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-rw-r--r--wqflask/base/trait.py1
-rw-r--r--wqflask/utility/helper_functions.py16
-rw-r--r--wqflask/wqflask/collect.py41
-rw-r--r--wqflask/wqflask/model.py2
-rw-r--r--wqflask/wqflask/templates/collections/add.html11
-rw-r--r--wqflask/wqflask/templates/collections/view.html235
-rw-r--r--wqflask/wqflask/templates/search_result_page.html2
7 files changed, 149 insertions, 159 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 9566c192..f18481a8 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -116,7 +116,6 @@ class GeneralTrait(object):
return stringy
-
def display_name(self):
stringy = ""
if self.dataset and self.name:
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 15f60765..149ee553 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -4,6 +4,8 @@ from base.trait import GeneralTrait
from base import data_set
from base.species import TheSpecies
+from wqflask import user_manager
+
def get_species_dataset_trait(self, start_vars):
#assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
@@ -23,13 +25,15 @@ def get_species_dataset_trait(self, start_vars):
def get_trait_db_obs(self, trait_db_list):
-
+ if isinstance(trait_db_list, basestring):
+ trait_db_list = trait_db_list.split(",")
+
self.trait_list = []
- for i, trait_db in enumerate(trait_db_list):
- if i == (len(trait_db_list) - 1):
- break
- trait_name, dataset_name = trait_db.split(":")
- #print("dataset_name:", dataset_name)
+ for trait in trait_db_list:
+ data, _separator, hmac = trait.rpartition(':')
+ data = data.strip()
+ assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?"
+ trait_name, dataset_name = data.split(":")
dataset_ob = data_set.create_dataset(dataset_name)
trait_ob = GeneralTrait(dataset=dataset_ob,
name=trait_name,
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 5484633b..7e7aba89 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -165,12 +165,19 @@ class UserCollection(object):
return create_new("Default")
else:
uc = model.UserCollection.query.get(params['existing_collection'])
- members = uc.members_as_set() #set(json.loads(uc.members))
+ members = list(uc.members_as_set()) #set(json.loads(uc.members))
len_before = len(members)
traits = process_traits(params['traits'])
-
- members_now = list(members | traits)
+
+ members_now = members
+ for trait in traits:
+ if trait in members:
+ continue
+ else:
+ members_now.append(trait)
+
+ #members_now = list(members | traits)
len_now = len(members_now)
uc.members = json.dumps(members_now)
@@ -184,28 +191,6 @@ class UserCollection(object):
# Probably have to change that
return redirect(url_for('view_collection', uc_id=uc.id))
- def remove_traits(self, params):
-
- #params = request.form
- print("params are:", params)
- uc_id = params['uc_id']
- uc = model.UserCollection.query.get(uc_id)
- traits_to_remove = params.getlist('traits[]')
- print("traits_to_remove are:", traits_to_remove)
- traits_to_remove = process_traits(traits_to_remove)
- print("\n\n after processing, traits_to_remove:", traits_to_remove)
- all_traits = uc.members_as_set()
- print(" all_traits:", all_traits)
- members_now = all_traits - traits_to_remove
- print(" members_now:", members_now)
- print("Went from {} to {} members in set.".format(len(all_traits), len(members_now)))
- uc.members = json.dumps(list(members_now))
- uc.changed_timestamp = datetime.datetime.utcnow()
- db_session.commit()
-
- # We need to return something so we'll return this...maybe in the future
- # we can use it to check the results
- return str(len(members_now))
def report_change(len_before, len_now):
new_length = len_now - len_before
@@ -218,8 +203,6 @@ def report_change(len_before, len_now):
print("No new traits were added.")
-
-
@app.route("/collections/add")
def collections_add():
traits=request.args['traits']
@@ -329,7 +312,6 @@ def list_collections():
@app.route("/collections/remove", methods=('POST',))
def remove_traits():
-
params = request.form
print("params are:", params)
@@ -337,14 +319,11 @@ def remove_traits():
uc_id = params['uc_id']
uc = model.UserCollection.query.get(uc_id)
traits_to_remove = params.getlist('traits[]')
- print("traits_to_remove are:", traits_to_remove)
traits_to_remove = process_traits(traits_to_remove)
print("\n\n after processing, traits_to_remove:", traits_to_remove)
all_traits = uc.members_as_set()
- print(" all_traits:", all_traits)
members_now = all_traits - traits_to_remove
print(" members_now:", members_now)
- print("Went from {} to {} members in set.".format(len(all_traits), len(members_now)))
uc.members = json.dumps(list(members_now))
uc.changed_timestamp = datetime.datetime.utcnow()
db_session.commit()
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 17343186..5321e420 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -177,12 +177,10 @@ class UserCollection(Base):
except:
return 0
-
#@property
#def display_num_members(self):
# return display_collapsible(self.num_members)
-
def members_as_set(self):
return set(json.loads(self.members))
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index c5598e84..47b87d73 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -6,16 +6,6 @@
</div>
<div class="modal-body">
<form action="/collections/new" data-validate="parsley" id="add_form">
-<!--
- <fieldset>
- <legend>Use your default collection</legend>
- <span class="help-block">Choose this if you're in a hurry or don't plan on using the collection again.</span>
- <span class="help-block"><em></em>If you are unsure this is probably the option you want.</em></span>
- <button type="submit" name="Default" class="btn">Continue</button>
- </fieldset>
- <hr />
--->
-
<input type="hidden" name="traits" value="{{ traits }}" />
<fieldset>
<legend>Create a new named collection</legend>
@@ -28,7 +18,6 @@
{% endif %}
<button type="submit" name="create_new" class="btn">Create and add traits</button>
</fieldset>
-
<hr />
<fieldset>
<legend>Or add to an existing collection</legend>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 68d2886f..6a11600c 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -21,64 +21,41 @@
<div class="container">
<div>
- <form action="/collections/delete" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% else %}
- <input type="hidden" name="collection_name" id="collection_name" value="{{ collection_name }}" />
- {% endif %}
- <div class="col-xs-3 controls">
- <input type="submit" class="btn btn-danger" value="Delete this collection" />
- </div>
- </form>
- <form action="/corr_matrix" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% endif %}
- <input type="hidden" name="trait_list" id="trait_list" value= "
- {% for this_trait in trait_obs %}
- {{ this_trait.name }}:{{ this_trait.dataset.name }},
- {% endfor %}" >
- <div class="col-xs-2 controls">
- <input type="submit" class="btn btn-primary" value="Correlation Matrix" />
- </div>
- </form>
- <form action="/wgcna_setup" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% endif %}
- <input type="hidden" name="trait_list" id="trait_list" value= "
- {% for this_trait in trait_obs %}
- {{ this_trait.name }}:{{ this_trait.dataset.name }},
- {% endfor %}" >
- <div class="col-xs-2 controls">
- <input type="submit" class="btn btn-primary" value="WGCNA Analysis" />
- </div>
- </form>
- <form action="/ctl_setup" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% endif %}
- <input type="hidden" name="trait_list" id="trait_list" value= "
- {% for this_trait in trait_obs %}
- {{ this_trait.name }}:{{ this_trait.dataset.name }},
- {% endfor %}" >
- <div class="col-xs-2 controls">
- <input type="submit" class="btn btn-primary" value="CTL Analysis" />
- </div>
- </form>
- <form action="/heatmap" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% endif %}
- <input type="hidden" name="trait_list" id="trait_list" value= "
- {% for this_trait in trait_obs %}
- {{ this_trait.name }}:{{ this_trait.dataset.name }},
- {% endfor %}" >
- <div class="col-xs-2 controls">
- <input type="submit" class="btn btn-primary" value="Heatmap" />
- </div>
- </form>
+ <form id="collection_form" action="/delete" method="post">
+ {% if uc %}
+ <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
+ {% endif %}
+ <input type="hidden" name="collection_name" id="collection_name" value="{{ collection_name }}" />
+ <input type="hidden" name="trait_list" id="trait_list" value= "
+ {% for this_trait in trait_obs %}
+ {{ this_trait.name }}:{{ this_trait.dataset.name }},
+ {% endfor %}" >
+ <div class="col-xs-3 controls">
+ <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" >
+ Delete this collection
+ </button>
+ </div>
+ <div class="col-xs-2 controls">
+ <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
+ Correlation Matrix
+ </button>
+ </div>
+ <div class="col-xs-2 controls">
+ <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
+ WGCNA Analysis
+ </button>
+ </div>
+ <div class="col-xs-2 controls">
+ <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
+ CTL Analysis
+ </button>
+ </div>
+ <div class="col-xs-2 controls">
+ <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
+ Heatmap
+ </button>
+ </div>
+ </form>
</div>
<div>
@@ -92,53 +69,54 @@
<button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
<br />
<br />
- <div style="background-color: #eeeeee; border: 1px solid black;">
- <table class="table table-hover table-striped" id='trait_table'>
- <thead>
- <tr>
- <th style="background-color: #eeeeee;"></th>
- <th style="background-color: #eeeeee;">Index</th>
- <th style="background-color: #eeeeee;">Record</th>
- <th style="background-color: #eeeeee;">Description</th>
- <th style="background-color: #eeeeee;">Location</th>
- <th style="background-color: #eeeeee;">Mean</th>
- <th style="background-color: #eeeeee;">Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
- <th style="background-color: #eeeeee;">Max LRS Location</th>
- <th style="background-color: #eeeeee;">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
- </tr>
- </thead>
-
- <tbody>
- {% for this_trait in trait_obs %}
- <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
- <TD>
- <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox"
- VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}">
- </TD>
- <TD>{{ loop.index }}</TD>
- <TD>
- <a href="{{ url_for('show_trait_page',
- trait_id = this_trait.name,
- dataset = this_trait.dataset.name
- )}}">
- {{ this_trait.name }}
- </a>
- </TD>
-
- <TD>{{ this_trait.description_display }}</TD>
- <TD>{{ this_trait.location_repr }}</TD>
- <TD>{{ this_trait.mean }}</TD>
- <TD>{{ this_trait.LRS_score_repr }}</TD>
- <TD>{{ this_trait.LRS_location_repr }}</TD>
- <TD>{{ this_trait.additive }}</TD>
-
- </TR>
- {% endfor %}
- </tbody>
-
- </table>
- </div>
- <br />
+ <div style="background-color: #eeeeee; border: 1px solid black;">
+ <table id="trait_table" class="table table-hover table-striped">
+ <thead>
+ <tr>
+ <th style="background-color: #eeeeee;"></th>
+ <th style="background-color: #eeeeee;">Index</th>
+ <th style="background-color: #eeeeee;">Dataset</th>
+ <th style="background-color: #eeeeee;">Record</th>
+ <th style="background-color: #eeeeee;">Description</th>
+ <th style="background-color: #eeeeee;">Location</th>
+ <th style="background-color: #eeeeee;">Mean</th>
+ <th style="background-color: #eeeeee;">Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+ <th style="background-color: #eeeeee;">Max LRS Location</th>
+ <th style="background-color: #eeeeee;">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+ </tr>
+ </thead>
+
+ <tbody>
+ {% for this_trait in trait_obs %}
+ <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
+ <TD>
+ <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox"
+ VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}">
+ </TD>
+ <TD>{{ loop.index }}</TD>
+ <TD>{{ this_trait.dataset.name }}</TD>
+ <TD>
+ <a href="{{ url_for('show_trait_page',
+ trait_id = this_trait.name,
+ dataset = this_trait.dataset.name
+ )}}">
+ {{ this_trait.name }}
+ </a>
+ </TD>
+ <TD>{{ this_trait.description_display }}</TD>
+ <TD>{{ this_trait.location_repr }}</TD>
+ <TD>{{ '%0.3f' % this_trait.mean|float }}</TD>
+ <TD>{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD>
+ <TD>{{ this_trait.LRS_location_repr }}</TD>
+ <TD>{{ '%0.3f' % this_trait.additive|float }}</TD>
+
+ </TR>
+ {% endfor %}
+ </tbody>
+
+ </table>
+ </div>
+ <br />
</div>
</div>
@@ -175,13 +153,14 @@
{ "type": "natural" },
{ "type": "natural" },
{ "type": "natural" },
+ { "type": "natural" },
{ "type": "natural",
"width": "35%" },
{ "type": "natural",
"width": "15%" },
{ "type": "cust-txt" },
{ "type": "natural",
- "width": "12%" },
+ "width": "9%" },
{ "type": "natural",
"width": "15%" },
{ "type": "natural" }
@@ -193,7 +172,7 @@
title: 'collection',
fieldBoundary: '"',
exportOptions: {
- columns: [1, 2, 3, 4, 5, 6, 7, 8]
+ columns: [1, 2, 3, 4, 5, 6, 7, 8, 9]
}
}
],
@@ -208,6 +187,48 @@
} );
console.timeEnd("Creating table");
+ submit_special = function(url) {
+ $("#collection_form").attr("action", url);
+ return $("#collection_form").submit();
+ };
+
+ $("#delete").on("click", function() {
+ url = $(this).data("url")
+ return submit_special(url)
+ });
+
+ $("#corr_matrix").on("click", function() {
+ traits = $("#trait_table input:checked").map(function() {
+ return $(this).val();
+ }).get();
+ $("#trait_list").val(traits)
+ url = $(this).data("url")
+ return submit_special(url)
+ });
+ $("#wgcna_setup").on("click", function() {
+ traits = $("#trait_table input:checked").map(function() {
+ return $(this).val();
+ }).get();
+ $("#trait_list").val(traits)
+ url = $(this).data("url")
+ return submit_special(url)
+ });
+ $("#ctl_setup").on("click", function() {
+ traits = $("#trait_table input:checked").map(function() {
+ return $(this).val();
+ }).get();
+ $("#trait_list").val(traits)
+ url = $(this).data("url")
+ return submit_special(url)
+ });
+ $("#heatmap").on("click", function() {
+ traits = $("#trait_table input:checked").map(function() {
+ return $(this).val();
+ }).get();
+ $("#trait_list").val(traits)
+ url = $(this).data("url")
+ return submit_special(url)
+ });
});
</script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 02c97862..bf1475ff 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -122,7 +122,7 @@
{{ this_trait.pubmed_text }}
</a>
</TD>
- <TD>{{ this_trait.LRS_score_repr }}</TD>
+ <TD>{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD>
<TD>{{ this_trait.LRS_location_repr }}</TD>
<TD>{{ '%0.3f' % this_trait.additive|float }}</TD>
{% elif dataset.type == 'Geno' %}