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authorBonfaceKilz2021-04-19 14:43:16 +0300
committerBonfaceKilz2021-04-23 17:42:26 +0300
commitb0ccb12682fed83bf72d22ff42f1f442a8e6176e (patch)
treed0a9bb84afa7fe6c72adf5b2a0ef46e7c77483a3 /wqflask
parenta04d089e7db0a924f7de0eb38c7dc0d043b1d75b (diff)
downloadgenenetwork2-b0ccb12682fed83bf72d22ff42f1f442a8e6176e.tar.gz
Remove stale comments
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/data_set.py11
-rw-r--r--wqflask/utility/helper_functions.py4
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py72
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html10
-rw-r--r--wqflask/wqflask/templates/submit_trait.html12
-rw-r--r--wqflask/wqflask/views.py23
6 files changed, 46 insertions, 86 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 178234fe..cc5a428c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -262,8 +262,6 @@ class Markers(object):
elif isinstance(p_values, dict):
filtered_markers = []
for marker in self.markers:
- #logger.debug("marker[name]", marker['name'])
- #logger.debug("p_values:", p_values)
if marker['name'] in p_values:
#logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
@@ -276,10 +274,6 @@ class Markers(object):
marker['lrs_value'] = - \
math.log10(marker['p_value']) * 4.61
filtered_markers.append(marker)
- # else:
- #logger.debug("marker {} NOT in p_values".format(i))
- # self.markers.remove(marker)
- #del self.markers[i]
self.markers = filtered_markers
@@ -306,7 +300,6 @@ class HumanMarkers(Markers):
marker['Mb'] = float(splat[3]) / 1000000
self.markers.append(marker)
- #logger.debug("markers is: ", pf(self.markers))
def add_pvalues(self, p_values):
super(HumanMarkers, self).add_pvalues(p_values)
@@ -520,7 +513,6 @@ def datasets(group_name, this_group=None):
break
if tissue_already_exists:
- #logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(dict(tissue=tissue_name,
@@ -735,9 +727,6 @@ class PhenotypeDataSet(DataSet):
DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
def setup(self):
-
- #logger.debug("IS A PHENOTYPEDATASET")
-
# Fields in the database table
self.search_fields = ['Phenotype.Post_publication_description',
'Phenotype.Pre_publication_description',
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 7eb7f013..15d5b3ab 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -10,7 +10,6 @@ import logging
logger = logging.getLogger(__name__ )
def get_species_dataset_trait(self, start_vars):
- #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
if "temp_trait" in list(start_vars.keys()):
if start_vars['temp_trait'] == "True":
self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group'])
@@ -27,9 +26,6 @@ def get_species_dataset_trait(self, start_vars):
get_qtl_info=True)
logger.debug("After creating trait")
- #if read_genotype:
- #self.dataset.group.read_genotype_file()
- #self.genotype = self.dataset.group.genotype
def get_trait_db_obs(self, trait_db_list):
if isinstance(trait_db_list, str):
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 6892f02b..ed55d473 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -138,17 +138,12 @@ class ShowTrait(object):
self.ncbi_summary = get_ncbi_summary(self.this_trait)
- #Get nearest marker for composite mapping
+ # Get nearest marker for composite mapping
if not self.temp_trait:
if check_if_attr_exists(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]
- #self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
else:
self.nearest_marker = ""
- #self.nearest_marker1 = ""
- #self.nearest_marker2 = ""
-
self.make_sample_lists()
@@ -168,16 +163,19 @@ class ShowTrait(object):
categorical_var_list = []
if not self.temp_trait:
- categorical_var_list = get_categorical_variables(self.this_trait, self.sample_groups[0]) #ZS: Only using first samplelist, since I think mapping only uses those samples
+ # ZS: Only using first samplelist, since I think mapping only uses those samples
+ categorical_var_list = get_categorical_variables(self.this_trait, self.sample_groups[0])
- #ZS: Get list of chromosomes to select for mapping
+ # ZS: Get list of chromosomes to select for mapping
self.chr_list = [["All", -1]]
for i, this_chr in enumerate(self.dataset.species.chromosomes.chromosomes):
self.chr_list.append([self.dataset.species.chromosomes.chromosomes[this_chr].name, i])
self.genofiles = self.dataset.group.get_genofiles()
- if "QTLReaper" or "R/qtl" in dataset.group.mapping_names: #ZS: No need to grab scales from .geno file unless it's using a mapping method that reads .geno files
+ # ZS: No need to grab scales from .geno file unless it's using
+ # a mapping method that reads .geno files
+ if "QTLReaper" or "R/qtl" in dataset.group.mapping_names:
if self.genofiles:
self.scales_in_geno = get_genotype_scales(self.genofiles)
else:
@@ -187,10 +185,15 @@ class ShowTrait(object):
self.has_num_cases = has_num_cases(self.this_trait)
- #ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width
+ # ZS: Needed to know whether to display bar chart + get max
+ # sample name length in order to set table column width
self.num_values = 0
- self.binary = "true" #ZS: So it knows whether to display the Binary R/qtl mapping method, which doesn't work unless all values are 0 or 1
- self.negative_vals_exist = "false" #ZS: Since we don't want to show log2 transform option for situations where it doesn't make sense
+ # ZS: So it knows whether to display the Binary R/qtl mapping
+ # method, which doesn't work unless all values are 0 or 1
+ self.binary = "true"
+ # ZS: Since we don't want to show log2 transform option for
+ # situations where it doesn't make sense
+ self.negative_vals_exist = "false"
max_samplename_width = 1
for group in self.sample_groups:
for sample in group.sample_list:
@@ -203,7 +206,8 @@ class ShowTrait(object):
if sample.value < 0:
self.negative_vals_exist = "true"
- #ZS: Check whether any attributes have few enough distinct values to show the "Block samples by group" option
+ # ZS: Check whether any attributes have few enough distinct
+ # values to show the "Block samples by group" option
self.categorical_attr_exists = "false"
for attribute in self.sample_groups[0].attributes:
if len(self.sample_groups[0].attributes[attribute].distinct_values) <= 10:
@@ -258,7 +262,6 @@ class ShowTrait(object):
if not self.temp_trait:
if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
hddn['control_marker'] = self.nearest_marker
- #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
hddn['do_control'] = False
hddn['maf'] = 0.05
hddn['mapping_scale'] = "physic"
@@ -268,7 +271,8 @@ class ShowTrait(object):
if len(self.scales_in_geno) < 2:
hddn['mapping_scale'] = self.scales_in_geno[list(self.scales_in_geno.keys())[0]][0][0]
- # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
+ # We'll need access to this_trait and hddn in the Jinja2
+ # Template, so we put it inside self
self.hddn = hddn
js_data = dict(trait_id = self.trait_id,
@@ -294,7 +298,8 @@ class ShowTrait(object):
self.js_data = js_data
def get_external_links(self):
- #ZS: There's some weirdness here because some fields don't exist while others are empty strings
+ # ZS: There's some weirdness here because some fields don't
+ # exist while others are empty strings
self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if check_if_attr_exists(self.this_trait, 'pubmed_id') else None
self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if check_if_attr_exists(self.this_trait, 'geneid') else None
self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if check_if_attr_exists(self.this_trait, 'omim') else None
@@ -320,7 +325,6 @@ class ShowTrait(object):
self.panther_link = webqtlConfig.PANTHER_URL % self.this_trait.symbol
self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol
self.protein_atlas_link = webqtlConfig.PROTEIN_ATLAS_URL % self.this_trait.symbol
- #self.open_targets_link = webqtlConfig.OPEN_TARGETS_URL % self.this_trait.symbol
if self.dataset.group.species == "mouse" or self.dataset.group.species == "human":
self.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize())
@@ -429,7 +433,9 @@ class ShowTrait(object):
all_samples_ordered.append(sample)
other_sample_names.append(sample)
- #ZS: CFW is here because the .geno file doesn't properly contain its full list of samples. This should probably be fixed.
+ # ZS: CFW is here because the .geno file doesn't properly
+ # contain its full list of samples. This should probably
+ # be fixed.
if self.dataset.group.species == "human" or (set(primary_sample_names) == set(parent_f1_samples)) or self.dataset.group.name == "CFW":
primary_sample_names += other_sample_names
other_sample_names = []
@@ -445,7 +451,8 @@ class ShowTrait(object):
sample_group_type='primary',
header=primary_header)
- #if other_sample_names and self.dataset.group.species != "human" and self.dataset.group.name != "CFW":
+ # if other_sample_names and self.dataset.group.species !=
+ # "human" and self.dataset.group.name != "CFW":
if len(other_sample_names) > 0:
other_sample_names.sort() #Sort other samples
if parent_f1_samples:
@@ -539,7 +546,8 @@ def get_z_scores(sample_groups):
def get_nearest_marker(this_trait, this_db):
this_chr = this_trait.locus_chr
this_mb = this_trait.locus_mb
- #One option is to take flanking markers, another is to take the two (or one) closest
+ # One option is to take flanking markers, another is to take the
+ # two (or one) closest
query = """SELECT Geno.Name
FROM Geno, GenoXRef, GenoFreeze
WHERE Geno.Chr = '{}' AND
@@ -552,7 +560,6 @@ def get_nearest_marker(this_trait, this_db):
if result == []:
return ""
- #return "", ""
else:
return result[0][0]
@@ -617,7 +624,8 @@ def check_if_attr_exists(the_trait, id_type):
def get_ncbi_summary(this_trait):
if check_if_attr_exists(this_trait, 'geneid'):
- #ZS: Need to switch this try/except to something that checks the output later
+ # ZS: Need to switch this try/except to something that checks
+ # the output later
try:
response = requests.get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=%s&retmode=json" % this_trait.geneid)
summary = json.loads(response.content)['result'][this_trait.geneid]['summary']
@@ -661,8 +669,8 @@ def get_genotype_scales(genofiles):
def get_scales_from_genofile(file_location):
geno_path = locate_ignore_error(file_location, 'genotype')
-
- if not geno_path: #ZS: This is just to allow the code to run when
+ # ZS: This is just to allow the code to run when
+ if not geno_path:
return [["physic", "Mb"]]
cm_and_mb_cols_exist = True
cm_column = None
@@ -670,7 +678,9 @@ def get_scales_from_genofile(file_location):
with open(geno_path, "r") as geno_fh:
for i, line in enumerate(geno_fh):
if line[0] == "#" or line[0] == "@":
- if "@scale" in line: #ZS: If the scale is made explicit in the metadata, use that
+ # ZS: If the scale is made explicit in the metadata,
+ # use that
+ if "@scale" in line:
scale = line.split(":")[1].strip()
if scale == "morgan":
return [["morgan", "cM"]]
@@ -690,12 +700,16 @@ def get_scales_from_genofile(file_location):
mb_column = 3
break
- #ZS: This attempts to check whether the cM and Mb columns are 'real', since some .geno files have one column be a copy of the other column, or have one column that is all 0s
+ # ZS: This attempts to check whether the cM and Mb columns are
+ # 'real', since some .geno files have one column be a copy of
+ # the other column, or have one column that is all 0s
cm_all_zero = True
mb_all_zero = True
cm_mb_all_equal = True
for i, line in enumerate(geno_fh):
- if first_marker_line <= i < first_marker_line + 10: #ZS: I'm assuming there won't be more than 10 markers where the position is listed as 0
+ # ZS: I'm assuming there won't be more than 10 markers
+ # where the position is listed as 0
+ if first_marker_line <= i < first_marker_line + 10:
if cm_column:
cm_val = line.split("\t")[cm_column].strip()
if cm_val != "0":
@@ -711,8 +725,8 @@ def get_scales_from_genofile(file_location):
if i > first_marker_line + 10:
break
-
- #ZS: This assumes that both won't be all zero, since if that's the case mapping shouldn't be an option to begin with
+ # ZS: This assumes that both won't be all zero, since if that's
+ # the case mapping shouldn't be an option to begin with
if mb_all_zero:
return [["morgan", "cM"]]
elif cm_mb_all_equal:
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 7f82b35c..87cf1b45 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -7,16 +7,6 @@
{% 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" style="min-width: 1210px;">
{{ flash_me() }}
diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html
index 68b06f55..334a608d 100644
--- a/wqflask/wqflask/templates/submit_trait.html
+++ b/wqflask/wqflask/templates/submit_trait.html
@@ -61,18 +61,6 @@
<img src="/static/new/images/step2.gif">
</div>
<div class="col-xs-10">
- <!--
- <div class="form-group" style="padding-left: 15px;">
- <p>
- <b>From a File:</b> You can enter data by entering a file name here. The file should contain a series of numbers representing trait values.
- The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual
- or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set,
- when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that
- you paste into the next section will be ignored.
- </p>
- <input type="file" name="trait_file" style="border-width: 1px; border-style: solid; border-color: #999999;">
- </div>
- -->
<div class="form-group" style="padding-left: 15px;">
<p>
<b>Paste or Type Multiple Values:</b> You can enter data by pasting a series of numbers representing trait values into this area.
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2c0ba586..c4b510d4 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -156,12 +156,6 @@ def index_page():
import_collections = params['import_collections']
if import_collections == "true":
g.user_session.import_traits_to_user(params['anon_id'])
- #if USE_GN_SERVER:
- # # The menu is generated using GN_SERVER
- # return render_template("index_page.html", gn_server_url = GN_SERVER_URL, version=GN_VERSION)
- #else:
-
- # Old style static menu (OBSOLETE)
return render_template("index_page_orig.html", version=GN_VERSION)
@@ -343,14 +337,10 @@ def intro():
@app.route("/tutorials")
def tutorials():
- #doc = Docs("links", request.args)
- #return render_template("docs.html", **doc.__dict__)
return render_template("tutorials.html")
@app.route("/credits")
def credits():
- #doc = Docs("links", request.args)
- #return render_template("docs.html", **doc.__dict__)
return render_template("credits.html")
@app.route("/update_text", methods=('POST',))
@@ -368,12 +358,9 @@ def submit_trait_form():
@app.route("/create_temp_trait", methods=('POST',))
def create_temp_trait():
logger.info(request.url)
-
- #template_vars = submit_trait.SubmitTrait(request.form)
-
doc = Docs("links")
return render_template("links.html", **doc.__dict__)
- #return render_template("show_trait.html", **template_vars.__dict__)
+
@app.route('/export_trait_excel', methods=('POST',))
def export_trait_excel():
@@ -487,21 +474,17 @@ def export_perm_data():
mimetype='text/csv',
headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"})
+
@app.route("/show_temp_trait", methods=('POST',))
def show_temp_trait_page():
logger.info(request.url)
template_vars = show_trait.ShowTrait(request.form)
- #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)
-
- #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("/show_trait")
def show_trait_page():
logger.info(request.url)