHRESH, - "%" + self.name + "%", webqtlConfig.PUBLICTHRESH)) - - the_results = results.fetchall() + "'" + self.name + "'", webqtlConfig.PUBLICTHRESH)) #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)): for dataset_item in the_results: @@ -317,14 +340,15 @@ class DatasetGroup(object): break if tissue_already_exists: - #print("dataset_menu:", dataset_menu[i]['datasets']) + #logger.debug("dataset_menu:", dataset_menu[i]['datasets']) dataset_menu[i]['datasets'].append((dataset, dataset_short)) else: dataset_menu.append(dict(tissue=tissue_name, datasets=[(dataset, dataset_short)])) - Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) - Redis.expire(key, 60*5) + if USE_REDIS: + Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*5) self._datasets = dataset_menu return self._datasets @@ -342,19 +366,19 @@ class DatasetGroup(object): self.parlist = [maternal, paternal] def get_samplelist(self): + result = None key = "samplelist:v2:" + self.name - #print("key is:", key) - #with Bench("Loading cache"): - result = Redis.get(key) + if USE_REDIS: + result = Redis.get(key) - if result: - #print("Sample List Cache hit!!!") - #print("Before unjsonifying {}: {}".format(type(result), result)) + if result is not None: + #logger.debug("Sample List Cache hit!!!") + #logger.debug("Before unjsonifying {}: {}".format(type(result), result)) self.samplelist = json.loads(result) - #print(" type: ", type(self.samplelist)) - #print(" self.samplelist: ", self.samplelist) + #logger.debug(" type: ", type(self.samplelist)) + #logger.debug(" self.samplelist: ", self.samplelist) else: - print("Cache not hit") + logger.debug("Cache not hit") genotype_fn = locate_ignore_error(self.name+".geno",'genotype') mapping_fn = locate_ignore_error(self.name+".fam",'mapping') @@ -364,9 +388,10 @@ class DatasetGroup(object): self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn) else: self.samplelist = None - print("Sample list: ",self.samplelist) - Redis.set(key, json.dumps(self.samplelist)) - Redis.expire(key, 60*5) + logger.debug("Sample list: ",self.samplelist) + if USE_REDIS: + Redis.set(key, json.dumps(self.samplelist)) + Redis.expire(key, 60*5) def all_samples_ordered(self): result = [] @@ -457,14 +482,14 @@ class DataSet(object): self.name, self.name)) - self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = g.db.execute(""" + self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetchone(""" SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name FROM ProbeSetFreeze, ProbeFreeze, Tissue WHERE ProbeSetFreeze.public > %s AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND ProbeFreeze.TissueId = Tissue.Id AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') - """ % (query_args)).fetchone() + """ % (query_args)) else: query_args = tuple(escape(x) for x in ( (self.type + "Freeze"), @@ -474,15 +499,15 @@ class DataSet(object): self.name)) self.tissue = "N/A" - self.id, self.name, self.fullname, self.shortname = g.db.execute(""" + self.id, self.name, self.fullname, self.shortname = fetchone(""" SELECT Id, Name, FullName, ShortName FROM %s WHERE public > %s AND (Name = '%s' OR FullName = '%s' OR ShortName = '%s') - """ % (query_args)).fetchone() + """ % (query_args)) except TypeError: - print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) + logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass def get_trait_data(self, sample_list=None): @@ -501,6 +526,7 @@ class DataSet(object): and Strain.SpeciesId=Species.Id and Species.name = '{}' """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) + logger.sql(query) results = dict(g.db.execute(query).fetchall()) sample_ids = [results[item] for item in self.samplelist] @@ -549,10 +575,11 @@ class DataSet(object): """.format(*mescape(self.type, self.type, self.type, self.type, self.name, dataset_type, self.type, self.type, dataset_type)) - #print("trait data query: ", query) + #logger.debug("trait data query: ", query) + logger.sql(query) results = g.db.execute(query).fetchall() - #print("query results:", results) + #logger.debug("query results:", results) trait_sample_data.append(results) trait_count = len(trait_sample_data[0]) @@ -571,7 +598,7 @@ class PhenotypeDataSet(DataSet): def setup(self): - #print("IS A PHENOTYPEDATASET") + #logger.debug("IS A PHENOTYPEDATASET") # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', @@ -635,6 +662,7 @@ class PhenotypeDataSet(DataSet): where PublishFreeze.InbredSetId=PublishXRef.InbredSetId and PublishFreeze.Id = {} """.format(escape(str(self.id))) + logger.sql(query) results = g.db.execute(query).fetchall() trait_data = {} for trait in results: @@ -683,12 +711,14 @@ class PhenotypeDataSet(DataSet): this_trait.LRS_location_value = 1000000 if this_trait.lrs: - result = g.db.execute(""" + query = """ select Geno.Chr, Geno.Mb from Geno, Species where Species.Name = %s and Geno.Name = %s and Geno.SpeciesId = Species.Id - """, (species, this_trait.locus)).fetchone() + """ % (species, this_trait.locus) + logger.sql(query) + result = g.db.execute(query).fetchone() if result: if result[0] and result[1]: @@ -726,6 +756,7 @@ class PhenotypeDataSet(DataSet): Order BY Strain.Name """ + logger.sql(query) results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -773,6 +804,7 @@ class GenotypeDataSet(DataSet): where GenoXRef.GenoId = Geno.Id and GenoFreezeId = {} """.format(escape(str(self.id))) + logger.sql(query) results = g.db.execute(query).fetchall() trait_data = {} for trait in results: @@ -817,6 +849,7 @@ class GenotypeDataSet(DataSet): Order BY Strain.Name """ + logger.sql(query) results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() @@ -899,6 +932,7 @@ class MrnaAssayDataSet(DataSet): where ProbeSetXRef.ProbeSetId = ProbeSet.Id and ProbeSetFreezeId = {} """.format(escape(str(self.id))) + logger.sql(query) results = g.db.execute(query).fetchall() trait_data = {} for trait in results: @@ -967,8 +1001,8 @@ class MrnaAssayDataSet(DataSet): """ % (escape(str(this_trait.dataset.id)), escape(this_trait.name))) - #print("query is:", pf(query)) - + #logger.debug("query is:", pf(query)) + logger.sql(query) result = g.db.execute(query).fetchone() mean = result[0] if result else 0 @@ -990,6 +1024,7 @@ class MrnaAssayDataSet(DataSet): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) + logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -1025,6 +1060,7 @@ class MrnaAssayDataSet(DataSet): ProbeSet.Name = %s ProbeSetFreeze.Name = %s """ % (escape(self.name), escape(self.dataset.name)) + logger.sql(query) results = g.db.execute(query).fetchone() return results[0] @@ -1045,8 +1081,9 @@ class MrnaAssayDataSet(DataSet): Order BY Strain.Name """ % (escape(trait), escape(self.name)) + logger.sql(query) results = g.db.execute(query).fetchall() - #print("RETRIEVED RESULTS HERE:", results) + #logger.debug("RETRIEVED RESULTS HERE:", results) return results @@ -1057,6 +1094,7 @@ class MrnaAssayDataSet(DataSet): where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) + logger.sql(query) results = g.db.execute(query).fetchall() return dict(results) @@ -1093,13 +1131,15 @@ class TempDataSet(DataSet): return desc def get_desc(self): - g.db.execute('SELECT description FROM Temp WHERE Name=%s', self.name) + query = 'SELECT description FROM Temp WHERE Name=%s' % self.name + logger.sql(query) + g.db.execute(query) desc = g.db.fetchone()[0] desc = self.handle_pca(desc) return desc def get_group(self): - self.cursor.execute(""" + query = """ SELECT InbredSet.Name, InbredSet.Id FROM @@ -1107,9 +1147,9 @@ class TempDataSet(DataSet): WHERE Temp.InbredSetId = InbredSet.Id AND Temp.Name = "%s" - """, self.name) - self.group, self.group_id = self.cursor.fetchone() - #return self.group + """ % self.name + logger.sql(query) + self.group, self.group_id = g.db.execute(query).fetchone() def retrieve_sample_data(self, trait): query = """ @@ -1125,17 +1165,18 @@ class TempDataSet(DataSet): Strain.Name """ % escape(trait.name) + logger.sql(query) results = g.db.execute(query).fetchall() def geno_mrna_confidentiality(ob): dataset_table = ob.type + "Freeze" - #print("dataset_table [%s]: %s" % (type(dataset_table), dataset_table)) + #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table)) query = '''SELECT Id, Name, FullName, confidentiality, - AuthorisedUsers FROM %s WHERE Name = %%s''' % (dataset_table) - - result = g.db.execute(query, ob.name) + AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table,ob.name) + logger.sql(query) + result = g.db.execute(query) (dataset_id, name, @@ -1145,4 +1186,3 @@ def geno_mrna_confidentiality(ob): if confidential: return True - diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 1f1be1e5..e99ef7b5 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -11,6 +11,9 @@ from MySQLdb import escape_string as escape from pprint import pformat as pf +from utility.logger import getLogger +logger = getLogger(__name__ ) + class MrnaAssayTissueData(object): def __init__(self, gene_symbols=None): @@ -54,7 +57,7 @@ class MrnaAssayTissueData(object): as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean; '''.format(in_clause) - + logger.sql(query) results = g.db.execute(query).fetchall() lower_symbols = [] @@ -97,7 +100,7 @@ class MrnaAssayTissueData(object): WHERE TissueProbeSetData.Id IN {} and TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list)) - print("TISSUE QUERY:", query) + logger.sql('tissue query',query) results = g.db.execute(query).fetchall() for result in results: @@ -156,4 +159,3 @@ class MrnaAssayTissueData(object): # # if len(tissue_data.gene_symbols): # return get_symbol_values_pairs(tissue_data) - diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 79d867c8..ce763fc3 100755..100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -10,6 +10,9 @@ from utility import Bunch from pprint import pformat as pf +from utility.logger import getLogger +logger = getLogger(__name__ ) + class TheSpecies(object): def __init__(self, dataset): self.dataset = dataset @@ -48,16 +51,17 @@ class Chromosomes(object): self.dataset = dataset self.chromosomes = collections.OrderedDict() - results = g.db.execute(""" + + query = """ Select Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet where Chr_Length.SpeciesId = InbredSet.SpeciesId AND - InbredSet.Name = %s + InbredSet.Name = '%s' Order by OrderId - """, self.dataset.group.name).fetchall() - #print("group: ", self.dataset.group.name) - #print("bike:", results) + """ % self.dataset.group.name + logger.sql(query) + results = g.db.execute(query).fetchall() for item in results: self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) @@ -120,4 +124,4 @@ class Chromosomes(object): # Testing #if __name__ == '__main__': -# foo = dict(bar=dict(length))
\ No newline at end of file +# foo = dict(bar=dict(length)) diff --git a/wqflask/base/template.py b/wqflask/base/template.py index aa8f90dc..aa8f90dc 100755..100644 --- a/wqflask/base/template.py +++ b/wqflask/base/template.py diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 4bce25ac..9566c192 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -9,7 +9,7 @@ from htmlgen import HTMLgen2 as HT from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction from utility import webqtlUtil from wqflask import app @@ -20,6 +20,9 @@ from pprint import pformat as pf from flask import Flask, g, request +from utility.logger import getLogger +logger = getLogger(__name__ ) + def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss print("{}: {}".format(stage, mem/1024)) @@ -253,6 +256,7 @@ class GeneralTrait(object): PublishFreeze.Id = %s """ % (self.name, self.dataset.id) + logger.sql(query) trait_info = g.db.execute(query).fetchone() @@ -272,6 +276,7 @@ class GeneralTrait(object): """ % (escape(display_fields_string), escape(self.dataset.name), escape(str(self.name))) + logger.sql(query) trait_info = g.db.execute(query).fetchone() #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name # to avoid the problem of same marker name from different species. @@ -289,9 +294,11 @@ class GeneralTrait(object): """ % (escape(display_fields_string), escape(self.dataset.name), escape(self.name)) + logger.sql(query) trait_info = g.db.execute(query).fetchone() else: #Temp type query = """SELECT %s FROM %s WHERE Name = %s""" + logger.sql(query) trait_info = g.db.execute(query, (string.join(self.dataset.display_fields,','), self.dataset.type, self.name)).fetchone() @@ -362,6 +369,7 @@ class GeneralTrait(object): InbredSet.SpeciesId = Species.Id AND Species.TaxonomyId = Homologene.TaxonomyId """ % (escape(str(self.geneid)), escape(self.dataset.group.name)) + logger.sql(query) result = g.db.execute(query).fetchone() #else: # result = None @@ -423,6 +431,7 @@ class GeneralTrait(object): ProbeSet.Name = "{}" AND ProbeSetXRef.ProbeSetFreezeId ={} """.format(self.name, self.dataset.id) + logger.sql(query) trait_qtl = g.db.execute(query).fetchone() if trait_qtl: self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl @@ -433,6 +442,7 @@ class GeneralTrait(object): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(self.dataset.group.species, self.locus) + logger.sql(query) result = g.db.execute(query).fetchone() if result: self.locus_chr = result[0] @@ -446,7 +456,7 @@ class GeneralTrait(object): if self.dataset.type == 'Publish': - trait_qtl = g.db.execute(""" + query = """ SELECT PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive FROM @@ -455,7 +465,9 @@ class GeneralTrait(object): PublishXRef.Id = %s AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND PublishFreeze.Id =%s - """, (self.name, self.dataset.id)).fetchone() + """ % (self.name, self.dataset.id) + logger.sql(query) + trait_qtl = g.db.execute(query).fetchone() if trait_qtl: self.locus, self.lrs, self.additive = trait_qtl if self.locus: @@ -465,6 +477,7 @@ class GeneralTrait(object): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(self.dataset.group.species, self.locus) + logger.sql(query) result = g.db.execute(query).fetchone() if result: self.locus_chr = result[0] @@ -651,12 +664,12 @@ class GeneralTrait(object): """ if self.cellid: - self.cursor.execute(""" - select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze - where - ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id) - probeDBName = self.cursor.fetchone()[0] + query = """ select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze where + ProbeFreeze.Id = + ProbeSetFreeze.ProbeFreezeId AND + ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id + logger.sql(query) + probeDBName = g.db.execute(query).fetchone()[0] return dict(name = probeDBName, url = None) else: @@ -724,4 +737,3 @@ def get_sample_data(): # jsonable_sample_data[sample] = trait_ob.data[sample].value # #return jsonable_sample_data - diff --git a/wqflask/base/trait_collection.py b/wqflask/base/trait_collection.py index d388a3af..d388a3af 100755..100644 --- a/wqflask/base/trait_collection.py +++ b/wqflask/base/trait_collection.py diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 411b0d24..c80fcb65 100755..100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -24,7 +24,12 @@ # # Last updated by GeneNetwork Core Team 2010/10/20 -print("Mr. Mojo Risin 2") +from utility.logger import getLogger +logger = getLogger(__name__) + +import utility.tools + +utility.tools.show_settings() class webqtlCaseData(object): """one case data in one trait""" @@ -70,4 +75,3 @@ class webqtlCaseData(object): return "%2.3f" % self.variance else: return "x" - diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index 10251756..10251756 100755..100644 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py diff --git a/wqflask/basicStatistics/BasicStatisticsFunctions.py b/wqflask/basicStatistics/BasicStatisticsFunctions.py index e748a822..1e5646a1 100755..100644 --- a/wqflask/basicStatistics/BasicStatisticsFunctions.py +++ b/wqflask/basicStatistics/BasicStatisticsFunctions.py @@ -16,7 +16,7 @@ from htmlgen import HTMLgen2 as HT #from utility import Plot from utility import webqtlUtil from base import webqtlConfig -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction def basicStatsTable(vals, trait_type=None, cellid=None, heritability=None): print("basicStatsTable called - len of vals", len(vals)) diff --git a/wqflask/basicStatistics/__init__.py b/wqflask/basicStatistics/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/basicStatistics/__init__.py +++ b/wqflask/basicStatistics/__init__.py diff --git a/wqflask/basicStatistics/corestats.py b/wqflask/basicStatistics/corestats.py index eba84c52..eba84c52 100755..100644 --- a/wqflask/basicStatistics/corestats.py +++ b/wqflask/basicStatistics/corestats.py diff --git a/wqflask/cfg/__init__.py b/wqflask/cfg/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/cfg/__init__.py +++ b/wqflask/cfg/__init__.py diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py index 88159321..5af61d5a 100755..100644 --- a/wqflask/cfg/default_settings.py +++ b/wqflask/cfg/default_settings.py @@ -1,21 +1 @@ -LOGFILE = """/tmp/flask_gn_log""" - -#This is needed because Flask turns key errors into a -#400 bad request response with no exception/log -TRAP_BAD_REQUEST_ERRORS = True - -# http://pythonhosted.org/Flask-Security/configuration.html -SECURITY_CONFIRMABLE = True -SECURITY_TRACKABLE = True -SECURITY_REGISTERABLE = True -SECURITY_RECOVERABLE = True - -SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org" - -SECURITY_POST_LOGIN_VIEW = "/thank_you" - -SQLALCHEMY_POOL_RECYCLE = 3600 - -SECURITY_PASSWORD_HASH = "bcrypt" -SESSION_TYPE = "filesystem" -SECRET_KEY = "secretkey" +# no longer in use diff --git a/wqflask/dbFunction/__init__.py b/wqflask/db/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/dbFunction/__init__.py +++ b/wqflask/db/__init__.py diff --git a/wqflask/db/call.py b/wqflask/db/call.py new file mode 100644 index 00000000..194a7650 --- /dev/null +++ b/wqflask/db/call.py @@ -0,0 +1,62 @@ +# Module for calling the backend + +from flask import g + +import string +import urllib2 +import json +from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL +from utility.benchmark import Bench + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +# from inspect import stack + +def fetch1(query, path=None, func=None): + """Fetch one result using either a SQL query or the URI path to +GN_SERVER (when USE_GN_SERVER is True). Apply func to GN_SERVER result +when set. + + """ + if USE_GN_SERVER and path: + result = gn_server(path) + if func != None: + return [func(result)] + else: + return [result] + else: + return fetchone(query) + +def fetchone(query): + """Return tuple containing one row by calling SQL directly (the +original fetchone, but with logging) + + """ + with Bench("SQL",LOG_SQL): + def helper(query): + res = g.db.execute(query) + return res.fetchone() + return logger.sql(query, helper) + +def fetchall(query): + """Return row iterator by calling SQL directly (the +original fetchall, but with logging) + + """ + with Bench("SQL",LOG_SQL): + def helper(query): + res = g.db.execute(query) + return res.fetchall() + return logger.sql(query, helper) + +def gn_server(path): + """Return JSON record by calling GN_SERVER + + """ + with Bench("GN_SERVER",LOG_SQL): + res = urllib2.urlopen(GN_SERVER_URL+path) + rest = res.read() + res2 = json.loads(rest) + logger.debug(res2) + return res2 diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py new file mode 100644 index 00000000..da224112 --- /dev/null +++ b/wqflask/db/gn_server.py @@ -0,0 +1,9 @@ +# Backend query functions (logic) + +from db.call import gn_server + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +def menu_main(): + return gn_server("/int/menu/main.json") diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py new file mode 100644 index 00000000..7fc096a9 --- /dev/null +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -0,0 +1,54 @@ +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU Affero General Public License for more details. +# +# This program is available from Source Forge: at GeneNetwork Project +# (sourceforge.net/projects/genenetwork/). +# +# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) +# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# +# +# +# This module is used by GeneNetwork project (www.genenetwork.org) + +from db.call import fetch1 + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +########################################################################### +#output: cursor instance +#function: connect to database and return cursor instance +########################################################################### +def getCursor(): + try: + logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)") + con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD) + cursor = con.cursor() + return cursor + except: + return None + +def retrieve_species(group): + """Get the species of a group (e.g. returns string "mouse" on "BXD" + + """ + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: r["species"])[0] + logger.debug("retrieve_species result:",result) + return result + + +def retrieve_species_id(group): + + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: r["species_id"])[0] + logger.debug("retrieve_species_id result:",result) + return result diff --git a/wqflask/dbFunction/webqtlDatabaseFunction.py b/wqflask/dbFunction/webqtlDatabaseFunction.py deleted file mode 100755 index 299114b4..00000000 --- a/wqflask/dbFunction/webqtlDatabaseFunction.py +++ /dev/null @@ -1,249 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) - - -from flask import Flask, g - -import MySQLdb -import string -from base import webqtlConfig - -########################################################################### -#output: cursor instance -#function: connect to database and return cursor instance -########################################################################### -def getCursor(): - try: - con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD) - cursor = con.cursor() - return cursor - except: - return None - - - -########################################################################### -#input: cursor, groupName (string) -#output: mappingMethodId (int) info, value will be Null or else -#function: retrieve mappingMethodId info from InbredSet table -########################################################################### - -def getMappingMethod(cursor=None, groupName=None): - cursor.execute("select MappingMethodId from InbredSet where Name= '%s'" % groupName) - mappingMethodId = cursor.fetchone()[0] - return mappingMethodId - -########################################################################### -#input: cursor, inbredSetId (int), strainId (int) -#output: isMappingId (bull) info, value will be 0,1,2 or else, 0 or Null means -# "can not do mapping", >0 means "can do mapping", >1 means "there exsists -# redundant data, user needs to choose one to do mapping function" -#function: retrieve isMappingId info from StrainXRef table -########################################################################### - -def isMapping(cursor=None, inbredSetId=None, strainId=None): - cursor.execute("select IsMapping from StrainXRef where InbredSetId='%d' and StrainId = '%d'" %(inbredSetId, strainId)) - isMappingId = cursor.fetchone()[0] - return isMappingId - -########################################################################### -#input: cursor, groupName (string) -#output: all species data info (array), value will be Null or else -#function: retrieve all species info from Species table -########################################################################### - -def getAllSpecies(cursor=None): - cursor.execute("select Id, Name, MenuName, FullName, TaxonomyId,OrderId from Species Order by OrderId") - allSpecies = cursor.fetchall() - return allSpecies - -########################################################################### -#input: cursor, RISet (string) -#output: specie's name (string), value will be None or else -#function: retrieve specie's name info based on RISet -########################################################################### - -def retrieve_species(group): - return g.db.execute("""select Species.Name - from Species, InbredSet - where InbredSet.Name = %s and - InbredSet.SpeciesId = Species.Id""", (group)).fetchone()[0] - -def retrieve_species_id(group): - return g.db.execute("select SpeciesId from InbredSet where Name = %s", (group)).fetchone()[0] - - -########################################################################### -# input: cursor -# output: tissProbeSetFreezeIdList (list), -# nameList (list), -# fullNameList (list) -# function: retrieve all TissueProbeSetFreezeId,Name,FullName info -# from TissueProbeSetFreeze table. -# These data will listed in the dropdown menu in the first page of Tissue Correlation -########################################################################### - -def getTissueDataSet(cursor=None): - tissProbeSetFreezeIdList=[] - nameList =[] - fullNameList = [] - - query = "select Id,Name,FullName from TissueProbeSetFreeze; " - try: - cursor.execute(query) - result = cursor.fetchall() - - for row in result: - tissProbeSetFreezeIdList.append(row[0]) - nameList.append(row[1]) - fullNameList.append(row[2]) - except: - return None - - return tissProbeSetFreezeIdList,nameList,fullNameList - -########################################################################### -# input: cursor,GeneSymbol (string), and TissueProbeSetFreezeId (string) -# output: geneId (string), dataId (string) -# function: retrieve geneId and DataId from TissueProbeSetXRef table -########################################################################### - -def getGeneIdDataIdForTissueBySymbol(cursor=None, GeneSymbol=None, TissueProbeSetFreezeId= 0): - query ="select GeneId, DataId from TissueProbeSetXRef where Symbol = '%s' and TissueProbeSetFreezeId=%s order by Mean desc" %(GeneSymbol,TissueProbeSetFreezeId) - try: - cursor.execute(query) - result = cursor.fetchone() - geneId = result[0] - dataId = result[1] - except: - geneId = 0 - dataId = 0 - - return geneId,dataId - -########################################################################### -# input: cursor, TissueProbeSetFreezeId (int) -# output: chipId (int) -# function: retrieve chipId from TissueProbeFreeze table -########################################################################### - -def getChipIdByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query = "select TissueProbeFreezeId from TissueProbeSetFreeze where Id =%s" % TissueProbeSetFreezeId - try: - cursor.execute(query) - result = cursor.fetchone() - TissueProbeFreezeId = result[0] - except: - TissueProbeFreezeId =0 - - query1 = "select ChipId from TissueProbeFreeze where Id =%s" % TissueProbeFreezeId - try: - cursor.execute(query1) - result1 = cursor.fetchone() - chipId = result1[0] - except: - chipId =0 - - return chipId - -########################################################################### -# input: cursor, TissueProbeSetFreezeId (int) -# output: TissueCount (int) -# function: retrieve how many tissue used in the specific dataset based on TissueProbeSetFreezeId -########################################################################### -def getTissueCountByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query1 ="select DataId from TissueProbeSetXRef where TissueProbeSetFreezeId =%s limit 1" % TissueProbeSetFreezeId - try: - cursor.execute(query1) - result1 = cursor.fetchone() - DataId = result1[0] - - query2 =" select count(*) from TissueProbeSetData where Id=%s" % DataId - try: - cursor.execute(query2) - result2 = cursor.fetchone() - TissueCount = result2[0] - except: - TissueCount =0 - except: - TissueCount =0 - - return TissueCount - -########################################################################### -# input: cursor, TissueProbeSetFreezeId (int) -# output: DataSetName(string),DataSetFullName(string) -# function: retrieve DataSetName, DataSetFullName based on TissueProbeSetFreezeId -########################################################################### -def getDataSetNamesByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query ="select Name, FullName from TissueProbeSetFreeze where Id=%s" % TissueProbeSetFreezeId - try: - cursor.execute(query) - result = cursor.fetchone() - DataSetName = result[0] - DataSetFullName =result[1] - except: - DataSetName =None - DataSetFullName =None - - return DataSetName, DataSetFullName - -########################################################################### -# input: cursor, geneIdLst (list) -# output: geneIdSymbolPair(dict),key is geneId, value is geneSymbol -# function: retrieve GeneId, GeneSymbol based on geneId List -########################################################################### -def getGeneIdSymbolPairByGeneId(cursor=None, geneIdLst =None): - geneIdSymbolPair={} - for geneId in geneIdLst: - geneIdSymbolPair[geneId]=None - - query ="select GeneId,GeneSymbol from GeneList where GeneId in (%s)" % string.join(geneIdLst, ", ") - try: - cursor.execute(query) - results = cursor.fetchall() - for item in results: - geneId =item[0] - geneSymbol =item[1] - geneIdSymbolPair[geneId]=geneSymbol - except: - geneIdSymbolPair=None - - return geneIdSymbolPair - - -def updateTissueProbesetXRefByProbesetId(cursor=None, probesetId=None): - query ="select Symbol,GeneId,Chr,Mb,description, Probe_Target_Description from ProbeSet where Id =%s"%probesetId - try: - cursor.execute(query) - result =cursor.fetchone() - - updateQuery =''' - Update TissueProbeSetXRef - Set Symbol='%s',GeneId='%s', Chr='%s', Mb='%s', description ='%s',Probe_Target_Description='%s' - where ProbesetId=%s - '''%(result[0],result[1],result[2],result[3],result[4],result[5],probesetId) - - cursor.execute(updateQuery) - - except: - return None diff --git a/wqflask/flask_security/__init__.py b/wqflask/flask_security/__init__.py index 81e6c89e..81e6c89e 100755..100644 --- a/wqflask/flask_security/__init__.py +++ b/wqflask/flask_security/__init__.py diff --git a/wqflask/flask_security/changeable.py b/wqflask/flask_security/changeable.py index 4447b655..4447b655 100755..100644 --- a/wqflask/flask_security/changeable.py +++ b/wqflask/flask_security/changeable.py diff --git a/wqflask/flask_security/confirmable.py b/wqflask/flask_security/confirmable.py index a7caf6cd..a7caf6cd 100755..100644 --- a/wqflask/flask_security/confirmable.py +++ b/wqflask/flask_security/confirmable.py diff --git a/wqflask/flask_security/core.py b/wqflask/flask_security/core.py index 0f3a231f..0f3a231f 100755..100644 --- a/wqflask/flask_security/core.py +++ b/wqflask/flask_security/core.py diff --git a/wqflask/flask_security/datastore.py b/wqflask/flask_security/datastore.py index 634399d9..634399d9 100755..100644 --- a/wqflask/flask_security/datastore.py +++ b/wqflask/flask_security/datastore.py diff --git a/wqflask/flask_security/decorators.py b/wqflask/flask_security/decorators.py index 0ea1105c..0ea1105c 100755..100644 --- a/wqflask/flask_security/decorators.py +++ b/wqflask/flask_security/decorators.py diff --git a/wqflask/flask_security/forms.py b/wqflask/flask_security/forms.py index 54677e77..54677e77 100755..100644 --- a/wqflask/flask_security/forms.py +++ b/wqflask/flask_security/forms.py diff --git a/wqflask/flask_security/passwordless.py b/wqflask/flask_security/passwordless.py index b0accb2c..b0accb2c 100755..100644 --- a/wqflask/flask_security/passwordless.py +++ b/wqflask/flask_security/passwordless.py diff --git a/wqflask/flask_security/recoverable.py b/wqflask/flask_security/recoverable.py index 6aafc111..6aafc111 100755..100644 --- a/wqflask/flask_security/recoverable.py +++ b/wqflask/flask_security/recoverable.py diff --git a/wqflask/flask_security/registerable.py b/wqflask/flask_security/registerable.py index 4606c7c6..4606c7c6 100755..100644 --- a/wqflask/flask_security/registerable.py +++ b/wqflask/flask_security/registerable.py diff --git a/wqflask/flask_security/script.py b/wqflask/flask_security/script.py index 9c9a2469..9c9a2469 100755..100644 --- a/wqflask/flask_security/script.py +++ b/wqflask/flask_security/script.py diff --git a/wqflask/flask_security/signals.py 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b/wqflask/flask_security/templates/security/register_user.html diff --git a/wqflask/flask_security/templates/security/reset_password.html b/wqflask/flask_security/templates/security/reset_password.html index e6fc3f58..e6fc3f58 100755..100644 --- a/wqflask/flask_security/templates/security/reset_password.html +++ b/wqflask/flask_security/templates/security/reset_password.html diff --git a/wqflask/flask_security/templates/security/send_confirmation.html b/wqflask/flask_security/templates/security/send_confirmation.html index 3e828407..3e828407 100755..100644 --- a/wqflask/flask_security/templates/security/send_confirmation.html +++ b/wqflask/flask_security/templates/security/send_confirmation.html diff --git a/wqflask/flask_security/templates/security/send_login.html b/wqflask/flask_security/templates/security/send_login.html index 15611c57..15611c57 100755..100644 --- a/wqflask/flask_security/templates/security/send_login.html +++ b/wqflask/flask_security/templates/security/send_login.html diff --git a/wqflask/flask_security/utils.py b/wqflask/flask_security/utils.py index 7397ab4f..7397ab4f 100755..100644 --- a/wqflask/flask_security/utils.py +++ b/wqflask/flask_security/utils.py diff --git a/wqflask/flask_security/views.py b/wqflask/flask_security/views.py index 1b8488d8..1b8488d8 100755..100644 --- a/wqflask/flask_security/views.py +++ b/wqflask/flask_security/views.py diff --git a/wqflask/maintenance/__init__.py b/wqflask/maintenance/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/maintenance/__init__.py +++ b/wqflask/maintenance/__init__.py diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index b1459bf3..d39bf4a5 100755..100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -5,6 +5,7 @@ It needs to be run manually when database has been changed. """ + # Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it @@ -36,11 +37,11 @@ from __future__ import print_function, division #print("cdict is:", cdict) import sys -import zach_settings # no hard code paths! +# import zach_settings # no hard code paths! -import MySQLdb +# import MySQLdb -import simplejson as json +# import simplejson as json import urlparse @@ -54,8 +55,8 @@ from pprint import pformat as pf #conn = Engine.connect() - - +print('ERROR: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!') +sys.exit() def parse_db_uri(db_uri): @@ -257,7 +258,7 @@ def build_datasets(species, group, type_name): def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" - parse_db_uri(zach_settings.DB_URI) + parse_db_uri(zach_settings.SQL_URI) species = get_species() groups = get_groups(species) @@ -296,6 +297,6 @@ def _test_it(): #print("build_datasets:", pf(datasets)) if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri(zach_settings.DB_URI)) + Conn = MySQLdb.Connect(**parse_db_uri(zach_settings.SQL_URI)) Cursor = Conn.cursor() main() diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index 84319a21..b7b2dc8e 100755..100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -4,7 +4,7 @@ from __future__ import absolute_import, print_function, division import sys -sys.path.insert(0, "..") +# sys.path.insert(0, "..") - why? import os import collections diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py index 2d48ce78..2d48ce78 100755..100644 --- a/wqflask/maintenance/get_group_samplelists.py +++ b/wqflask/maintenance/get_group_samplelists.py diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py index ae327cf3..ae327cf3 100755..100644 --- a/wqflask/maintenance/print_benchmark.py +++ b/wqflask/maintenance/print_benchmark.py diff --git a/wqflask/other_config/dot.pylintrc b/wqflask/other_config/dot.pylintrc index 2774300a..2774300a 100755..100644 --- a/wqflask/other_config/dot.pylintrc +++ b/wqflask/other_config/dot.pylintrc diff --git a/wqflask/other_config/nginx-old.conf b/wqflask/other_config/nginx-old.conf index 65ee768c..65ee768c 100755..100644 --- a/wqflask/other_config/nginx-old.conf +++ b/wqflask/other_config/nginx-old.conf diff --git a/wqflask/other_config/nginx_conf/gn2-zach.conf b/wqflask/other_config/nginx_conf/gn2-zach.conf index 38347292..38347292 100755..100644 --- a/wqflask/other_config/nginx_conf/gn2-zach.conf +++ b/wqflask/other_config/nginx_conf/gn2-zach.conf diff --git a/wqflask/other_config/nginx_conf/gn2.conf b/wqflask/other_config/nginx_conf/gn2.conf index a51b4113..a51b4113 100755..100644 --- a/wqflask/other_config/nginx_conf/gn2.conf +++ b/wqflask/other_config/nginx_conf/gn2.conf diff --git a/wqflask/other_config/nginx_conf/gn2_lei.conf b/wqflask/other_config/nginx_conf/gn2_lei.conf index 6589d298..6589d298 100755..100644 --- a/wqflask/other_config/nginx_conf/gn2_lei.conf +++ b/wqflask/other_config/nginx_conf/gn2_lei.conf diff --git a/wqflask/other_config/nginx_conf/gn2_sam.conf b/wqflask/other_config/nginx_conf/gn2_sam.conf index f9abbbd2..f9abbbd2 100755..100644 --- a/wqflask/other_config/nginx_conf/gn2_sam.conf +++ b/wqflask/other_config/nginx_conf/gn2_sam.conf diff --git a/wqflask/other_config/nginx_conf/penguin.conf b/wqflask/other_config/nginx_conf/penguin.conf index c819951c..c819951c 100755..100644 --- a/wqflask/other_config/nginx_conf/penguin.conf +++ b/wqflask/other_config/nginx_conf/penguin.conf diff --git a/wqflask/other_config/pylintrc b/wqflask/other_config/pylintrc index b23af7a4..b23af7a4 100755..100644 --- a/wqflask/other_config/pylintrc +++ b/wqflask/other_config/pylintrc diff --git a/wqflask/runserver.py b/wqflask/runserver.py index e4392b3f..12ec904e 100755..100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -1,36 +1,51 @@ -from wqflask import app - -# Please note, running with host set externally below combined with debug mode -# is a big security no-no -# Unless you have a firewall setup -# -# Something like /sbin/iptables -A INPUT -p tcp -i eth0 -s ! 71.236.239.43 --dport 5000 -j DROP -# should do the trick +# Starts the webserver with the ./bin/genenetwork2 command # -# You'll probably have to firewall the main port and the +# Please note, running with host set externally below combined with +# debug mode is a security risk unless you have a firewall setup, e.g. # -# For more info see: http://www.cyberciti.biz/faq/iptables-block-port/ +# /sbin/iptables -A INPUT -p tcp -i eth0 -s ! 71.236.239.43 --dport 5003 -j DROP -#import logging -#logging.basicConfig(filename="/tmp/flask_gn_log", level=logging.INFO) -# -#_log = logging.getLogger("search") -#_ch = logging.StreamHandler() -#_log.addHandler(_ch) - -print app.config +from wqflask import app import logging -file_handler = logging.FileHandler(app.config['LOGFILE']) -file_handler.setLevel(logging.DEBUG) -app.logger.addHandler(file_handler) - -# import logging_tree -# logging_tree.printout() - -app.run(host='0.0.0.0', - port=app.config['SERVER_PORT'], - debug=True, - use_debugger=True, - threaded=True, - use_reloader=True) +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +BLUE = '\033[94m' +GREEN = '\033[92m' +BOLD = '\033[1m' +ENDC = '\033[0m' + +logger.info("GN2 is running. Visit %shttp://localhost:5003/%s" % (BLUE,ENDC)) + +import os +app.config['SECRET_KEY'] = os.urandom(24) + +from utility.tools import WEBSERVER_MODE + +werkzeug_logger = logging.getLogger('werkzeug') + +if WEBSERVER_MODE == 'DEBUG': + app.run(host='0.0.0.0', + port=app.config['SERVER_PORT'], + debug=True, + use_debugger=True, + threaded=False, + use_reloader=True) +elif WEBSERVER_MODE == 'DEV': + werkzeug_logger.setLevel(logging.WARNING) + app.run(host='0.0.0.0', + port=app.config['SERVER_PORT'], + debug=False, + use_debugger=False, + threaded=False, + processes=0, + use_reloader=True) +else: #production mode + app.run(host='0.0.0.0', + port=app.config['SERVER_PORT'], + debug=False, + use_debugger=False, + threaded=True, + processes=8, + use_reloader=True) diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py index 083d1c0d..d70acfcd 100755..100644 --- a/wqflask/utility/AJAX_table.py +++ b/wqflask/utility/AJAX_table.py @@ -68,6 +68,8 @@ class AJAX_table: workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+file)) worksheet = workbook.add_worksheet() + logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)") + con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) cursor = con.cursor() diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 063de387..d60e2bb2 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -29,8 +29,6 @@ from __future__ import print_function import piddle as pid from pprint import pformat as pf -print("Lysol") - from math import * import random import sys, os @@ -38,14 +36,15 @@ from numarray import linear_algebra as la from numarray import ones, array, dot, swapaxes import reaper -sys.path.append("..") -print(sys.path) +# sys.path.append("..") Never in a running webserver from basicStatistics import corestats import svg import webqtlUtil from base import webqtlConfig +import utility.logger +logger = utility.logger.getLogger(__name__ ) def cformat(d, rank=0): 'custom string format' @@ -297,10 +296,10 @@ def find_outliers(vals): """ - print("xerxes vals is:", pf(vals)) + logger.debug("xerxes vals is:", pf(vals)) if vals: - #print("vals is:", pf(vals)) + #logger.debug("vals is:", pf(vals)) stats = corestats.Stats(vals) low_hinge = stats.percentile(25) up_hinge = stats.percentile(75) @@ -313,7 +312,7 @@ def find_outliers(vals): upper_bound = None lower_bound = None - print(pf(locals())) + logger.debug(pf(locals())) return upper_bound, lower_bound @@ -436,7 +435,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \ color=pid.blue,size=3) - #print (catMean, catMedian, cat25per, cat75per) + #print(catMean, catMedian, cat25per, cat75per) pass XCoord += stepX diff --git a/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py index 8de8e050..8de8e050 100755..100644 --- a/wqflask/utility/TDCell.py +++ b/wqflask/utility/TDCell.py diff --git a/wqflask/utility/THCell.py b/wqflask/utility/THCell.py index dde221b5..dde221b5 100755..100644 --- a/wqflask/utility/THCell.py +++ b/wqflask/utility/THCell.py diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index d9856eed..d9856eed 100755..100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py index a3bb85e9..a3bb85e9 100755..100644 --- a/wqflask/utility/after.py +++ b/wqflask/utility/after.py diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index d5b32703..8c97370d 100755..100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -3,34 +3,39 @@ from __future__ import print_function, division, absolute_import import collections import inspect import time +from utility.tools import LOG_BENCH +from utility.logger import getLogger +logger = getLogger(__name__ ) class Bench(object): entries = collections.OrderedDict() - def __init__(self, name=None): + def __init__(self, name=None, write_output=True): self.name = name + self.write_output = write_output def __enter__(self): - if self.name: - print("Starting benchmark: %s" % (self.name)) - else: - print("Starting benchmark at: %s [%i]" % (inspect.stack()[1][3], inspect.stack()[1][2])) + if self.write_output: + if self.name: + logger.debug("Starting benchmark: %s" % (self.name)) + else: + logger.debug("Starting benchmark at: %s [%i]" % (inspect.stack()[1][3], inspect.stack()[1][2])) self.start_time = time.time() def __exit__(self, type, value, traceback): - if self.name: - name = self.name - else: - name = "That" - time_taken = time.time() - self.start_time - print(" %s took: %f seconds" % (name, (time_taken))) + if self.write_output: + if self.name: + name = self.name + else: + name = "That" + + logger.info(" %s took: %f seconds" % (name, (time_taken))) if self.name: Bench.entries[self.name] = Bench.entries.get(self.name, 0) + time_taken - @classmethod def report(cls): total_time = sum((time_taken for time_taken in cls.entries.itervalues())) @@ -42,4 +47,4 @@ class Bench(object): def reset(cls): """Reset the entries""" - cls.entries = collections.OrderedDict()
\ No newline at end of file + cls.entries = collections.OrderedDict() diff --git a/wqflask/utility/corr_result_helpers.py b/wqflask/utility/corr_result_helpers.py index ef644d85..ef644d85 100755..100644 --- a/wqflask/utility/corr_result_helpers.py +++ b/wqflask/utility/corr_result_helpers.py diff --git a/wqflask/utility/db_tools.py b/wqflask/utility/db_tools.py index 4034f39c..4034f39c 100755..100644 --- a/wqflask/utility/db_tools.py +++ b/wqflask/utility/db_tools.py diff --git a/wqflask/utility/formatting.py b/wqflask/utility/formatting.py index e53dda22..e53dda22 100755..100644 --- a/wqflask/utility/formatting.py +++ b/wqflask/utility/formatting.py diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 15f60765..15f60765 100755..100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py new file mode 100644 index 00000000..86ee1c52 --- /dev/null +++ b/wqflask/utility/logger.py @@ -0,0 +1,137 @@ +# GeneNetwork logger +# +# The standard python logging module is very good. This logger adds a +# few facilities on top of that. Main one being that it picks up +# settings for log levels (global and by module) and (potentially) +# offers some fine grained log levels for the standard levels. +# +# All behaviour is defined here. Global settings (defined in +# default_settings.py). +# +# To use logging and settings put this at the top of a module: +# +# import utility.logger +# logger = utility.logger.getLogger(__name__ ) +# +# To override global behaviour set the LOG_LEVEL in default_settings.py +# or use an environment variable, e.g. +# +# env LOG_LEVEL=INFO ./bin/genenetwork2 +# +# To override log level for a module replace that with, for example, +# +# import logging +# import utility.logger +# logger = utility.logger.getLogger(__name__,level=logging.DEBUG) +# +# We'll add more overrides soon. + +import logging +import string +from inspect import isfunction +from pprint import pformat as pf +from inspect import stack + +from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT + +class GNLogger: + """A logger class with some additional functionality, such as + multiple parameter logging, SQL logging, timing, colors, and lazy + functions. + + """ + + def __init__(self,name): + self.logger = logging.getLogger(name) + + def setLevel(self,value): + """Set the undelying log level""" + self.logger.setLevel(value) + + def debug(self,level=0,*args): + """Call logging.debug for multiple args. Use level=num to filter on +LOG_LEVEL_DEBUG. + + """ + if level <= LOG_LEVEL_DEBUG: + self.collect(self.logger.debug,*args) + + def info(self,*args): + """Call logging.info for multiple args""" + self.collect(self.logger.info,*args) + + def warning(self,*args): + """Call logging.warning for multiple args""" + self.collect(self.logger.warning,*args) + self.logger.warning(self.collect(*args)) + + def error(self,*args): + """Call logging.error for multiple args""" + self.collect(self.logger.error,*args) + + def infof(self,*args): + """Call logging.info for multiple args lazily""" + # only evaluate function when logging + if self.logger.getEffectiveLevel() < 30: + self.collectf(self.logger.debug,*args) + + def debugf(self,level=0,*args): + """Call logging.debug for multiple args lazily""" + # only evaluate function when logging + if level <= LOG_LEVEL_DEBUG: + if self.logger.getEffectiveLevel() < 20: + self.collectf(self.logger.debug,*args) + + def sql(self, sqlcommand, fun = None): + """Log SQL command, optionally invoking a timed fun""" + if LOG_SQL: + caller = stack()[1][3] + if caller in ['fetchone','fetch1','fetchall']: + caller = stack()[2][3] + self.info(caller,sqlcommand) + if fun: + result = fun(sqlcommand) + if LOG_SQL: + self.info(result) + return result + + def collect(self,fun,*args): + """Collect arguments and use fun to output""" + out = "."+stack()[2][3] + for a in args: + if len(out)>1: + out += ": " + if isinstance(a, str): + out = out + a + else: + out = out + pf(a,width=160) + fun(out) + + def collectf(self,fun,*args): + """Collect arguments and use fun to output one by one""" + out = "."+stack()[2][3] + for a in args: + if len(out)>1: + out += ": " + if isfunction(a): + out += a() + else: + if isinstance(a, str): + out = out + a + else: + out = out + pf(a,width=160) + fun(out) + +# Get the module logger. You can override log levels at the +# module level +def getLogger(name, level = None): + gnlogger = GNLogger(name) + logger = gnlogger.logger + + if level: + logger.setLevel(level) + else: + logger.setLevel(LOG_LEVEL) + + logger.info("Log level of "+name+" set to "+logging.getLevelName(logger.getEffectiveLevel())) + return gnlogger diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index 512bc9e6..512bc9e6 100755..100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 5bf700c9..5bf700c9 100755..100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 11441d7a..bb8241f5 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -5,14 +5,18 @@ import os import sys from wqflask import app +# Use the standard logger here to avoid a circular dependency +import logging +logger = logging.getLogger(__name__ ) + def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in - app.config, with get_valid_path is a function checking whether the + app.config, with valid_path is a function checking whether the path points to an expected directory and returns the full path to the binary command guess = os.environ.get('HOME')+'/pylmm' - get_setting('PYLMM_PATH',guess) + valid_path(get_setting('PYLMM_PATH',guess)) first tries the environment variable in +id+, next gets the Flask app setting for the same +id+ and finally does an educated @@ -31,23 +35,39 @@ def get_setting(command_id,guess=None): """ def value(command): if command: - sys.stderr.write("Found path "+command+"\n") + # sys.stderr.write("Found "+command+"\n") return command else: return None # ---- Check whether environment exists - sys.stderr.write("Looking for "+command_id+"\n") + logger.debug("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) - if not command: + if command is None or command == "": # ---- Check whether setting exists in app command = value(app.config.get(command_id)) - if not command: + if command is None: command = value(guess) - if not command: - raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path') + if command is None or command == "": + print command + raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') + logger.debug("Set "+command_id+"="+str(command)) return command +def get_setting_bool(id): + v = get_setting(id) + if v not in [0,False,'False','FALSE',None]: + return True + return False + +def get_setting_int(id): + v = get_setting(id) + if isinstance(v, str): + return int(v) + if v is None: + return 0 + return v + def valid_bin(bin): if os.path.islink(bin) or valid_file(bin): return bin @@ -100,7 +120,7 @@ def locate(name, subdir=None): if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): - print("Found: file "+lookfor+"\n") + logger.info("Found: file "+lookfor+"\n") return lookfor else: raise Exception("Can not locate "+lookfor) @@ -120,18 +140,52 @@ def locate_ignore_error(name, subdir=None): if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): - print("Found: file "+name+"\n") + logger.debug("Found: file "+name+"\n") return lookfor - sys.stderr.write("WARNING: file "+name+" not found\n") + logger.info("WARNING: file "+name+" not found\n") return None def tempdir(): return valid_path(get_setting("TEMPDIR","/tmp")) +BLUE = '\033[94m' +GREEN = '\033[92m' +BOLD = '\033[1m' +ENDC = '\033[0m' + +def show_settings(): + from utility.tools import LOG_LEVEL + + print("Set global log level to "+BLUE+LOG_LEVEL+ENDC) + log_level = getattr(logging, LOG_LEVEL.upper()) + logging.basicConfig(level=log_level) + + logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) + print "runserver.py: ****** The webserver has the following configuration ******" + keylist = app.config.keys() + keylist.sort() + for k in keylist: + try: + print("%s %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC)) + except: + print("%s %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)) + # Cached values -PYLMM_COMMAND = pylmm_command() -GEMMA_COMMAND = gemma_command() -PLINK_COMMAND = plink_command() -FLAT_FILES = flat_files() -TEMPDIR = tempdir() +WEBSERVER_MODE = get_setting('WEBSERVER_MODE') +GN_SERVER_URL = get_setting('GN_SERVER_URL') +SQL_URI = get_setting('SQL_URI') +LOG_LEVEL = get_setting('LOG_LEVEL') +LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG') +LOG_SQL = get_setting_bool('LOG_SQL') +LOG_SQLALCHEMY = get_setting_bool('LOG_SQLALCHEMY') +LOG_BENCH = get_setting_bool('LOG_BENCH') +LOG_FORMAT = "%(message)s" # not yet in use +USE_REDIS = get_setting_bool('USE_REDIS') +USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') + +PYLMM_COMMAND = pylmm_command() +GEMMA_COMMAND = gemma_command() +PLINK_COMMAND = plink_command() +FLAT_FILES = flat_files() +TEMPDIR = tempdir() diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 4fc978f5..4fc978f5 100755..100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 478d0a71..af271d02 100755..100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -1,19 +1,24 @@ from __future__ import absolute_import, division, print_function import sys -print("sys.path is:", sys.path) - import jinja2 from flask import Flask from utility import formatting +import logging +logger = logging.getLogger(__name__ ) +logging.basicConfig(level=logging.INFO) + app = Flask(__name__) app.config.from_object('cfg.default_settings') # Get the defaults from cfg.default_settings app.config.from_envvar('WQFLASK_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files -print("Current application configuration:", app.config) +logger.debug("System path is") +logger.debug(sys.path) +logger.debug("App.config is") +logger.debug(app.config) app.jinja_env.globals.update( undefined = jinja2.StrictUndefined, diff --git a/wqflask/wqflask/correlation/__init__.py b/wqflask/wqflask/correlation/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/wqflask/correlation/__init__.py +++ b/wqflask/wqflask/correlation/__init__.py diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 96afef1e..96afef1e 100755..100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py index b25005d3..80a0818c 100755..100644 --- a/wqflask/wqflask/correlation/correlation_functions.py +++ b/wqflask/wqflask/correlation/correlation_functions.py @@ -34,7 +34,7 @@ import string from utility import webqtlUtil from base.mrna_assay_tissue_data import MrnaAssayTissueData from base.trait import GeneralTrait -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction from flask import Flask, g diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index b852a99c..401059fd 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -21,7 +21,7 @@ from __future__ import absolute_import, print_function, division import sys -sys.path.append(".") +# sys.path.append(".") Never in a running webserver import gc import string @@ -46,7 +46,7 @@ from utility.TDCell import TDCell from base.trait import GeneralTrait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench diff --git a/wqflask/wqflask/correlation_matrix/__init__.py b/wqflask/wqflask/correlation_matrix/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/wqflask/correlation_matrix/__init__.py +++ b/wqflask/wqflask/correlation_matrix/__init__.py diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 5c3354f1..caf48a45 100755..100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -21,7 +21,7 @@ from __future__ import absolute_import, print_function, division import sys -sys.path.append(".") +# sys.path.append(".") Never do this in a webserver! import gc import string @@ -48,7 +48,7 @@ from utility.TDCell import TDCell from base.trait import GeneralTrait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench diff --git a/wqflask/wqflask/ctl/__init__.py b/wqflask/wqflask/ctl/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/wqflask/ctl/__init__.py +++ b/wqflask/wqflask/ctl/__init__.py diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py index 22c96a49..4df872ad 100755..100644 --- a/wqflask/wqflask/database.py +++ b/wqflask/wqflask/database.py @@ -1,11 +1,15 @@ +# Module to initialize sqlalchemy with flask + from sqlalchemy import create_engine from sqlalchemy.orm import scoped_session, sessionmaker from sqlalchemy.ext.declarative import declarative_base +from utility.tools import SQL_URI + +import utility.logger +logger = utility.logger.getLogger(__name__ ) -from wqflask import app -#engine = create_engine('sqlite:////tmp/test.db', convert_unicode=True) -engine = create_engine(app.config['DB_URI'], convert_unicode=True) +engine = create_engine(SQL_URI, convert_unicode=True) db_session = scoped_session(sessionmaker(autocommit=False, autoflush=False, @@ -13,20 +17,14 @@ db_session = scoped_session(sessionmaker(autocommit=False, Base = declarative_base() Base.query = db_session.query_property() -#import logging -# -#logging.basicConfig() -#logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO) - def init_db(): # import all modules here that might define models so that # they will be registered properly on the metadata. Otherwise # you will have to import them first before calling init_db() #import yourapplication.models import wqflask.model - print("database.py: Creating all model metadata..") + logger.debug("Creating all model metadata") Base.metadata.create_all(bind=engine) - print("database.py: Done creating all model metadata...") - print("Point your browser at http://localhost:5003/") + logger.info("Done creating all model metadata") init_db() diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index d89facfe..ad3eab79 100755..100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -1,6 +1,3 @@ -#!/usr/bin/python - - from __future__ import print_function, division import string @@ -11,10 +8,13 @@ from MySQLdb import escape_string as escape from pprint import pformat as pf import sys -sys.path.append("..") +# sys.path.append("..") Never in a running webserver -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction +import logging +from utility.logger import getLogger +logger = getLogger(__name__) class DoSearch(object): """Parent class containing parameters/functions used for all searches""" @@ -30,15 +30,15 @@ class DoSearch(object): self.dataset = dataset if self.dataset: - print("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) - print("self.dataset.group is: ", pf(self.dataset.group)) + logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) + logger.debug("self.dataset.group is: ", pf(self.dataset.group)) #Get group information for dataset and the species id self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) def execute(self, query): """Executes query and returns results""" query = self.normalize_spaces(query) - print("in do_search query is:", pf(query)) + logger.sql(query) results = g.db.execute(query, no_parameters=True).fetchall() return results @@ -56,7 +56,7 @@ class DoSearch(object): def mescape(self, *items): """Multiple escape""" escaped = [escape(str(item)) for item in items] - print("escaped is:", escaped) + logger.debug("escaped is:", escaped) return tuple(escaped) def normalize_spaces(self, stringy): @@ -66,13 +66,13 @@ class DoSearch(object): @classmethod def get_search(cls, search_type): - print("search_types are:", pf(cls.search_types)) + logger.debug("search_types are:", pf(cls.search_types)) search_type_string = search_type['dataset_type'] if 'key' in search_type: search_type_string += '_' + search_type['key'] - print("search_type_string is:", search_type_string) + logger.debug("search_type_string is:", search_type_string) if search_type_string in cls.search_types: return cls.search_types[search_type_string] @@ -100,7 +100,7 @@ class QuickMrnaAssaySearch(DoSearch): def run(self): """Generates and runs a search for assays across all mRNA expression datasets""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") query = self.base_query + """WHERE (MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, @@ -108,8 +108,6 @@ class QuickMrnaAssaySearch(DoSearch): AGAINST ('%s' IN BOOLEAN MODE)) """ % (escape(self.search_term[0])) - print("final query is:", pf(query)) - return self.execute(query) @@ -175,15 +173,12 @@ class MrnaAssaySearch(DoSearch): """ % (escape(from_clause), where_clause, escape(str(self.dataset.id)))) - - #print("query is:", pf(query)) - return query def run_combined(self, from_clause = '', where_clause = ''): """Generates and runs a combined search of an mRNA expression dataset""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") #query = self.base_query + from_clause + " WHERE " + where_clause from_clause = self.normalize_spaces(from_clause) @@ -198,19 +193,15 @@ class MrnaAssaySearch(DoSearch): where_clause, escape(str(self.dataset.id)))) - print("final query is:", pf(query)) - return self.execute(query) def run(self): """Generates and runs a simple search of an mRNA expression dataset""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") where_clause = self.get_where_clause() query = self.base_query + "WHERE " + where_clause + "ORDER BY ProbeSet.symbol ASC" - #print("final query is:", pf(query)) - return self.execute(query) @@ -290,14 +281,12 @@ class PhenotypeSearch(DoSearch): escape(str(self.dataset.group.id)), escape(str(self.dataset.id)))) - print("query is:", pf(query)) - return query def run_combined(self, from_clause, where_clause): """Generates and runs a combined search of an phenotype dataset""" - print("Running PhenotypeSearch") + logger.debug("Running PhenotypeSearch") from_clause = self.normalize_spaces(from_clause) @@ -313,9 +302,6 @@ class PhenotypeSearch(DoSearch): escape(str(self.dataset.group.id)), escape(str(self.dataset.id)))) - print("final query is:", pf(query)) - - return self.execute(query) def run(self): @@ -364,8 +350,6 @@ class QuickPhenotypeSearch(PhenotypeSearch): PublishXRef.InbredSetId = InbredSet.Id and InbredSet.SpeciesId = Species.Id""" % where_clause) - print("query is:", pf(query)) - return query def run(self): @@ -408,7 +392,7 @@ class GenotypeSearch(DoSearch): where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type, field), self.search_term)) - print("hello ;where_clause is:", pf(where_clause)) + logger.debug("hello ;where_clause is:", pf(where_clause)) where_clause = "(%s) " % ' OR '.join(where_clause) return where_clause @@ -432,8 +416,6 @@ class GenotypeSearch(DoSearch): and GenoFreeze.Id = %s"""% (where_clause, escape(str(self.dataset.id)))) - print("query is:", pf(query)) - return query def run(self): @@ -586,7 +568,7 @@ class LrsSearch(DoSearch): self.species_id) else: # Deal with >, <, >=, and <= - print("self.search_term is:", self.search_term) + logger.debug("self.search_term is:", self.search_term) where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, self.search_term[0]) @@ -787,7 +769,7 @@ class MeanSearch(MrnaAssaySearch): def get_final_query(self): self.where_clause = self.get_where_clause() - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -795,7 +777,7 @@ class MeanSearch(MrnaAssaySearch): def run(self): self.where_clause = self.get_where_clause() - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -825,7 +807,7 @@ class RangeSearch(MrnaAssaySearch): WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s """ % (escape(self.search_term[0])) - print("where_clause is:", pf(where_clause)) + logger.debug("where_clause is:", pf(where_clause)) return where_clause @@ -927,10 +909,11 @@ class PvalueSearch(MrnaAssaySearch): self.search_operator, self.search_term[0]) - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) + logger.sql(self.query) return self.execute(self.query) class AuthorSearch(PhenotypeSearch): @@ -966,7 +949,7 @@ if __name__ == "__main__": from base.data_set import create_dataset from base.templatePage import templatePage from utility import webqtlUtil - from dbFunction import webqtlDatabaseFunction + from db import webqtlDatabaseFunction db_conn = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, @@ -992,7 +975,7 @@ if __name__ == "__main__": # ProbeSet.Id = ProbeSetXRef.ProbeSetId and # ProbeSetXRef.ProbeSetFreezeId = 112""") - #print(pf(cursor.fetchall())) + #logger.debug(pf(cursor.fetchall())) #results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run() results = PvalueSearch(['0.005'], '<', dataset, cursor, db_conn).run() #results = RifSearch("diabetes", dataset, cursor, db_conn).run() @@ -1004,4 +987,4 @@ if __name__ == "__main__": #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run() #results = GoSearch("0045202", dataset, cursor, db_conn).run() - print("results are:", pf(results)) + logger.debug("results are:", pf(results)) diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index a8363a1f..a8363a1f 100755..100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 23b7f869..64d638b2 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -3,10 +3,13 @@ from __future__ import absolute_import, print_function, division from flask import Flask, g from base.data_set import create_dataset from base.trait import GeneralTrait -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction from utility.benchmark import Bench +from utility.logger import getLogger +logger = getLogger(__name__) + class GSearch(object): def __init__(self, kw): @@ -42,6 +45,7 @@ class GSearch(object): LIMIT 6000 """ % (self.terms) with Bench("Running query"): + logger.sql(sql) re = g.db.execute(sql).fetchall() self.trait_list = [] with Bench("Creating trait objects"): @@ -84,6 +88,7 @@ class GSearch(object): ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id` LIMIT 6000 """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms) + logger.sql(sql) re = g.db.execute(sql).fetchall() self.trait_list = [] with Bench("Creating trait objects"): diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index c766d677..56ff11cd 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -1,7 +1,7 @@ from __future__ import absolute_import, print_function, division import sys -sys.path.append(".") +# sys.path.append(".") Never in a running webserver import gc import string diff --git a/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py b/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py index c5cf9e7f..c5cf9e7f 100755..100644 --- a/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py +++ b/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py diff --git a/wqflask/wqflask/interval_analyst/__init__.py b/wqflask/wqflask/interval_analyst/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/wqflask/interval_analyst/__init__.py +++ b/wqflask/wqflask/interval_analyst/__init__.py diff --git a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py index a9e0328c..deb47ad0 100755..100644 --- a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py +++ b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py @@ -37,7 +37,7 @@ from base.webqtlTrait import webqtlTrait from base.templatePage import templatePage from utility import webqtlUtil from base import webqtlConfig -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction from base.GeneralObject import GeneralObject import reaper diff --git a/wqflask/wqflask/marker_regression/__init__.py b/wqflask/wqflask/marker_regression/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/wqflask/marker_regression/__init__.py +++ b/wqflask/wqflask/marker_regression/__init__.py diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py index 8bc6b889..8bc6b889 100755..100644 --- a/wqflask/wqflask/news.py +++ b/wqflask/wqflask/news.py diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index 35070b8c..ea7ab1b9 100755..100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -23,6 +23,9 @@ import re from pprint import pformat as pf +from utility.logger import getLogger +logger = getLogger(__name__ ) + def parse(pstring): """ @@ -40,13 +43,13 @@ def parse(pstring): separators = [re.escape(x) for x in ("<=", ">=", ":", "=", "<", ">")] separators = '(%s)' % ("|".join(separators)) - print("separators:", separators) + logger.debug("separators:", separators) for item in pstring: splat = re.split(separators, item) - print("splat is:", splat) + logger.debug("splat is:", splat) # splat is an array of 1 if no match, otherwise more than 1 if len(splat) > 1: @@ -72,7 +75,7 @@ def parse(pstring): search_term=[item]) items.append(term) - print("* items are:", pf(items) + "\n") + logger.debug("* items are:", pf(items) + "\n") return(items) #def encregexp(self,str): @@ -108,4 +111,4 @@ if __name__ == '__main__': parse("LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)") parse("sal1 LRS=(9 99 Chr4 122 155) sal2 cisLRS=(9 999 10)") parse("sal1 sal3 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)") - parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)")
\ No newline at end of file + parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)") diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py index f7f61a09..f7f61a09 100755..100644 --- a/wqflask/wqflask/pbkdf2.py +++ b/wqflask/wqflask/pbkdf2.py diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index a62f2d51..a924c7c9 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -1,8 +1,5 @@ -from __future__ import absolute_import, print_function, division +# from __future__ import absolute_import, print_function, division -from wqflask import app - -from flask import render_template import os import cPickle @@ -10,8 +7,6 @@ import re import uuid from math import * import time -#import pyXLWriter as xl -#import pp - Note from Sam: is this used? import math import datetime import collections @@ -20,32 +15,28 @@ from pprint import pformat as pf import json -from flask import Flask, g -from MySQLdb import escape_string as escape - -# Instead of importing HT we're going to build a class below until we can eliminate it -# from htmlgen import HTMLgen2 as HT - -from utility.benchmark import Bench from base.data_set import create_dataset from base.trait import GeneralTrait from wqflask import parser from wqflask import do_search -from utility import webqtlUtil -from dbFunction import webqtlDatabaseFunction +from utility import webqtlUtil,tools +from db import webqtlDatabaseFunction + +from flask import render_template from utility import formatting -#class QuickSearchResult(object): - #def __init__(self, key, result_fields): - # self.key = key - # self.result_fields = result_fields +from utility.logger import getLogger +logger = getLogger(__name__ ) class SearchResultPage(object): #maxReturn = 3000 - def __init__(self, kw): + """This class gets invoked after hitting submit on the main menu (in +views.py). + + """ ########################################### # Names and IDs of group / F2 set @@ -64,9 +55,9 @@ class SearchResultPage(object): #else: self.uc_id = uuid.uuid4() - print("uc_id:", self.uc_id) + logger.debug("uc_id:", self.uc_id) # contains a unique id - print("kw is:", kw) + logger.debug("kw is:", kw) # dict containing search terms if kw['search_terms_or']: self.and_or = "or" self.search_terms = kw['search_terms_or'] @@ -75,14 +66,14 @@ class SearchResultPage(object): self.search_terms = kw['search_terms_and'] self.search_term_exists = True self.results = [] - if kw['type'] == "Phenotypes": + if kw['type'] == "Phenotypes": # split datatype on type field dataset_type = "Publish" elif kw['type'] == "Genotypes": dataset_type = "Geno" else: - dataset_type = "ProbeSet" + dataset_type = "ProbeSet" # ProbeSet is default self.dataset = create_dataset(kw['dataset'], dataset_type) - print("KEYWORD:", self.search_terms) + logger.debug("search_terms:", self.search_terms) self.search() if self.search_term_exists: self.gen_search_result() @@ -97,16 +88,16 @@ class SearchResultPage(object): self.trait_list = [] species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name) - # result_set represents the results for each search term; a search of # "shh grin2b" would have two sets of results, one for each term - print("self.results is:", pf(self.results)) + logger.debug("self.results is:", pf(self.results)) for result in self.results: if not result: continue #### Excel file needs to be generated #### + #logger.debug("foo locals are:", locals()) trait_id = result[0] this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) @@ -118,12 +109,16 @@ class SearchResultPage(object): # self.species_groups[item['result_fields']['species']].append( # item['result_fields']['group_name']) - def search(self): + """This function sets up the actual search query in the form of a SQL +statement and executes + + """ self.search_terms = parser.parse(self.search_terms) - print("After parsing:", self.search_terms) + logger.debug("After parsing:", self.search_terms) if len(self.search_terms) > 1: + logger.debug("len(search_terms)>1") combined_from_clause = "" combined_where_clause = "" previous_from_clauses = [] #The same table can't be referenced twice in the from clause @@ -150,9 +145,11 @@ class SearchResultPage(object): if self.search_term_exists: combined_where_clause = "(" + combined_where_clause + ")" final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause) + # logger.debug("final_query",final_query) results = the_search.execute(final_query) self.results.extend(results) else: + logger.debug("len(search_terms)<=1") if self.search_terms == []: self.search_term_exists = False else: @@ -168,19 +165,19 @@ class SearchResultPage(object): self.header_fields = the_search.header_fields def get_search_ob(self, a_search): - print("[kodak] item is:", pf(a_search)) + logger.debug("[kodak] item is:", pf(a_search)) search_term = a_search['search_term'] search_operator = a_search['separator'] search_type = {} search_type['dataset_type'] = self.dataset.type if a_search['key']: search_type['key'] = a_search['key'].upper() - print("search_type is:", pf(search_type)) + logger.debug("search_type is:", pf(search_type)) search_ob = do_search.DoSearch.get_search(search_type) if search_ob: search_class = getattr(do_search, search_ob) - print("search_class is: ", pf(search_class)) + logger.debug("search_class is: ", pf(search_class)) the_search = search_class(search_term, search_operator, self.dataset, diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py index bf5d0dd8..bf5d0dd8 100755..100644 --- a/wqflask/wqflask/send_mail.py +++ b/wqflask/wqflask/send_mail.py diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 363b1efe..5e3b092e 100755..100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -12,6 +12,9 @@ from pprint import pformat as pf import itertools +import utility.logger +logger = utility.logger.getLogger(__name__ ) + class SampleList(object): def __init__(self, dataset, @@ -29,7 +32,7 @@ class SampleList(object): self.sample_attribute_values = {} self.get_attributes() - print("camera: attributes are:", pf(self.attributes)) + logger.debug("camera: attributes are:", pf(self.attributes)) if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet': self.get_extra_attribute_values() @@ -41,7 +44,7 @@ class SampleList(object): try: sample = self.this_trait.data[sample_name] except KeyError: - print("No sample %s, let's create it now" % sample_name) + logger.debug("No sample %s, let's create it now" % sample_name) sample = webqtlCaseData.webqtlCaseData(sample_name) #sampleNameAdd = '' @@ -52,7 +55,7 @@ class SampleList(object): sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" sample.extra_info['css_class'] = "fs12" - print(" type of sample:", type(sample)) + logger.debug(" type of sample:", type(sample)) if sample_group_type == 'primary': sample.this_id = "Primary_" + str(counter) @@ -62,17 +65,17 @@ class SampleList(object): #### For extra attribute columns; currently only used by several datasets - Zach if self.sample_attribute_values: sample.extra_attributes = self.sample_attribute_values.get(sample_name, {}) - print("sample.extra_attributes is", pf(sample.extra_attributes)) + logger.debug("sample.extra_attributes is", pf(sample.extra_attributes)) self.sample_list.append(sample) - print("self.attributes is", pf(self.attributes)) + logger.debug("self.attributes is", pf(self.attributes)) self.do_outliers() #do_outliers(the_samples) - print("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list))) - for sample in self.sample_list: - print("apple:", type(sample), sample) + logger.debug("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list))) + #for sample in self.sample_list: + # logger.debug("apple:", type(sample), sample) #return the_samples def __repr__(self): @@ -105,7 +108,7 @@ class SampleList(object): self.attributes = {} for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)): key, name = attr - print("radish: %s - %s" % (key, name)) + logger.debug("radish: %s - %s" % (key, name)) self.attributes[key] = Bunch() self.attributes[key].name = name self.attributes[key].distinct_values = [item.Value for item in values] diff --git a/wqflask/wqflask/show_trait/__init__.py b/wqflask/wqflask/show_trait/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/wqflask/show_trait/__init__.py +++ b/wqflask/wqflask/show_trait/__init__.py diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index ac3cd366..ac3cd366 100755..100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 73acde22..3eea3f4a 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -18,7 +18,7 @@ from wqflask.show_trait.SampleList import SampleList from utility import webqtlUtil, Plot, Bunch, helper_functions from base.trait import GeneralTrait from base import data_set -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction from basicStatistics import BasicStatisticsFunctions from pprint import pformat as pf @@ -26,6 +26,9 @@ from pprint import pformat as pf from utility.tools import flat_files MAPPING_PATH = flat_files("mapping") +from utility.logger import getLogger +logger = getLogger(__name__ ) + ############################################### # # Todo: Put in security to ensure that user has permission to access confidential data sets @@ -36,7 +39,7 @@ MAPPING_PATH = flat_files("mapping") class ShowTrait(object): def __init__(self, kw): - print("in ShowTrait, kw are:", kw) + logger.debug("in ShowTrait, kw are:", kw) if kw['trait_id'] != None: self.temp_trait = False @@ -97,7 +100,7 @@ class ShowTrait(object): #Get nearest marker for composite mapping - print("self.dataset.type:", self.dataset.type) + logger.debug("self.dataset.type:", self.dataset.type) if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish": self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset) #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0] @@ -143,7 +146,7 @@ class ShowTrait(object): else: self.sample_group_types['samples_primary'] = self.dataset.group.name sample_lists = [group.sample_list for group in self.sample_groups] - print("sample_lists is:", pf(sample_lists)) + logger.debug("sample_lists is:", pf(sample_lists)) self.get_mapping_methods() @@ -204,7 +207,7 @@ class ShowTrait(object): except ValueError: return None - print("bottle samplelist is:", samplelist) + logger.debug("bottle samplelist is:", samplelist) if traitfiledata: tt = traitfiledata.split() values = map(webqtlUtil.StringAsFloat, tt) @@ -212,17 +215,17 @@ class ShowTrait(object): tt = traitpastedata.split() values = map(webqtlUtil.StringAsFloat, tt) else: - print("mapping formdataasfloat") + logger.debug("mapping formdataasfloat") #values = map(self.FormDataAsFloat, samplelist) values = [to_float(getattr(self, key)) for key in samplelist] - print("rocket values is:", values) + logger.debug("rocket values is:", values) if len(values) < len(samplelist): values += [None] * (len(samplelist) - len(values)) elif len(values) > len(samplelist): values = values[:len(samplelist)] - print("now values is:", values) + logger.debug("now values is:", values) if variancefiledata: @@ -253,7 +256,7 @@ class ShowTrait(object): if values[i] != None: self.allTraitData[_sample] = webqtlCaseData( _sample, values[i], variances[i], nsamples[i]) - print("allTraitData is:", pf(self.allTraitData)) + logger.debug("allTraitData is:", pf(self.allTraitData)) def dispTraitInformation(self, args, title1Body, hddn, this_trait): @@ -403,6 +406,7 @@ class ShowTrait(object): ProbeSet.Name = '{}' AND Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""".format(this_trait.dataset.name, this_trait.name) + logger.sql(query) seqs = g.db.execute(query).fetchall() for seqt in seqs: @@ -447,6 +451,7 @@ class ShowTrait(object): FROM Probe, ProbeSet WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (this_trait.name) #query database for number of probes associated with trait; if count > 0, set probe tool button and text + logger.sql(query) probeResult = g.db.execute(query).fetchone() if probeResult[0] > 0: self.show_probes = "True" @@ -504,7 +509,7 @@ class ShowTrait(object): txst = int(txst*1000000) txen = int(txen*1000000) if self.species_name == "mouse": - print("this_trait.symbol:", this_trait.symbol) + logger.debug("this_trait.symbol:", this_trait.symbol) result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone() if result != None: this_chr, txst, txen = result[0], result[1], result[2] @@ -752,14 +757,14 @@ class ShowTrait(object): primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples #XZ: note that fd.f1list and fd.parlist are added. all_samples = primary_samples + other_samples other_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_samples #XZ: note that fd.f1list and fd.parlist are added. - print("ac1") # This is the one used for first sall3 + logger.debug("ac1") # This is the one used for first sall3 self.MDP_menu.append(('All Cases','0')) self.MDP_menu.append(('%s Only' % fd.group, '1')) self.MDP_menu.append(('Non-%s Only' % fd.group, '2')) else: if (len(other_samples) > 0) and (len(primary_samples) + len(other_samples) > 3): - print("ac2") + logger.debug("ac2") self.MDP_menu.append(('All Cases','0')) self.MDP_menu.append(('%s Only' % fd.group,'1')) self.MDP_menu.append(('Non-%s Only' % fd.group,'2')) @@ -768,7 +773,7 @@ class ShowTrait(object): all_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_samples primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples else: - print("ac3") + logger.debug("ac3") all_samples = samplelist other_samples.sort(key=webqtlUtil.natsort_key) @@ -785,18 +790,18 @@ class ShowTrait(object): for sampleNameOrig in all_samples: sampleName = sampleNameOrig.replace("_2nd_", "") - print("* type of this_trait:", type(this_trait)) - print(" name:", this_trait.__class__.__name__) - print(" this_trait:", this_trait) - print(" type of this_trait.data[sampleName]:", type(this_trait.data[sampleName])) - print(" name:", this_trait.data[sampleName].__class__.__name__) - print(" this_trait.data[sampleName]:", this_trait.data[sampleName]) + logger.debug("* type of this_trait:", type(this_trait)) + logger.debug(" name:", this_trait.__class__.__name__) + logger.debug(" this_trait:", this_trait) + logger.debug(" type of this_trait.data[sampleName]:", type(this_trait.data[sampleName])) + logger.debug(" name:", this_trait.data[sampleName].__class__.__name__) + logger.debug(" this_trait.data[sampleName]:", this_trait.data[sampleName]) thisval = this_trait.data[sampleName].value - print(" thisval:", thisval) + logger.debug(" thisval:", thisval) thisvar = this_trait.data[sampleName].variance - print(" thisvar:", thisvar) + logger.debug(" thisvar:", thisvar) thisValFull = [sampleName, thisval, thisvar] - print(" thisValFull:", thisValFull) + logger.debug(" thisValFull:", thisValFull) vals1.append(thisValFull) @@ -1202,9 +1207,9 @@ class ShowTrait(object): this_trait=this_trait, sample_group_type='primary', header="%s Only" % (self.dataset.group.name)) - print("primary_samples is: ", pf(primary_samples)) + logger.debug("primary_samples is: ", pf(primary_samples)) - print("other_sample_names2:", other_sample_names) + logger.debug("other_sample_names2:", other_sample_names) if other_sample_names and self.dataset.group.species != "human": parent_f1_samples = None if self.dataset.group.parlist and self.dataset.group.f1list: @@ -1214,7 +1219,7 @@ class ShowTrait(object): if parent_f1_samples: other_sample_names = parent_f1_samples + other_sample_names - print("other_sample_names:", other_sample_names) + logger.debug("other_sample_names:", other_sample_names) other_samples = SampleList(dataset=self.dataset, sample_names=other_sample_names, @@ -1229,14 +1234,14 @@ class ShowTrait(object): #TODO: Figure out why this if statement is written this way - Zach #if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0])) # or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))): - # print("hjs") + # logger.debug("hjs") self.dataset.group.allsamples = all_samples_ordered def get_nearest_marker(this_trait, this_db): this_chr = this_trait.locus_chr - print("this_chr:", this_chr) + logger.debug("this_chr:", this_chr) this_mb = this_trait.locus_mb - print("this_mb:", this_mb) + logger.debug("this_mb:", this_mb) #One option is to take flanking markers, another is to take the two (or one) closest query = """SELECT Geno.Name FROM Geno, GenoXRef, GenoFreeze @@ -1245,10 +1250,9 @@ def get_nearest_marker(this_trait, this_db): GenoFreeze.Id = GenoXRef.GenoFreezeId AND GenoFreeze.Name = '{}' ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb) - print("query:", query) - + logger.sql(query) result = g.db.execute(query).fetchall() - print("result:", result) + logger.debug("result:", result) if result == []: return "" @@ -1267,5 +1271,3 @@ def get_trait_table_width(sample_groups): table_width += len(sample_groups[0].attributes)*10 return table_width - - diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py index de818a64..de818a64 100755..100644 --- a/wqflask/wqflask/show_trait/show_trait_page.py +++ b/wqflask/wqflask/show_trait/show_trait_page.py diff --git a/wqflask/wqflask/static/new/css/bar_chart.css b/wqflask/wqflask/static/new/css/bar_chart.css index 20730c2f..20730c2f 100755..100644 --- a/wqflask/wqflask/static/new/css/bar_chart.css +++ b/wqflask/wqflask/static/new/css/bar_chart.css diff --git a/wqflask/wqflask/static/new/css/box_plot.css b/wqflask/wqflask/static/new/css/box_plot.css index 4c743b33..4c743b33 100755..100644 --- a/wqflask/wqflask/static/new/css/box_plot.css +++ b/wqflask/wqflask/static/new/css/box_plot.css diff --git a/wqflask/wqflask/static/new/css/corr_matrix.css b/wqflask/wqflask/static/new/css/corr_matrix.css index cd2b0a80..cd2b0a80 100755..100644 --- a/wqflask/wqflask/static/new/css/corr_matrix.css +++ b/wqflask/wqflask/static/new/css/corr_matrix.css diff --git a/wqflask/wqflask/static/new/css/corr_scatter_plot.css b/wqflask/wqflask/static/new/css/corr_scatter_plot.css index c62d4c9a..c62d4c9a 100755..100644 --- a/wqflask/wqflask/static/new/css/corr_scatter_plot.css +++ b/wqflask/wqflask/static/new/css/corr_scatter_plot.css diff --git a/wqflask/wqflask/static/new/css/main.css b/wqflask/wqflask/static/new/css/main.css index 017bbdb8..017bbdb8 100755..100644 --- a/wqflask/wqflask/static/new/css/main.css +++ b/wqflask/wqflask/static/new/css/main.css diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css index d81b5021..d81b5021 100755..100644 --- a/wqflask/wqflask/static/new/css/marker_regression.css +++ b/wqflask/wqflask/static/new/css/marker_regression.css diff --git a/wqflask/wqflask/static/new/css/parsley.css b/wqflask/wqflask/static/new/css/parsley.css index 7d244579..7d244579 100755..100644 --- a/wqflask/wqflask/static/new/css/parsley.css +++ b/wqflask/wqflask/static/new/css/parsley.css diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee index 7558de80..7558de80 100755..100644 --- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js index 7ec35148..7ec35148 100755..100644 --- a/wqflask/wqflask/static/new/javascript/bar_chart.js +++ b/wqflask/wqflask/static/new/javascript/bar_chart.js diff --git a/wqflask/wqflask/static/new/javascript/box.js b/wqflask/wqflask/static/new/javascript/box.js index aae80f05..aae80f05 100755..100644 --- a/wqflask/wqflask/static/new/javascript/box.js +++ b/wqflask/wqflask/static/new/javascript/box.js diff --git a/wqflask/wqflask/static/new/javascript/box_plot.coffee b/wqflask/wqflask/static/new/javascript/box_plot.coffee index edd5e968..edd5e968 100755..100644 --- a/wqflask/wqflask/static/new/javascript/box_plot.coffee +++ b/wqflask/wqflask/static/new/javascript/box_plot.coffee diff --git a/wqflask/wqflask/static/new/javascript/box_plot.js b/wqflask/wqflask/static/new/javascript/box_plot.js index 566a8eb8..566a8eb8 100755..100644 --- a/wqflask/wqflask/static/new/javascript/box_plot.js +++ b/wqflask/wqflask/static/new/javascript/box_plot.js diff --git a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee index b1d2305e..b1d2305e 100755..100644 --- a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee +++ b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee diff --git a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js index c661edc7..c661edc7 100755..100644 --- a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js +++ b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js diff --git a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js index 553423cf..553423cf 100755..100644 --- a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js +++ b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 12a30e84..4ff90ca8 100755..100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -4827,4 +4827,4 @@ ] } } -}
\ No newline at end of file +} diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee deleted file mode 100755 index 83264da3..00000000 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee +++ /dev/null @@ -1,129 +0,0 @@ -$ -> - - ## Handle menu changes - - process_json = (data) -> - window.jdata = data - populate_species() - apply_default() - - $.ajax '/static/new/javascript/dataset_menu_structure.json', - dataType: 'json' - success: process_json - - populate_species = -> - species_list = @jdata.species - redo_dropdown($('#species'), species_list) - populate_group() - window.populate_species = populate_species - - populate_group = -> - console.log("in populate group") - species = $('#species').val() - group_list = @jdata.groups[species] - redo_dropdown($('#group'), group_list) - populate_type() - window.populate_group = populate_group - - populate_type = -> - species = $('#species').val() - group = $('#group').val() - type_list = @jdata.types[species][group] - redo_dropdown($('#type'), type_list) - populate_dataset() - window.populate_type = populate_type - - populate_dataset = -> - species = $('#species').val() - group = $('#group').val() - type = $('#type').val() - console.log("sgt:", species, group, type) - dataset_list = @jdata.datasets[species][group][type] - console.log("pop_dataset:", dataset_list) - redo_dropdown($('#dataset'), dataset_list) - window.populate_dataset = populate_dataset - - redo_dropdown = (dropdown, items) -> - console.log("in redo:", dropdown, items) - dropdown.empty() - for item in items - dropdown.append($("<option />").val(item[0]).text(item[1])) - - $('#species').change => - populate_group() - - $('#group').change => - populate_type() - - $('#type').change => - populate_dataset() - - ## Info buttons - - open_window = (url, name) -> - options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900" - open(url, name, options).focus() - - # Link to info on selected group; use of "Cross" - # in the url is outdated and should be changed to group - group_info = -> - species = $('#species').val() - group = $('#group').val() - url = "/" + species + "Cross.html#" + group - open_window(url, "Group Info") - - $('#group_info').click(group_info) - - # Link to dataset info - dataset_info = -> - dataset = $('#dataset').val() - url = "/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset - open_window(url, "Dataset Info") - - $('#dataset_info').click(dataset_info) - - - ## Handle setting new default drop downs - - make_default = -> - holder = {} - for item in ['species', 'group', 'type', 'dataset'] - holder[item] = $("##{item}").val() - jholder = JSON.stringify(holder) - $.cookie('search_defaults', jholder, - expires: 365) - - apply_default = -> - defaults = $.cookie('search_defaults') - if defaults - # defaults are stored as a JSON string in a cookie - defaults = $.parseJSON(defaults) - else - # If user hasn't set a default we use this - # (Most of GN's data is from BXD mice) - defaults = - species: "mouse" - group: "BXD" - type: "Hippocampus mRNA" - dataset: "HC_M2_0606_P" - - for item in [['species', 'group'] - ['group', 'type'] - ['type', 'dataset'], - ['dataset', null]] - $("##{item[0]}").val(defaults[item[0]]) - - if item[1] - populate_function = "populate_" + item[1] - console.log("Calling:", populate_function) - window[populate_function]() - - check_search_term = -> - search_term = $('#tfor').val() - console.log("search_term:", search_term) - if (search_term == "") - alert("Please enter one or more search terms or search equations.") - return false - - $("#make_default").click(make_default) - $("#btsearch").click(check_search_term)
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js index 1fe4cf75..43b0960c 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js @@ -1,54 +1,67 @@ -// Generated by CoffeeScript 1.8.0 $(function() { - var apply_default, check_search_term, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown; - process_json = function(data) { - window.jdata = data; + var gndata; // loaded once for all to use + process_json = function(data) { + populate_species(); + return apply_default(); + }; + $.getJSON(gn_server_url+"/int/menu/main.json", + function(data) { + gndata = data; + console.log("***** GOT DATA from GN_SERVER ****"); + console.log(gndata); populate_species(); - return apply_default(); - }; - $.ajax('/static/new/javascript/dataset_menu_structure.json', { - dataType: 'json', - success: process_json + }).error(function() { + console.log("ERROR: GN_SERVER not responding"); + alert("ERROR: GN_SERVER internal REST API is not responding"); }); - populate_species = function() { - var species_list; - species_list = this.jdata.species; + + var populate_species = function() { + var species_list = Object.keys(gndata.menu).map(function(species) { + var mitem = gndata.menu[species].menu + // console.log("Species menu:",species,mitem) + return [species,mitem]; + }); redo_dropdown($('#species'), species_list); return populate_group(); }; window.populate_species = populate_species; - populate_group = function() { - var group_list, species; - console.log("in populate group"); - species = $('#species').val(); - group_list = this.jdata.groups[species]; - redo_dropdown($('#group'), group_list); + + var populate_group = function() { + var species = $('#species').val(); + var groups = gndata.groups[species].map(function(item) { + console.log("group:",item); + return item.slice(1,3); + }) + redo_dropdown($('#group'), groups); return populate_type(); }; window.populate_group = populate_group; - populate_type = function() { - var group, species, type_list; - console.log("in populate type"); - species = $('#species').val(); - group = $('#group').val(); - type_list = this.jdata.types[species][group]; + + var populate_type = function() { + var species = $('#species').val(); + var group = $('#group').val(); + var type_list = gndata.menu[species].types[group].map(function(item) { + return [item,item]; + }); + redo_dropdown($('#type'), type_list); return populate_dataset(); }; window.populate_type = populate_type; - populate_dataset = function() { - var dataset_list, group, species, type; - console.log("in populate dataset"); - species = $('#species').val(); - group = $('#group').val(); - type = $('#type').val(); - console.log("sgt:", species, group, type); - dataset_list = this.jdata.datasets[species][group][type]; - console.log("pop_dataset:", dataset_list); + + var populate_dataset = function() { + var species = $('#species').val(); + var group = $('#group').val(); + var type = $('#type').val(); + var dataset_list = gndata.datasets[species][group][type].map(function(item) { + return item.slice(1,3); + }) + return redo_dropdown($('#dataset'), dataset_list); }; window.populate_dataset = populate_dataset; - redo_dropdown = function(dropdown, items) { + + var redo_dropdown = function(dropdown, items) { var item, _i, _len, _results; console.log("in redo:", dropdown, items); dropdown.empty(); @@ -83,7 +96,7 @@ $(function() { options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900"; return open(url, name, options).focus(); }; - group_info = function() { + var group_info = function() { var group, species, url; species = $('#species').val(); group = $('#group').val(); @@ -91,14 +104,14 @@ $(function() { return open_window(url, "Group Info"); }; $('#group_info').click(group_info); - dataset_info = function() { + var dataset_info = function() { var dataset, url; accession_id = $('#dataset option:selected').data("id"); url = "http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + accession_id; return open_window(url, "Dataset Info"); }; $('#dataset_info').click(dataset_info); - make_default = function() { + var make_default = function() { var holder, item, jholder, _i, _len, _ref; alert("The current settings are now your default.") holder = {}; @@ -112,7 +125,7 @@ $(function() { expires: 365 }); }; - apply_default = function() { + var apply_default = function() { var defaults, item, populate_function, _i, _len, _ref, _results; defaults = $.cookie('search_defaults'); if (defaults) { @@ -140,7 +153,7 @@ $(function() { } return _results; }; - check_search_term = function() { + var check_search_term = function() { var or_search_term, and_search_term; or_search_term = $('#or_search').val(); and_search_term = $('#and_search').val(); diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js new file mode 100644 index 00000000..1fe4cf75 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -0,0 +1,156 @@ +// Generated by CoffeeScript 1.8.0 +$(function() { + var apply_default, check_search_term, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown; + process_json = function(data) { + window.jdata = data; + populate_species(); + return apply_default(); + }; + $.ajax('/static/new/javascript/dataset_menu_structure.json', { + dataType: 'json', + success: process_json + }); + populate_species = function() { + var species_list; + species_list = this.jdata.species; + redo_dropdown($('#species'), species_list); + return populate_group(); + }; + window.populate_species = populate_species; + populate_group = function() { + var group_list, species; + console.log("in populate group"); + species = $('#species').val(); + group_list = this.jdata.groups[species]; + redo_dropdown($('#group'), group_list); + return populate_type(); + }; + window.populate_group = populate_group; + populate_type = function() { + var group, species, type_list; + console.log("in populate type"); + species = $('#species').val(); + group = $('#group').val(); + type_list = this.jdata.types[species][group]; + redo_dropdown($('#type'), type_list); + return populate_dataset(); + }; + window.populate_type = populate_type; + populate_dataset = function() { + var dataset_list, group, species, type; + console.log("in populate dataset"); + species = $('#species').val(); + group = $('#group').val(); + type = $('#type').val(); + console.log("sgt:", species, group, type); + dataset_list = this.jdata.datasets[species][group][type]; + console.log("pop_dataset:", dataset_list); + return redo_dropdown($('#dataset'), dataset_list); + }; + window.populate_dataset = populate_dataset; + redo_dropdown = function(dropdown, items) { + var item, _i, _len, _results; + console.log("in redo:", dropdown, items); + dropdown.empty(); + _results = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + if (item.length > 2){ + _results.push(dropdown.append($("<option data-id=\""+item[0]+"\" />").val(item[1]).text(item[2]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + return _results; + }; + $('#species').change((function(_this) { + return function() { + return populate_group(); + }; + })(this)); + $('#group').change((function(_this) { + return function() { + return populate_type(); + }; + })(this)); + $('#type').change((function(_this) { + return function() { + return populate_dataset(); + }; + })(this)); + open_window = function(url, name) { + var options; + options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900"; + return open(url, name, options).focus(); + }; + group_info = function() { + var group, species, url; + species = $('#species').val(); + group = $('#group').val(); + url = "/" + species + "Cross.html#" + group; + return open_window(url, "Group Info"); + }; + $('#group_info').click(group_info); + dataset_info = function() { + var dataset, url; + accession_id = $('#dataset option:selected').data("id"); + url = "http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + accession_id; + return open_window(url, "Dataset Info"); + }; + $('#dataset_info').click(dataset_info); + make_default = function() { + var holder, item, jholder, _i, _len, _ref; + alert("The current settings are now your default.") + holder = {}; + _ref = ['species', 'group', 'type', 'dataset']; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + item = _ref[_i]; + holder[item] = $("#" + item).val(); + } + jholder = JSON.stringify(holder); + return $.cookie('search_defaults', jholder, { + expires: 365 + }); + }; + apply_default = function() { + var defaults, item, populate_function, _i, _len, _ref, _results; + defaults = $.cookie('search_defaults'); + if (defaults) { + defaults = $.parseJSON(defaults); + } else { + defaults = { + species: "mouse", + group: "BXD", + type: "Hippocampus mRNA", + dataset: "HC_M2_0606_P" + }; + } + _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]]; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + item = _ref[_i]; + $("#" + item[0]).val(defaults[item[0]]); + if (item[1]) { + populate_function = "populate_" + item[1]; + console.log("Calling:", populate_function); + _results.push(window[populate_function]()); + } else { + _results.push(void 0); + } + } + return _results; + }; + check_search_term = function() { + var or_search_term, and_search_term; + or_search_term = $('#or_search').val(); + and_search_term = $('#and_search').val(); + console.log("or_search_term:", or_search_term); + console.log("and_search_term:", and_search_term); + if (or_search_term === "" && and_search_term === "") { + alert("Please enter one or more search terms or search equations."); + return false; + } + }; + $("#make_default").click(make_default); + return $("#btsearch").click(check_search_term); +}); diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee index 07be824f..07be824f 100755..100644 --- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee +++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js index a73eafe4..a73eafe4 100755..100644 --- 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a/wqflask/wqflask/templates/environments.html b/wqflask/wqflask/templates/environments.html index 5ef91a95..5ef91a95 100755..100644 --- a/wqflask/wqflask/templates/environments.html +++ b/wqflask/wqflask/templates/environments.html diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 70cafcfe..70cafcfe 100755..100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 9be0349f..9be0349f 100755..100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 9e029911..dc7e058c 100755..100644 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -7,15 +7,15 @@ <header class="jumbotron subhead" id="overview"> <div class="container"> <h1>GeneNetwork</h1> - <p class="lead">Open source bioinformatics for systems genetics</p> + <p class="lead">Open source bioinformatics for systems genetics</p> </div> </header> --> <div class="container-fluid"> - + {{ flash_me() }} - + <div class="row" style="width: 1400px !important;"> <div class="col-xs-5"> @@ -90,7 +90,7 @@ <!-- GET ANY HELP --> <div class="form-group"> <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> - <div class="col-xs-10 controls"> + <div class="col-xs-10 controls"> <div class="col-xs-12 controls"> Enter terms, genes, ID numbers in the <b>Search</b> field.<br> Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br> @@ -113,7 +113,7 @@ <div class="col-xs-10 controls"> <div class="col-xs-2 controls" style="width: 100px !important;"> <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search"> - </div> + </div> </div> </div> @@ -267,15 +267,19 @@ {%endblock%} {% block js %} + + <script> + gn_server_url = "{{ gn_server_url }}"; + </script> <script src="/static/new/javascript/dataset_select_menu.js"></script> <script> function pressed(e) { // Has the enter key been pressed? - if ( (window.event ? event.keyCode : e.which) == 13) { + if ( (window.event ? event.keyCode : e.which) == 13) { // If enter key has been pressed and the search fields are non-empty - // manually submit the <form> - if( event.target.value.trim() != "" ) { + // manually submit the <form> + if( event.target.value.trim() != "" ) { document.forms[1].submit(); } } diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html new file mode 100755 index 00000000..9fba0e31 --- /dev/null +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -0,0 +1,285 @@ +{% extends "base.html" %} +{% block title %}GeneNetwork{% endblock %} +{% block content %} +<!-- Start of body --> + +<!-- + <header class="jumbotron subhead" id="overview"> + <div class="container"> + <h1>GeneNetwork</h1> + <p class="lead">Open source bioinformatics for systems genetics</p> + </div> + </header> +--> + + <div class="container-fluid"> + + {{ flash_me() }} + + <div class="row" style="width: 1400px !important;"> + + <div class="col-xs-5"> + <section id="search"> + <div class="page-header"> + <h1>Select and search</h1> + </div> + <form method="get" action="/search" name="SEARCHFORM"> + <fieldset> + <div style="padding: 20px" class="form-horizontal"> + + <div class="form-group"> + <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label> + <div class="col-xs-10 controls input-append" style="padding-right: 0px;"> + <div class="col-xs-8"> + <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select> + </div> + <div class="col-xs-4"> + <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button> + </div> + </div> + </div> + + <div class="form-group"> + <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label> + <div class="col-xs-10 controls input-append"> + <div class="col-xs-8"> + <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select> + <i class="icon-question-sign"></i> + </div> + </div> + </div> + + <div class="form-group"> + <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label> + <div class="col-xs-10 controls"> + <div class="col-xs-8"> + <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select> + </div> + </div> + </div> + + <div class="form-group"> + <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label> + <div class="col-xs-10 controls input-append"> + <div class="col-xs-10"> + <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select> + <i class="icon-question-sign"></i> + </div> + <div class="col-xs-2"> + <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button> + </div> + </div> + </div> + + <!-- USER HELP --> + <!--<p >Databases marked with <b>**</b>--> + <!-- suffix are not public yet.<br>--> + <!-- Access requires <a href="/account.html" target=--> + <!-- "_blank" class="fs14">user login</a>.</p>--> + <!-- GET ANY SEARCH --> + + <div class="form-group"> + <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label> + <div class="col-xs-10 controls"> + <div class="col-xs-8"> + <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea> + </div> + </div> + </div> + + <!-- GET ANY HELP --> + <div class="form-group"> + <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> + <div class="col-xs-10 controls"> + <div class="col-xs-12 controls"> + Enter terms, genes, ID numbers in the <b>Search</b> field.<br> + Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br> + Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>. + </div> + </div> + </div> + + <div class="form-group"> + <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label> + <div class="col-xs-10 controls"> + <div class="col-xs-8"> + <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea> + </div> + </div> + </div> + + <div class="form-group"> + <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> + <div class="col-xs-10 controls"> + <div class="col-xs-2 controls" style="width: 100px !important;"> + <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search"> + </div> + </div> + </div> + + <!-- SEARCH, MAKE DEFAULT --> + + <div class="form-group"> + </div> + + <input type="hidden" name="FormID" value="searchResult" class="form-control"> + <!--!<input type="hidden" name="RISet" value="BXD">--> + </div> + </fieldset> + </form> + </section> + <section id="advanced"> + <div class="page-header"> + <h2>Advanced commands</h2> + </div> + + <p>You can also use advanced commands. Copy these simple examples into the Get Any or Combined search fields:</p> + + <ul> + <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on + chromosome 1 between 25 and 30 Mb.</li> + + <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds + highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a> + linkage between 23 and 46.</li> + + <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF" target="_blank"> + GeneRIF</a> links.</li> + + <li><b>WIKI=nicotine</b> searches <a href="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank"> + GeneWiki</a> for genes that you or other users have annotated + with the word <i>nicotine</i>.</li> + + <li><b>GO:0045202</b> searches for synapse-associated genes listed in the + <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank"> + Gene Ontology</a>.</li> + + <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b> + finds synapse-associated genes with <a href="http://www.genenetwork.org/glossary.html#E" target="_blank"> + cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores + between 9 and 999.</li> + + <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b> + finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E" target="_blank"> + trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS + scores between 9 and 999.</li> + </ul> + </section> + </div> + <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;"> + <!-- + <section id="tour-info"> + <div class="page-header"> + <h1>Tour and more info</h1> + </div> + + <h3>Thirty minute tour</h3> + <p> + Take the 30 minute + GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target="_blank" class="fs14">tour</a> that includes screen shots and + typical steps in the analysis. + </p> + + <h3>Even more info</h3> + <p> + For information about + resources and methods, select the Info buttons next to the Group + and Database fields above. + </p> + + <p>The <a href="/conditionsofUse.html" target="_blank">conditions</a> + and <a href="/statusandContact.html" target="_blank">contact + </a> pages have information on the status of data sets + and advice on their use and citation.</p> + + </section> + --> + + <section id="websites"> + <div class="page-header"> + <h1>Affiliates and mirrors</h1> + </div> + <h3>Websites affiliated with GeneNetwork</h3> + <ul> + <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome + browser</a> at UTHSC</li> + + <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at + UTHSC</li> + + <li>GeneNetwork 1 at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon + Cloud (EC2)</a></li> + + <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li> + + <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2" target="_blank">GitHub</a></li> + </ul> + <h3>GN1 Mirror and development sites</h3> + + <ul> + <li><a href="http://www.genenetwork.org/" target="_blank">Main GN1 site at UTHSC</a> (main site)</li> + <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">Germany at the HZI</a></li> + <li><a href="http://genenetwork.memphis.edu/" target="_blank">Memphis at the U of M</a></li> + </ul> + </section> + + <!--<section id="getting-started"> + <div class="page-header"> + <h1>Getting started</h1> + </div> + + <ol style="font-size:12px;font-family:verdana;color:black"> + <li>Select <b>Species</b> (or All)</li> + + <li>Select <b>Group</b> (a specific sample)</li> + + <li>Select <b>Type</b> of data: + + <ul> + <li>Phenotype (traits)</li> + + <li>Genotype (markers)</li> + + <li>Expression (mRNAs)</li> + </ul> + </li> + + <li>Select a <b>Dataset</b></li> + + <li>Enter terms in the search field: words, + genes, ID numbers, probes, advanced search commands</li> + + <li>Click the <b>Search</b> button</li> + + <li>Optional: Use the <b>Make Default</b> button to save your preferences</li> + </ol> + + <h3>User Guide</h3> + <h5>Read the + <a href="http://www.genenetwork.org/index4.html" target="_blank"> + user guide</a>.</h5> + + </section>--> + </div> + </div> + </div> + +{%endblock%} + +{% block js %} + <script src="/static/new/javascript/dataset_select_menu_orig.js"></script> + + <script> + function pressed(e) { + // Has the enter key been pressed? + if ( (window.event ? event.keyCode : e.which) == 13) { + // If enter key has been pressed and the search fields are non-empty + // manually submit the <form> + if( event.target.value.trim() != "" ) { + document.forms[1].submit(); + } + } + } + </script> + +{% endblock %} diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html index 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a/wqflask/wqflask/templates/show_trait_progress_bar.html +++ b/wqflask/wqflask/templates/show_trait_progress_bar.html diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 3ee8bdea..3ee8bdea 100755..100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html diff --git a/wqflask/wqflask/tracer.py b/wqflask/wqflask/tracer.py index a1043d28..a1043d28 100755..100644 --- a/wqflask/wqflask/tracer.py +++ b/wqflask/wqflask/tracer.py diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py index 166649a4..68bea9d6 100644 --- a/wqflask/wqflask/update_search_results.py +++ b/wqflask/wqflask/update_search_results.py @@ -5,10 +5,13 @@ import json from flask import Flask, g from base.data_set import create_dataset from base.trait import GeneralTrait -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction from utility.benchmark import Bench +from utility.logger import getLogger +logger = getLogger(__name__) + class GSearch(object): def __init__(self, kw): @@ -45,6 +48,7 @@ class GSearch(object): LIMIT 6000 """ % (self.terms) with Bench("Running query"): + logger.sql(sql) re = g.db.execute(sql).fetchall() self.trait_list = [] with Bench("Creating trait objects"): @@ -87,6 +91,7 @@ class GSearch(object): ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id` LIMIT 6000 """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms) + logger.sql(sql) re = g.db.execute(sql).fetchall() self.trait_list = [] with Bench("Creating trait objects"): @@ -123,7 +128,3 @@ class GSearch(object): json_results = json.dumps(json_dict) return json_results - - - - diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 1e454292..10fac06d 100755..100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -46,8 +46,11 @@ from wqflask.database import db_session from wqflask import model from utility import Bunch, Struct, after +from utility.tools import LOG_SQL, LOG_SQLALCHEMY - +import logging +from utility.logger import getLogger +logger = getLogger(__name__) from base.data_set import create_datasets_list @@ -64,10 +67,10 @@ class AnonUser(object): def __init__(self): self.cookie = request.cookies.get(self.cookie_name) if self.cookie: - print("already is cookie") + logger.debug("already is cookie") self.anon_id = verify_cookie(self.cookie) else: - print("creating new cookie") + logger.debug("creating new cookie") self.anon_id, self.cookie = create_signed_cookie() @after.after_this_request @@ -87,7 +90,7 @@ def create_signed_cookie(): the_uuid = str(uuid.uuid4()) signature = actual_hmac_creation(the_uuid) uuid_signed = the_uuid + ":" + signature - print("uuid_signed:", uuid_signed) + logger.debug("uuid_signed:", uuid_signed) return the_uuid, uuid_signed class UserSession(object): @@ -102,7 +105,7 @@ class UserSession(object): session_id = verify_cookie(cookie) self.redis_key = self.cookie_name + ":" + session_id - print("self.redis_key is:", self.redis_key) + logger.debug("self.redis_key is:", self.redis_key) self.session_id = session_id self.record = Redis.hgetall(self.redis_key) @@ -123,10 +126,10 @@ class UserSession(object): if Redis.ttl(self.redis_key) < THREE_DAYS: # (Almost) everytime the user does something we extend the session_id in Redis... - print("Extending ttl...") + logger.debug("Extending ttl...") Redis.expire(self.redis_key, THREE_DAYS) - print("record is:", self.record) + logger.debug("record is:", self.record) self.logged_in = True @property @@ -142,8 +145,8 @@ class UserSession(object): """Actual sqlalchemy record""" # Only look it up once if needed, then store it try: - logging.basicConfig() - logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG) + if LOG_SQLALCHEMY: + logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG) # Already did this before return self.db_object @@ -156,7 +159,7 @@ class UserSession(object): def delete_session(self): # And more importantly delete the redis record Redis.delete(self.cookie_name) - print("At end of delete_session") + logger.debug("At end of delete_session") @app.before_request def before_request(): @@ -165,26 +168,26 @@ def before_request(): class UsersManager(object): def __init__(self): self.users = model.User.query.all() - print("Users are:", self.users) + logger.debug("Users are:", self.users) class UserManager(object): def __init__(self, kw): self.user_id = kw['user_id'] - print("In UserManager locals are:", pf(locals())) + logger.debug("In UserManager locals are:", pf(locals())) #self.user = model.User.get(user_id) - #print("user is:", user) + #logger.debug("user is:", user) self.user = model.User.query.get(self.user_id) - print("user is:", self.user) + logger.debug("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) + logger.debug("\n Name:", dataset.name) + logger.debug(" Type:", dataset.type) + logger.debug(" ID:", dataset.id) + logger.debug(" Confidential:", dataset.check_confidentiality()) + #logger.debug(" ---> self.datasets:", self.datasets) class RegisterUser(object): @@ -215,7 +218,7 @@ class RegisterUser(object): if self.errors: return - print("No errors!") + logger.debug("No errors!") set_password(password, self.user) @@ -233,10 +236,10 @@ class RegisterUser(object): "Click the button above to sign in using an existing account.") return - print("Adding verification email to queue") + logger.debug("Adding verification email to queue") #self.send_email_verification() VerificationEmail(self.new_user) - print("Added verification email to queue") + logger.debug("Added verification email to queue") self.thank_you_mode = True @@ -259,8 +262,8 @@ def set_password(password, user): # One more check on password length assert len(password) >= 6, "Password shouldn't be so short here" - print("pwfields:", vars(pwfields)) - print("locals:", locals()) + logger.debug("pwfields:", vars(pwfields)) + logger.debug("locals:", locals()) enc_password = Password(password, pwfields.salt, @@ -324,14 +327,14 @@ class ForgotPasswordEmail(VerificationEmail): class Password(object): def __init__(self, unencrypted_password, salt, iterations, keylength, hashfunc): hashfunc = getattr(hashlib, hashfunc) - print("hashfunc is:", hashfunc) + logger.debug("hashfunc is:", hashfunc) # On our computer it takes around 1.4 seconds in 2013 start_time = time.time() salt = base64.b64decode(salt) self.password = pbkdf2.pbkdf2_hex(str(unencrypted_password), salt, iterations, keylength, hashfunc) self.encrypt_time = round(time.time() - start_time, 3) - print("Creating password took:", self.encrypt_time) + logger.debug("Creating password took:", self.encrypt_time) def basic_info(): @@ -355,7 +358,7 @@ def verify_email(): @app.route("/n/password_reset") def password_reset(): - print("in password_reset request.url is:", request.url) + logger.debug("in password_reset request.url is:", request.url) # We do this mainly just to assert that it's in proper form for displaying next page # Really not necessary but doesn't hurt @@ -365,7 +368,7 @@ def password_reset(): @app.route("/n/password_reset_step2", methods=('POST',)) def password_reset_step2(): - print("in password_reset request.url is:", request.url) + logger.debug("in password_reset request.url is:", request.url) errors = [] @@ -373,13 +376,13 @@ def password_reset_step2(): verification_code, separator, hmac = user_encode.partition(':') hmac_verified = actual_hmac_creation(verification_code) - print("locals are:", locals()) + logger.debug("locals are:", locals()) assert hmac == hmac_verified, "Someone has been naughty" user = DecodeUser.actual_get_user(ForgotPasswordEmail.key_prefix, verification_code) - print("user is:", user) + logger.debug("user is:", user) password = request.form['password'] @@ -408,9 +411,9 @@ class DecodeUser(object): @staticmethod def actual_get_user(code_prefix, verification_code): data = Redis.get(code_prefix + ":" + verification_code) - print("in get_coded_user, data is:", data) + logger.debug("in get_coded_user, data is:", data) data = json.loads(data) - print("data is:", data) + logger.debug("data is:", data) return model.User.query.get(data['id']) @app.route("/n/login", methods=('GET', 'POST')) @@ -428,14 +431,14 @@ class LoginUser(object): def standard_login(self): """Login through the normal form""" params = request.form if request.form else request.args - print("in login params are:", params) + logger.debug("in login params are:", params) if not params: return render_template("new_security/login_user.html") else: try: user = model.User.query.filter_by(email_address=params['email_address']).one() except sqlalchemy.orm.exc.NoResultFound: - print("No account exists for that email address") + logger.debug("No account exists for that email address") valid = False user = None else: @@ -446,9 +449,9 @@ class LoginUser(object): pwfields.iterations, pwfields.keylength, pwfields.hashfunc) - print("\n\nComparing:\n{}\n{}\n".format(encrypted.password, pwfields.password)) + logger.debug("\n\nComparing:\n{}\n{}\n".format(encrypted.password, pwfields.password)) valid = pbkdf2.safe_str_cmp(encrypted.password, pwfields.password) - print("valid is:", valid) + logger.debug("valid is:", valid) if valid and not user.confirmed: VerificationEmail(user) @@ -458,7 +461,7 @@ class LoginUser(object): if valid: if params.get('remember'): - print("I will remember you") + logger.debug("I will remember you") self.remember_me = True return self.actual_login(user) @@ -492,14 +495,14 @@ class LoginUser(object): #session_id = "session_id:{}".format(login_rec.session_id) session_id_signature = actual_hmac_creation(login_rec.session_id) session_id_signed = login_rec.session_id + ":" + session_id_signature - print("session_id_signed:", session_id_signed) + logger.debug("session_id_signed:", session_id_signed) session = dict(login_time = time.time(), user_id = user.id, user_email_address = user.email_address) key = UserSession.cookie_name + ":" + login_rec.session_id - print("Key when signing:", key) + logger.debug("Key when signing:", key) Redis.hmset(key, session) if self.remember_me: expire_time = self.remember_time @@ -518,7 +521,7 @@ class LoginUser(object): @app.route("/n/logout") def logout(): - print("Logging out...") + logger.debug("Logging out...") UserSession().delete_session() flash("You are now logged out. We hope you come back soon!") response = make_response(redirect(url_for('index_page'))) @@ -610,7 +613,7 @@ def register(): params = request.form if request.form else request.args if params: - print("Attempting to register the user...") + logger.debug("Attempting to register the user...") result = RegisterUser(params) errors = result.errors @@ -656,16 +659,16 @@ def data_hmac(stringy): def verify_url_hmac(url): """Pass in a url that was created with url_hmac and this assures it hasn't been tampered with""" - print("url passed in to verify is:", url) + logger.debug("url passed in to verify is:", url) # Verify parts are correct at the end - we expect to see &hm= or ?hm= followed by an hmac assert url[-23:-20] == "hm=", "Unexpected url (stage 1)" assert url[-24] in ["?", "&"], "Unexpected url (stage 2)" hmac = url[-20:] url = url[:-24] # Url without any of the hmac stuff - #print("before urlsplit, url is:", url) + #logger.debug("before urlsplit, url is:", url) #url = divide_up_url(url)[1] - #print("after urlsplit, url is:", url) + #logger.debug("after urlsplit, url is:", url) hm = actual_hmac_creation(url) @@ -706,4 +709,4 @@ class GroupsManager(object): class RolesManager(object): def __init__(self): self.roles = model.Role.query.all() - print("Roles are:", self.roles) + logger.debug("Roles are:", self.roles) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index f88a9cdb..71de9340 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1,9 +1,10 @@ # -*- coding: utf-8 -*- +# +# Main routing table for GN2 + from __future__ import absolute_import, division, print_function import sys -print("sys.path is:", sys.path) - import csv import xlsxwriter import StringIO # Todo: Use cStringIO? @@ -14,7 +15,6 @@ import cPickle as pickle import uuid import simplejson as json -#import json import yaml #Switching from Redis to StrictRedis; might cause some issues @@ -25,20 +25,17 @@ import flask import base64 import array import sqlalchemy -#import config - from wqflask import app - -from flask import (render_template, request, make_response, Response, - Flask, g, config, jsonify, redirect, url_for, send_from_directory) - +from flask import g, request, render_template +# from flask import (render_template, request, make_response, Response, +# Flask, g, config, jsonify, redirect, url_for, +# send_from_directory) from wqflask import search_results from wqflask import gsearch from wqflask import update_search_results from wqflask import docs from wqflask import news 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.heatmap import heatmap @@ -47,12 +44,11 @@ from wqflask.marker_regression import marker_regression_gn1 from wqflask.correlation import show_corr_results from wqflask.correlation_matrix import show_corr_matrix from wqflask.correlation import corr_scatter_plot - from wqflask.wgcna import wgcna_analysis from wqflask.ctl import ctl_analysis from utility import temp_data -from utility.tools import TEMPDIR +from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL from base import webqtlFormData from base.webqtlConfig import GENERATED_IMAGE_DIR @@ -62,14 +58,26 @@ from pprint import pformat as pf from wqflask import user_manager from wqflask import collect +from wqflask.database import db_session -#import logging -#logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO) -#_log = logging.getLogger("correlation") +import utility.logger +logger = utility.logger.getLogger(__name__ ) @app.before_request def connect_db(): - g.db = sqlalchemy.create_engine(app.config['DB_URI']) + db = getattr(g, '_database', None) + if db is None: + logger.debug("Get new database connector") + g.db = g._database = sqlalchemy.create_engine(SQL_URI) + logger.debug(g.db) + +@app.teardown_appcontext +def shutdown_session(exception=None): + db = getattr(g, '_database', None) + if db is not None: + logger.debug("remove db_session") + db_session.remove() + g.db = None #@app.before_request #def trace_it(): @@ -78,28 +86,21 @@ 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") + logger.info("Sending index_page") + if USE_GN_SERVER: + # The menu is generated using GN_SERVER + return render_template("index_page.html", gn_server_url = GN_SERVER_URL) + else: + # Old style static menu (OBSOLETE) + return render_template("index_page_orig.html") @app.route("/tmp/<img_path>") def tmp_page(img_path): - print("In tmp_page") - print("img_path:", img_path) + logger.info("In tmp_page") + logger.info("img_path:", img_path) initial_start_vars = request.form - print("initial_start_vars:", initial_start_vars) + logger.info("initial_start_vars:", initial_start_vars) imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") @@ -110,15 +111,15 @@ def tmp_page(img_path): #@app.route("/data_sharing") #def data_sharing_page(): -# print("In data_sharing") +# logger.info("In data_sharing") # fd = webqtlFormData.webqtlFormData(request.args) -# print("1Have fd") +# logger.info("1Have fd") # sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None) # info, htmlfilelist = sharingInfoObject.getBody(infoupdate="") -# print("type(htmlfilelist):", type(htmlfilelist)) +# logger.info("type(htmlfilelist):", type(htmlfilelist)) # htmlfilelist = htmlfilelist.encode("utf-8") # #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None) -# print("1 Made it to rendering") +# logger.info("1 Made it to rendering") # return render_template("data_sharing.html", # info=info, # htmlfilelist=htmlfilelist) @@ -126,32 +127,35 @@ def tmp_page(img_path): @app.route("/search", methods=('GET',)) def search_page(): - print("in search_page") + logger.info("in search_page") if 'info_database' in request.args: - print("Going to sharing_info_page") + logger.info("Going to sharing_info_page") template_vars = sharing_info_page() if template_vars.redirect_url: - print("Going to redirect") + logger.info("Going to redirect") return flask.redirect(template_vars.redirect_url) else: return render_template("data_sharing.html", **template_vars.__dict__) else: - key = "search_results:v1:" + 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"): - result = pickle.loads(result) + result = None + if USE_REDIS: + with Bench("Trying Redis cache"): + key = "search_results:v1:" + json.dumps(request.args, sort_keys=True) + logger.debug("key is:", pf(key)) + result = Redis.get(key) + if result: + logger.info("Redis cache hit on search results!") + result = pickle.loads(result) else: - print("calling search_results.SearchResultPage") - print("request.args is", request.args) - the_search = search_results.SearchResultPage(request.args) - result = the_search.__dict__ + logger.info("Skipping Redis cache (USE_REDIS=False)") + + logger.info("request.args is", request.args) + the_search = search_results.SearchResultPage(request.args) + result = the_search.__dict__ - print("result: ", pf(result)) + logger.debugf("result", result) + + if USE_REDIS: Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) @@ -171,7 +175,7 @@ def gsearchact(): @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): - print("REQUEST ARGS:", request.values) + logger.info("REQUEST ARGS:", request.values) result = update_search_results.GSearch(request.args).__dict__ return result['results'] # type = request.args['type'] @@ -179,7 +183,7 @@ def gsearch_updating(): # return render_template("gsearch_gene_updating.html", **result) # elif type == "phenotype": # return render_template("gsearch_pheno.html", **result) - + @app.route("/docedit") def docedit(): doc = docs.Docs(request.args['entry']) @@ -196,12 +200,12 @@ def help(): @app.route("/wgcna_setup", methods=('POST',)) def wcgna_setup(): - print("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis + logger.info("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis return render_template("wgcna_setup.html", **request.form) # Display them using the template @app.route("/wgcna_results", methods=('POST',)) def wcgna_results(): - print("In wgcna, request.form is:", request.form) + logger.info("In wgcna, request.form is:", request.form) wgcna = wgcna_analysis.WGCNA() # Start R, load the package and pointers and create the analysis wgcnaA = wgcna.run_analysis(request.form) # Start the analysis, a wgcnaA object should be a separate long running thread result = wgcna.process_results(wgcnaA) # After the analysis is finished store the result @@ -209,12 +213,12 @@ def wcgna_results(): @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): - print("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis + logger.info("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis return render_template("ctl_setup.html", **request.form) # Display them using the template @app.route("/ctl_results", methods=('POST',)) def ctl_results(): - print("In ctl, request.form is:", request.form) + logger.info("In ctl, request.form is:", request.form) ctl = ctl_analysis.CTL() # Start R, load the package and pointers and create the analysis ctlA = ctl.run_analysis(request.form) # Start the analysis, a ctlA object should be a separate long running thread result = ctl.process_results(ctlA) # After the analysis is finished store the result @@ -253,11 +257,11 @@ def environments(): @app.route('/export_trait_excel', methods=('POST',)) def export_trait_excel(): """Excel file consisting of the sample data from the trait data and analysis page""" - print("In export_trait_excel") - print("request.form:", request.form) + logger.info("In export_trait_excel") + logger.info("request.form:", request.form) sample_data = export_trait_data.export_sample_table(request.form) - print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) + logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) buff = StringIO.StringIO() workbook = xlsxwriter.Workbook(buff, {'in_memory': True}) @@ -278,11 +282,11 @@ def export_trait_excel(): @app.route('/export_trait_csv', methods=('POST',)) def export_trait_csv(): """CSV file consisting of the sample data from the trait data and analysis page""" - print("In export_trait_csv") - print("request.form:", request.form) + logger.info("In export_trait_csv") + logger.info("request.form:", request.form) sample_data = export_trait_data.export_sample_table(request.form) - print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) + logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) buff = StringIO.StringIO() writer = csv.writer(buff) @@ -322,22 +326,22 @@ def export_perm_data(): def show_trait_page(): # Here it's currently too complicated not to use an fd that is a webqtlFormData #fd = webqtlFormData.webqtlFormData(request.args) - #print("stp y1:", pf(vars(fd))) + #logger.info("stp y1:", pf(vars(fd))) template_vars = show_trait.ShowTrait(request.args) - #print("js_data before dump:", template_vars.js_data) + #logger.info("js_data before dump:", template_vars.js_data) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") # Sorting the keys messes up the ordered dictionary, so don't do that #sort_keys=True) - #print("js_data after dump:", template_vars.js_data) - #print("show_trait template_vars:", pf(template_vars.__dict__)) + #logger.info("js_data after dump:", template_vars.js_data) + #logger.info("show_trait template_vars:", pf(template_vars.__dict__)) return render_template("show_trait.html", **template_vars.__dict__) @app.route("/heatmap", methods=('POST',)) def heatmap_page(): - print("In heatmap, request.form is:", pf(request.form)) + logger.info("In heatmap, request.form is:", pf(request.form)) start_vars = request.form temp_uuid = uuid.uuid4() @@ -346,17 +350,17 @@ def heatmap_page(): if traits[0] != "": version = "v5" key = "heatmap:{}:".format(version) + json.dumps(start_vars, sort_keys=True) - print("key is:", pf(key)) + logger.info("key is:", pf(key)) with Bench("Loading cache"): result = Redis.get(key) if result: - print("Cache hit!!!") + logger.info("Cache hit!!!") with Bench("Loading results"): result = pickle.loads(result) else: - print("Cache miss!!!") + logger.info("Cache miss!!!") template_vars = heatmap.Heatmap(request.form, temp_uuid) template_vars.js_data = json.dumps(template_vars.js_data, @@ -366,10 +370,10 @@ def heatmap_page(): result = template_vars.__dict__ for item in template_vars.__dict__.keys(): - print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) + logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) - print("pickled result length:", len(pickled_result)) + logger.info("pickled result length:", len(pickled_result)) Redis.set(key, pickled_result) Redis.expire(key, 60*60) @@ -425,7 +429,7 @@ def marker_regression_page(): 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno' ) - print("Marker regression called with initial_start_vars:", initial_start_vars) + logger.info("Marker regression called with initial_start_vars:", initial_start_vars) start_vars = {} for key, value in initial_start_vars.iteritems(): if key in wanted or key.startswith(('value:')): @@ -433,21 +437,21 @@ def marker_regression_page(): version = "v3" key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True) - print("key is:", pf(key)) + logger.info("key is:", pf(key)) with Bench("Loading cache"): result = None # Just for testing #result = Redis.get(key) - #print("************************ Starting result *****************") - #print("result is [{}]: {}".format(type(result), result)) - #print("************************ Ending result ********************") + #logger.info("************************ Starting result *****************") + #logger.info("result is [{}]: {}".format(type(result), result)) + #logger.info("************************ Ending result ********************") if result: - print("Cache hit!!!") + logger.info("Cache hit!!!") with Bench("Loading results"): result = pickle.loads(result) else: - print("Cache miss!!!") + logger.info("Cache miss!!!") with Bench("Total time in MarkerRegression"): template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid) @@ -460,9 +464,9 @@ def marker_regression_page(): if result['pair_scan']: with Bench("Rendering template"): img_path = result['pair_scan_filename'] - print("img_path:", img_path) + logger.info("img_path:", img_path) initial_start_vars = request.form - print("initial_start_vars:", initial_start_vars) + logger.info("initial_start_vars:", initial_start_vars) imgfile = open(TEMPDIR + img_path, 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") @@ -471,12 +475,12 @@ def marker_regression_page(): rendered_template = render_template("pair_scan_results.html", **result) else: #for item in template_vars.__dict__.keys(): - # print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) + # logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__ pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) - print("pickled result length:", len(pickled_result)) + logger.info("pickled result length:", len(pickled_result)) Redis.set(key, pickled_result) Redis.expire(key, 1*60) @@ -486,9 +490,9 @@ def marker_regression_page(): # with Bench("Rendering template"): # if result['pair_scan'] == True: # img_path = result['pair_scan_filename'] - # print("img_path:", img_path) + # logger.info("img_path:", img_path) # initial_start_vars = request.form - # print("initial_start_vars:", initial_start_vars) + # logger.info("initial_start_vars:", initial_start_vars) # imgfile = open(TEMPDIR + '/' + img_path, 'rb') # imgdata = imgfile.read() # imgB64 = imgdata.encode("base64") @@ -504,7 +508,7 @@ def marker_regression_page(): @app.route("/export", methods = ('POST',)) def export(): - print("request.form:", request.form) + logger.info("request.form:", request.form) svg_xml = request.form.get("data", "Invalid data") filename = request.form.get("filename", "manhattan_plot_snp") response = Response(svg_xml, mimetype="image/svg+xml") @@ -514,9 +518,9 @@ def export(): @app.route("/export_pdf", methods = ('POST',)) def export_pdf(): import cairosvg - print("request.form:", request.form) + logger.info("request.form:", request.form) svg_xml = request.form.get("data", "Invalid data") - print("svg_xml:", svg_xml) + logger.info("svg_xml:", svg_xml) filename = request.form.get("filename", "interval_map_pdf") filepath = GENERATED_IMAGE_DIR+filename pdf_file = cairosvg.svg2pdf(bytestring=svg_xml) @@ -526,14 +530,14 @@ def export_pdf(): @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): - print("In corr_compute, request.form is:", pf(request.form)) + logger.info("In corr_compute, request.form is:", pf(request.form)) #fd = webqtlFormData.webqtlFormData(request.form) template_vars = show_corr_results.CorrelationResults(request.form) return render_template("correlation_page.html", **template_vars.__dict__) @app.route("/corr_matrix", methods=('POST',)) def corr_matrix_page(): - print("In corr_matrix, request.form is:", pf(request.form)) + logger.info("In corr_matrix, request.form is:", pf(request.form)) start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] @@ -559,7 +563,7 @@ def corr_scatter_plot_page(): # Todo: Can we simplify this? -Sam def sharing_info_page(): """Info page displayed when the user clicks the "Info" button next to the dataset selection""" - print("In sharing_info_page") + logger.info("In sharing_info_page") fd = webqtlFormData.webqtlFormData(request.args) template_vars = SharingInfoPage.SharingInfoPage(fd) return template_vars @@ -570,12 +574,6 @@ def get_temp_data(): temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) - - -################################################################################################### - - - ########################################################################## def json_default_handler(obj): @@ -590,7 +588,7 @@ def json_default_handler(obj): if hasattr(obj, '__dict__'): return obj.__dict__ #elif type(obj) == "Dataset": - # print("Not going to serialize Dataset") + # logger.info("Not going to serialize Dataset") # return None else: raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % ( diff --git a/wqflask/wqflask/wgcna/__init__.py b/wqflask/wqflask/wgcna/__init__.py index e69de29b..e69de29b 100755..100644 --- a/wqflask/wqflask/wgcna/__init__.py +++ b/wqflask/wqflask/wgcna/__init__.py |
