diff options
| -rw-r--r-- | misc/notes.txt | 6 | ||||
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 72 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/CorrelationPage.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee | 28 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/trait_data_and_analysis.html | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 6 |
7 files changed, 83 insertions, 70 deletions
diff --git a/misc/notes.txt b/misc/notes.txt index be023c1d..9d31fb5d 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -36,6 +36,12 @@ coffee --help (for information about setting options) =========================================== +Unset ASKPASS when trying to git push + +unset SSH_ASKPASS + +=========================================== + Python stuff: Classes should always inherit "object" \ No newline at end of file diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index 177c72a2..9f58d437 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -63,7 +63,7 @@ class webqtlFormData: for item in start_vars: self.__dict__[item] = start_vars[item] - #print(" Now self.dict is:", pf(self.__dict__)) + print(" Now self.dict is:", pf(self.__dict__)) #Todo: This can't be good below...rework try: @@ -216,6 +216,13 @@ class webqtlFormData: #### Todo: Rewrite below when we get to someone submitting their own trait ##### + def to_float(item): + try: + return float(item) + except ValueError: + return None + + print("bottle strainlist is:", strainlist) if traitfiledata: tt = traitfiledata.split() values = map(webqtlUtil.StringAsFloat, tt) @@ -223,12 +230,17 @@ class webqtlFormData: tt = traitpastedata.split() values = map(webqtlUtil.StringAsFloat, tt) else: - values = map(self.FormDataAsFloat, strainlist) + print("mapping formdataasfloat") + #values = map(self.FormDataAsFloat, strainlist) + values = [to_float(getattr(self, key)) for key in strainlist] + print("rocket values is:", values) + if len(values) < len(strainlist): values += [None] * (len(strainlist) - len(values)) elif len(values) > len(strainlist): values = values[:len(strainlist)] + print("now values is:", values) if variancefiledata: @@ -257,40 +269,48 @@ class webqtlFormData: self.allTraitData = {} for i, _strain in enumerate(strainlist): if values[i] != None: - self.allTraitData[_strain] = webqtlCaseData(values[i], variances[i], nstrains[i]) + self.allTraitData[_strain] = webqtlCaseData( + _strain, values[i], variances[i], nstrains[i]) + print("allTraitData is:", pf(self.allTraitData)) - def informativeStrains(self, strainlst=[], incVars = 0): - '''if readData was called, use this to output the informative strains - (strain with values)''' - if not strainlst: - strainlst = self.strainlist + def informativeStrains(self, strainlist=None, include_variances = None): + '''if readData was called, use this to output informative strains (strain with values)''' + + if not strainlist: + strainlist = self.strainlist + strains = [] - vals = [] - vars = [] - for _strain in strainlst: - if self.allTraitData.has_key(_strain): - _val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var + values = [] + variances = [] + + #print("self.allTraitData is:", pf(self.allTraitData)) + + for strain in strainlist: + if strain in self.allTraitData: + _val, _var = self.allTraitData[strain].value, self.allTraitData[strain].variance if _val != None: - if incVars: + if include_variances: if _var != None: - strains.append(_strain) - vals.append(_val) - vars.append(_var) + strains.append(strain) + values.append(_val) + variances.append(_var) else: - strains.append(_strain) - vals.append(_val) - vars.append(None) - return strains, vals, vars, len(strains) + strains.append(strain) + values.append(_val) + variances.append(None) + + return strains, values, variances, len(strains) - def FormDataAsFloat(self, key): - try: - return float(self.formdata.getfirst(key)) - except: - return None + #def FormDataAsFloat(self, key): + # + # #try: + # # return float(self.key) + # #except: + # # return None def FormVarianceAsFloat(self, key): diff --git a/wqflask/wqflask/correlation/CorrelationPage.py b/wqflask/wqflask/correlation/CorrelationPage.py index 62e4c4ab..0af5297a 100644 --- a/wqflask/wqflask/correlation/CorrelationPage.py +++ b/wqflask/wqflask/correlation/CorrelationPage.py @@ -157,7 +157,7 @@ def get_correlation_method_key(form_data): #XZ, 09/28/2008: if user select "4", then display 1, 3 and 4. #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5. - method = form_data.formdata.getvalue("method") + method = form_data.method if method not in ["1", "2", "3" ,"4", "5"]: return "1" @@ -166,7 +166,7 @@ def get_correlation_method_key(form_data): def get_custom_trait(form_data, cursor): """Pulls the custom trait, if it exists, out of the form data""" - trait_name = form_data.formdata.getvalue('fullname') + trait_name = form_data.fullname if trait_name: trait = webqtlTrait(fullname=trait_name, cursor=cursor) @@ -178,7 +178,7 @@ def get_custom_trait(form_data, cursor): #XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form. def get_sample_data(fd): - print("fd is:", pf(fd.__dict__)) + #print("fd is:", pf(fd.__dict__)) if fd.allstrainlist: mdpchoice = fd.MDPChoice #XZ, in HTML source code, it is "BXD Only", "BXH Only", and so on @@ -277,10 +277,10 @@ class CorrelationPage(templatePage): return templatePage.error(heading = heading, detail = [message], error=error) def __init__(self, fd): - print("in CorrelationPage __init__ fd is:", pf(fd.__dict__)) + #print("in CorrelationPage __init__ fd is:", pf(fd.__dict__)) # Call the superclass constructor templatePage.__init__(self, fd) - print("in CorrelationPage __init__ now fd is:", pf(fd.__dict__)) + #print("in CorrelationPage __init__ now fd is:", pf(fd.__dict__)) # Connect to the database if not self.openMysql(): return @@ -290,6 +290,7 @@ class CorrelationPage(templatePage): fd.readGenotype() sample_list = get_sample_data(fd) + print("sample_list is", pf(sample_list)) # Whether the user chose BXD Only, Non-BXD Only, or All Strains # (replace BXD with whatever the group/inbredset name is) @@ -321,17 +322,18 @@ class CorrelationPage(templatePage): #XZ, 09/18/2008: filter out the strains that have no value. self.sample_names, vals, vars, N = fd.informativeStrains(sample_list) - #CF - If less than a minimum number of strains/cases in common, don't calculate anything + print("samplenames is:", pf(self.sample_names)) + #CF - If less than a minimum number of strains/cases in common, don't calculate anything if len(self.sample_names) < self.corrMinInformative: detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corrMinInformative, fd.RISet)] self.error(heading=None, detail=detail) - self.method = get_correlation_method_key(fd) + self.method = fd.method correlation_method = self.CORRELATION_METHODS[self.method] rankOrder = self.RANK_ORDERS[self.method] - # CF - Number of results returned + # CF - Number of results returned self.returnNumber = int(fd.criteria) self.record_count = 0 diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee index 7bfa6d01..5c153ccb 100644 --- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee +++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee @@ -166,20 +166,20 @@ $ -> $('select[name=corr_method]').change(on_corr_method_change) - on_corr_submit = -> - console.log("in beginning of on_corr_submit") - values = $('#trait_data_form').serialize() - console.log("in on_corr_submit, values are:", values) - - params = $.param(values) - window.location.href = "/corr_compute?" + params - - #$.ajax "/corr_compute", - # type: 'GET' - # dataType: 'html' - # data: values - - $('#corr_compute').click(on_corr_submit) + #on_corr_submit = -> + # console.log("in beginning of on_corr_submit") + # values = $('#trait_data_form').serialize() + # console.log("in on_corr_submit, values are:", values) + # + # params = $.param(values) + # window.location.href = "/corr_compute?" + params + # + # #$.ajax "/corr_compute", + # # type: 'GET' + # # dataType: 'html' + # # data: values + # + #$('#corr_compute').click(on_corr_submit) ### End Calculate Correlations Code diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js index e1f870d9..55acbada 100644 --- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js +++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js @@ -10,7 +10,7 @@ }; $(function() { - var edit_data_change, hide_tabs, make_table, on_corr_method_change, on_corr_submit, process_id, show_hide_outliers, stats_mdp_change, update_stat_values; + var edit_data_change, hide_tabs, make_table, on_corr_method_change, process_id, show_hide_outliers, stats_mdp_change, update_stat_values; hide_tabs = function(start) { var x, _i, _results; _results = []; @@ -199,15 +199,6 @@ return $('#' + corr_method + "_r_desc").show().effect("highlight"); }; $('select[name=corr_method]').change(on_corr_method_change); - on_corr_submit = function() { - var params, values; - console.log("in beginning of on_corr_submit"); - values = $('#trait_data_form').serialize(); - console.log("in on_corr_submit, values are:", values); - params = $.param(values); - return window.location.href = "/corr_compute?" + params; - }; - $('#corr_compute').click(on_corr_submit); /* End Calculate Correlations Code */ diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index a5d0e05c..c25db7c4 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -8,7 +8,7 @@ <table width="100%" cellspacing="0" cellpadding="5"> <tr> <td valign="top" width="100%" bgcolor="#FAFAFA"> - <form method="post" action="/webqtl/main.py" name="dataInput" id="trait_data_form"> + <form method="post" action="/corr_compute" name="dataInput" id="trait_data_form"> {# <input type="hidden" name="isSE" value="yes"> <input type="hidden" name="permCheck"> <input type="hidden" name="otherStrainVals" value="_"> @@ -683,13 +683,7 @@ <p class="sectionheader" id="title3" style="border-radius: 5px;"> Calculate Correlations</p> - <p id="sectionbody3"></p><script language="Javascript" type="text/javascript"> -<!-- - - $(function() { $("#corr_tabs").tabs(); }); - - //--> - </script> + <p id="sectionbody3"></p> <table class="target4" cellpadding="0" cellspacing="0" width="100%"> <tr> @@ -771,7 +765,7 @@ "sample_method" value="spearman"><br> <br> - <input type="button" name="corr_compute" id="corr_compute" class="button" value="Compute"><br><br> + <input type="submit" name="corr_compute" id="corr_compute" class="button" value="Compute"><br><br> <span id="sample_r_desc" class="correlation_desc fs12"> The <a href="/correlationAnnotation.html#sample_r" target="_blank">Sample Correlation</a> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 114ec458..677c7f43 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -75,10 +75,10 @@ def showDatabaseBXD(): print("showDatabaseBXD template_vars:", pf(template_vars.__dict__)) return render_template("trait_data_and_analysis.html", **template_vars.__dict__) -@app.route("/corr_compute") +@app.route("/corr_compute", methods=('POST',)) def corr_compute(): - print("In corr_compute") - fd = webqtlFormData.webqtlFormData(request.args) + #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") |