diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 7 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 78 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 133 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression.html | 51 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_mapping_tools.html | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 63 |
9 files changed, 160 insertions, 215 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 612b9209..36d4acaf 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -16,11 +16,11 @@ # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # -# +#we # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import print_function, division +from __future__ import absolute_import, print_function, division import os from flask import Flask, g @@ -29,7 +29,7 @@ from htmlgen import HTMLgen2 as HT import reaper -import webqtlConfig +from base import webqtlConfig from base import species from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil @@ -50,6 +50,7 @@ def create_dataset(dataset_name): WHERE DBList.Name = '%s' and DBType.Id = DBList.DBTypeId """ % (escape(dataset_name)) + print("query is: ", pf(query)) dataset_type = g.db.execute(query).fetchone().Name #dataset_type = cursor.fetchone()[0] diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 8c9e3b10..241bf2ab 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -1,12 +1,12 @@ -from __future__ import division, print_function +from __future__ import absolute_import, division, print_function import string from htmlgen import HTMLgen2 as HT -import webqtlConfig -from webqtlCaseData import webqtlCaseData -from data_set import create_dataset +from base import webqtlConfig +from base.webqtlCaseData import webqtlCaseData +from base.data_set import create_dataset from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil @@ -24,76 +24,28 @@ class GeneralTrait: def __init__(self, **kw): print("in GeneralTrait") - self.dataset = kw.get('dataset', None) # database name - self.name = kw.get('name', None) # Trait ID, ProbeSet ID, Published ID, etc. - self.cellid = kw.get('cellid', None) + self.dataset = kw.get('dataset') # database name + self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. + self.cellid = kw.get('cellid') self.identification = kw.get('identification', 'un-named trait') - #self.group = kw.get('group', None) self.haveinfo = kw.get('haveinfo', False) - self.sequence = kw.get('sequence', None) # Blat sequence, available for ProbeSet + self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet self.data = kw.get('data', {}) - + if kw.get('fullname'): name2 = value.split("::") if len(name2) == 2: self.dataset, self.name = name2 + # self.cellid is set to None above elif len(name2) == 3: self.dataset, self.name, self.cellid = name2 - - #if self.dataset and isinstance(self.dataset, basestring): - self.dataset = create_dataset(self.dataset) - print("self.dataset is:", self.dataset, type(self.dataset)) - #if self.dataset: - - #self.dataset.get_group() + self.dataset = create_dataset(self.dataset) - #if self.dataset.type == "Temp": - # self.cursor.execute(''' - # SELECT - # InbredSet.Name - # FROM - # InbredSet, Temp - # WHERE - # Temp.InbredSetId = InbredSet.Id AND - # Temp.Name = "%s" - # ''', self.name) - # self.group = self.cursor.fetchone()[0] - #else: - # self.group = self.dataset.get_group() - - #print("trinity, self.group is:", self.group) - - # - # In ProbeSet, there are maybe several annotations match one sequence - # so we need use sequence(BlatSeq) as the identification, when we update - # one annotation, we update the others who match the sequence also. - # - # Hongqiang Li, 3/3/2008 - # - - #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield. - # The variable self.sequence should be changed to self.BlatSeq - # It also should be changed in other places where it are used. - - #if self.dataset: - #if self.dataset.type == 'ProbeSet': - # print("Doing ProbeSet Query") - # query = ''' - # SELECT - # ProbeSet.BlatSeq - # FROM - # ProbeSet, ProbeSetFreeze, ProbeSetXRef - # WHERE - # ProbeSet.Id=ProbeSetXRef.ProbeSetId and - # ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and - # ProbeSet.Name = %s and - # ProbeSetFreeze.Name = %s - # ''', (self.name, self.dataset.name) - # print("query is:", query) - # self.sequence = g.db.execute(*query).fetchone()[0] - # #self.sequence = self.cursor.fetchone()[0] - # print("self.sequence is:", self.sequence) + # Todo: These two lines are necessary most of the time, but perhaps not all of the time + # So we could add a simple if statement to short-circuit this if necessary + self.retrieve_info() + self.retrieve_sample_data() def get_name(self): diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index fc45395c..a2eddfc6 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -63,7 +63,7 @@ class DoSearch(object): class MrnaAssaySearch(DoSearch): """A search within an mRNA expression dataset""" - DoSearch.search_types['ProbeSet'] = "ProbeSetSearch" + DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch" base_query = """SELECT ProbeSet.Name as TNAME, 0 as thistable, diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index c605cb58..807761a2 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -34,45 +34,26 @@ from pprint import pformat as pf class ShowTrait(object): - def __init__(self, args): - print("in ShowTrait, args are:", args) - #self.group = args.group - self.trait_id = args['trait_id'] + def __init__(self, kw): + print("in ShowTrait, kw are:", kw) + self.trait_id = kw['trait_id'] - self.dataset = create_dataset(args['dataset']) - - #self.dataset = create_dataset(args['dataset']) - self.cell_id = None + self.dataset = create_dataset(kw['dataset']) + + #self.cell_id = None - #assert self.openMysql(), "No database!" - #print("red3 fd.group:", fd.group) - this_trait = self.get_this_trait() + this_trait = GeneralTrait(dataset=self.dataset.name, + name=self.trait_id, + cellid=None) - #print("red4 fd.group:", fd.group) - ##read genotype file - #fd.group = this_trait.group - #print("[red5] fd.group is:", fd.group) self.dataset.group.read_genotype_file() - #fd.readGenotype() if not self.dataset.group.genotype: - self.read_data(include_f1=True) #incf1=1) + self.read_data(include_f1=True) - ## determine data editing page format - #variance_data_page = 0 - #if fd.formID == 'varianceChoice': - # variance_data_page = 1 - # - #if variance_data_page: - # fmID='dataEditing' - #else: - # if fd.enablevariance: - # fmID='pre_dataEditing' - # else: - # fmID='dataEditing' - + # Todo: Add back in the ones we actually need from below, as we discover we need them hddn = OrderedDict() @@ -111,55 +92,19 @@ class ShowTrait(object): # export_data = None # ) - #if fd.enablevariance: - # hddn['enablevariance']='ON' - #if fd.incparentsf1: - # hddn['incparentsf1']='ON' - #if this_trait: - # hddn['fullname'] = str(this_trait) - # try: - # hddn['normalPlotTitle'] = this_trait.symbol - # hddn['normalPlotTitle'] += ": " - # hddn['normalPlotTitle'] += this_trait.name - # except: - # hddn['normalPlotTitle'] = str(this_trait.name) - # hddn['fromDataEditingPage'] = 1 # if this_trait.dataset and this_trait.dataset.type and this_trait.dataset.type == 'ProbeSet': - # hddn['trait_type'] = this_trait.dataset.type - # if this_trait.cellid: - # hddn['cellid'] = this_trait.cellid - # else: # self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" % # this_trait.mysqlid) # heritability = self.cursor.fetchone() - # hddn['heritability'] = heritability - # - # hddn['attribute_names'] = "" - # + #hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor, # groupName=fd.group) - # - #if fd.identification: - # hddn['identification'] = fd.identification - #else: - # hddn['identification'] = "Un-named trait" #If no identification, set identification to un-named - - self.dispTraitInformation(args, "", hddn, this_trait) #Display trait information + function buttons - if this_trait == None: - this_trait = webqtlTrait(data=args['allTraitData'], dataset=None) + self.dispTraitInformation(kw, "", hddn, this_trait) #Display trait information + function buttons - ## Variance submit page only - #if fd.enablevariance and not variance_data_page: - # pass - # #title2Body.append("Click the next button to go to the variance submission form.", - # # HT.Center(next,reset)) - #else: - # pass - # # We'll get this part working later - # print("Calling dispBasicStatistics") - # self.dispBasicStatistics(fd, this_trait) + #if this_trait == None: + # this_trait = webqtlTrait(data=kw['allTraitData'], dataset=None) self.build_correlation_tools(this_trait) @@ -168,9 +113,6 @@ class ShowTrait(object): if self.dataset.group.allsamples: hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ') - #if args['varianceDispName'] != 'Variance': - # hddn['isSE'] = "yes" - # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self self.this_trait = this_trait self.hddn = hddn @@ -188,34 +130,23 @@ class ShowTrait(object): self.js_data = js_data - def get_this_trait(self): - # When is traitInfos used? - #if traitInfos: - # database, ProbeSetID, CellID = traitInfos - #else: - #dataset = self.fd['dataset'] - #trait_id = self.fd['trait_id'] - #cell_id = self.fd.get('CellID') - - this_trait = GeneralTrait(dataset=self.dataset.name, - name=self.trait_id, - cellid=self.cell_id) - - ##identification, etc. - self.identification = '%s : %s' % (self.dataset.shortname, self.trait_id) - this_trait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\ - &ProbeSetID=%s&group=%s&parentsf1=on' %(self.dataset, self.trait_id, self.dataset.group.name) - - if self.cell_id: - self.identification = '%s/%s'%(self.identification, self.cell_id) - this_trait.returnURL = '%s&CellID=%s' % (this_trait.returnURL, self.cell_id) - - print("yellow1:", self.dataset.group) - this_trait.retrieve_info() - print("yellow2:", self.dataset.group) - this_trait.retrieve_sample_data() - print("yellow3:", self.dataset.group) - return this_trait + #def get_this_trait(self): + # this_trait = GeneralTrait(dataset=self.dataset.name, + # name=self.trait_id, + # cellid=self.cell_id) + # + # ###identification, etc. + # #self.identification = '%s : %s' % (self.dataset.shortname, self.trait_id) + # #this_trait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\ + # # &ProbeSetID=%s&group=%s&parentsf1=on' %(self.dataset, self.trait_id, self.dataset.group.name) + # # + # #if self.cell_id: + # # self.identification = '%s/%s'%(self.identification, self.cell_id) + # # this_trait.returnURL = '%s&CellID=%s' % (this_trait.returnURL, self.cell_id) + # + # this_trait.retrieve_info() + # this_trait.retrieve_sample_data() + # return this_trait def read_data(self, include_f1=False): diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee index b1f5b186..d0fc869d 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee @@ -1,11 +1,17 @@ $ -> - run_marker_regression = -> - console.log("In marker regression") - url = "/marker_regression" + submit_special = -> + # Add submit_special class plus a data-url field to any button + # And it will submit to that url + # No js changes necessary + console.log("In submit_special") + console.log("this is:", this) + console.log("$(this) is:", $(this)) + url = $(this).data("url") + console.log("url is:", url) $("#trait_data_form").attr("action", url); $("#trait_data_form").submit() - $("#do_marker_regression").click(run_marker_regression) + $(".submit_special").click(submit_special) composite_mapping_fields = -> @@ -14,10 +20,10 @@ $ -> $("#use_composite_choice").change(composite_mapping_fields) + #### Todo: Redo below so its like submit_special and requires no js hardcoding toggle_enable_disable = (elem) -> - $(elem).prop("disabled", !$(elem.prop("disabled"))) + $(elem).prop("disabled", !$(elem).prop("disabled")) - $("#choose_closet_control").change(-> toggle_enable_disable("#control_locus") ) diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index c8328498..c6766288 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -2,21 +2,24 @@ (function() { $(function() { - var composite_mapping_fields, run_marker_regression, toggle_enable_disable; - run_marker_regression = function() { + var composite_mapping_fields, submit_special, toggle_enable_disable; + submit_special = function() { var url; - console.log("In marker regression"); - url = "/marker_regression"; + console.log("In submit_special"); + console.log("this is:", this); + console.log("$(this) is:", $(this)); + url = $(this).data("url"); + console.log("url is:", url); $("#trait_data_form").attr("action", url); return $("#trait_data_form").submit(); }; - $("#do_marker_regression").click(run_marker_regression); + $(".submit_special").click(submit_special); composite_mapping_fields = function() { return $(".composite_fields").toggle(); }; $("#use_composite_choice").change(composite_mapping_fields); toggle_enable_disable = function(elem) { - return $(elem).prop("disabled", !$(elem.prop("disabled"))); + return $(elem).prop("disabled", !$(elem).prop("disabled")); }; $("#choose_closet_control").change(function() { return toggle_enable_disable("#control_locus"); diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html new file mode 100644 index 00000000..db2de604 --- /dev/null +++ b/wqflask/wqflask/templates/marker_regression.html @@ -0,0 +1,51 @@ +{% extends "base.html" %} +{% block title %}Marker Regression{% endblock %} +{% block content %} <!-- Start of body --> + + <header class="jumbotron subhead" id="overview"> + <div class="container"> + <h1>Marker Regression</h1> + <p class="lead"> + {{ this_trait.name }}: {{ this_trait.description_fmt }} + </p> + </div> + </header> + + <dl class="dl-horizontal"> + <dt>Aliases</dt> + <dd>{{ this_trait.alias_fmt }}</dd> + + <dt>Location</dt> + <dd>{{ this_trait.location_fmt }}</dd> + + <dt>Database</dt> + <dd> + <a href="{{ url_for('static', filename='/dbdoc/' + dataset.fullname + '.html') }}" target="_blank"> + {{ dataset.name }} + </a> + </dd> + + {% if this_trait.probe_set_specificity %} + <dt> + <a href="/blatInfo.html" target="_blank" + title="Values higher than 2 for the specificity are good"> + BLAT Specifity + </a> + </dt> + <dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd> + {% endif %} + {% if this_trait.probe_set_blat_score %} + <dt>BLAT Score</dt> + <dd>{{ "%i" % (this_trait.probe_set_blat_score) }}</dd> + {% endif %} + </dl> + + <!-- End of body --> + +{% endblock %} + +{% block js %} + <script> + js_data = {{ js_data | safe }} + </script> +{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 8436703d..72b152fa 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -101,7 +101,8 @@ <div class="control-group"> <div class="controls"> - <button id="do_interval_mapping" class="btn btn-inverse" + <button class="btn btn-inverse submit_special" + data-url="/interval_mapping" title="Compute Interval Mapping"> <i class="icon-ok-circle icon-white"></i> Compute </button> @@ -135,8 +136,9 @@ <div class="control-group"> <div class="controls"> - <button id="do_marker_regression" - class="btn btn-inverse" title="Compute Marker Regression"> + <button class="btn btn-inverse submit_special" + data-url="/marker_regression" + title="Compute Marker Regression"> <i class="icon-ok-circle icon-white"></i> Compute </button> </div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 503b0972..f6c0dfb0 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -18,6 +18,7 @@ from flask import render_template, request, make_response, Response, Flask, g, c from wqflask import search_results from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data +from wqflask.marker_regression import marker_regression from wqflask.correlation import CorrelationPage from wqflask.dataSharing import SharingInfo, SharingInfoPage @@ -89,27 +90,6 @@ def whats_new_page(): print("\nnews_item is: %s\n" % (news_item)) return render_template("whats_new.html", news_items=news_items) - -@app.route("/show_trait") -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))) - template_vars = show_trait.ShowTrait(request.args) - - print("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__)) - return render_template("show_trait.html", **template_vars.__dict__) - @app.route('/export_trait_csv', methods=('POST',)) def export_trait_excel(): """Excel file consisting of the sample data from the trait data and analysis page""" @@ -150,33 +130,52 @@ def export_trait_csv(): mimetype='text/csv', headers={"Content-Disposition":"attachment;filename=test.csv"}) +@app.route("/show_trait") +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))) + template_vars = show_trait.ShowTrait(request.args) + print("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__)) + return render_template("show_trait.html", **template_vars.__dict__) + +@app.route("/marker_regression", methods=('POST',)) +def marker_regression_page(): + template_vars = marker_regression.MarkerRegression(request.form) + #print("js_data before dump:", template_vars.js_data) + #template_vars.js_data = json.dumps(template_vars.js_data, + # default=json_default_handler, + # indent=" ") + #print("js_data after dump:", template_vars.js_data) + print("marker_regression template_vars:", pf(template_vars.__dict__)) + return render_template("marker_regression.html", **template_vars.__dict__) @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): - #print("In corr_compute, request.args is:", pf(request.form)) + print("In corr_compute, request.args is:", pf(request.form)) fd = webqtlFormData.webqtlFormData(request.form) - print("Have fd") template_vars = CorrelationPage.CorrelationPage(fd) - print("Made it to rendering") return render_template("correlation_page.html", **template_vars.__dict__) @app.route("/int_mapping", methods=('POST',)) def interval_mapping_page(): - fd = webqtlFormData.webqtlFormData(request.form) - print("Have fd") - template_vars = CorrelationPage.CorrelationPage(fd) - print("Made it to rendering") - return render_template("correlation_page.html", **template_vars.__dict__) - + template_vars = interval_mapping.IntervalMapping(request.args) + return render_template("interval_mapping.html", **template_vars.__dict__) # 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") fd = webqtlFormData.webqtlFormData(request.args) - print("2Have fd") template_vars = SharingInfoPage.SharingInfoPage(fd) - print("2 Made it to rendering") return template_vars |