3 participants
example url with an example of a study with multiple identified GWAS relations <localhost>/study/19010793
remember to purge() and populate() first
wejendorp
commented
Now the Study documents have a list of names of diseases (csv), and are fully searchable again.
Are we ready to close this one yet? Thinking we should be moving this off the production line so we can start on to the pagination story
wejendorp
commented
Merge it! I have it under wraps ^^
wejendorp
closed this
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
This page is out of date. Refresh to see the latest.
Showing 8 changed files with 150 additions and 84 deletions. Show Diff Stats
@@ -36,7 +36,7 @@ def AddStudyDocument(study): |
||
| 36 | 36 |
doc = search.Document(doc_id=study.pubmed_id, # Treat pubmed_id as key |
| 37 | 37 |
fields=[ |
| 38 | 38 |
search.TextField(name='name', value=study.name), |
| 39 |
- search.TextField(name='disease_trait', value=study.disease_trait),
|
|
| 39 |
+ search.TextField(name='disease_trait', value=','.join([s.name for s in study.diseases])),
|
|
| 40 | 40 |
search.TextField(name='id', value=study.pubmed_id) |
| 41 | 41 |
]) |
| 42 | 42 |
search.Index(name=study._index).add(doc) |
@@ -100,44 +100,49 @@ def populate(path="gwascatalog.txt", limit=100): |
||
| 100 | 100 |
# read all GWAS into a dictionary, using pubmed_id as key |
| 101 | 101 |
# - collecting all GWAS assorted with the same study under same key |
| 102 | 102 |
for doc in docs: |
| 103 |
- pubid = doc["PUBMEDID"] |
|
| 103 |
+ pubid = doc["PUBMEDID"].strip()
|
|
| 104 | 104 |
if pubids.has_key(pubid): |
| 105 | 105 |
pubids[pubid].append(doc) |
| 106 | 106 |
else: |
| 107 | 107 |
pubids[pubid] = [doc] |
| 108 | 108 |
|
| 109 | 109 |
i = 0 |
| 110 |
- for pid, line in pubids.iteritems(): |
|
| 110 |
+ for pid, lines in pubids.iteritems():
|
|
| 111 | 111 |
i += 1 |
| 112 |
- if i == limit:
|
|
| 112 |
+ if i == 100:
|
|
| 113 | 113 |
break |
| 114 |
- rel = line[0] |
|
| 114 |
+ print i |
|
| 115 |
+ # create a new study object for each new iteration |
|
| 116 |
+ # - use the first line to initiate the study model |
|
| 117 |
+ init = lines[0] |
|
| 115 | 118 |
|
| 116 |
- # create or get disease with disease_name as key |
|
| 117 |
- disease_name = rel["Disease/Trait"].strip().lower() |
|
| 118 |
- disease = Disease.get_or_insert(disease_name, |
|
| 119 |
- name=disease_name) |
|
| 120 |
- AddDiseaseDocument(disease) |
|
| 121 |
- |
|
| 122 |
- # create or get study with study_id |
|
| 123 | 119 |
study = Study.get_or_insert(pid, |
| 124 |
- name=rel["Study"].strip(), |
|
| 125 |
- disease_trait = disease_name, |
|
| 126 |
- disease_ref = disease, |
|
| 127 |
- pubmed_id = pid) |
|
| 128 |
- |
|
| 129 |
- # parse date of study |
|
| 130 |
- date = datetime.strptime(rel["Date"].strip(), "%m/%d/%Y").date() |
|
| 131 |
- # populate model |
|
| 132 |
- study.date = date |
|
| 133 |
- study.pubmed_url=rel["Link"].strip() |
|
| 134 |
- study.init_sample = rel["Initial Sample Size"].strip() |
|
| 135 |
- study.repl_sample= rel["Replication Sample Size"].strip() |
|
| 136 |
- study.platform = rel["Platform [SNPs passing QC]"].strip() |
|
| 120 |
+ name=init["Study"].strip(), |
|
| 121 |
+ pubmed_id = pid) # disease_ref = disease, |
|
| 122 |
+ |
|
| 123 |
+ # populate study with static data |
|
| 124 |
+ # date = datetime.strptime(init["Date"].strip(), "%m/%d/%Y").date() |
|
| 125 |
+ study.date = datetime.strptime(init["Date"].strip(), "%m/%d/%Y").date() |
|
| 126 |
+ study.pubmed_url=init["Link"].strip() |
|
| 127 |
+ study.init_sample = init["Initial Sample Size"].strip() |
|
| 128 |
+ study.repl_sample= init["Replication Sample Size"].strip() |
|
| 129 |
+ study.platform = init["Platform [SNPs passing QC]"].strip() |
|
| 137 | 130 |
study.put() |
| 138 | 131 |
AddStudyDocument(study) |
| 139 | 132 |
|
| 140 |
- for rel in line: |
|
| 133 |
+ disease_name = None |
|
| 134 |
+ disease = None |
|
| 135 |
+ for line in lines: |
|
| 136 |
+ # if the disease in this GWAS row differs from the other |
|
| 137 |
+ # ones in this study, create new disease relation: |
|
| 138 |
+ tmp = line["Disease/Trait"].strip().lower() |
|
| 139 |
+ if disease_name != tmp: |
|
| 140 |
+ disease_name = tmp |
|
| 141 |
+ disease = Disease.get_or_insert(disease_name, |
|
| 142 |
+ name=disease_name) |
|
| 143 |
+ study.add_disease(disease) |
|
| 144 |
+ AddDiseaseDocument(disease) |
|
| 145 |
+ |
|
| 141 | 146 |
# A gwas has either a direct gene or a |
| 142 | 147 |
# down-stream and up-stream gene |
| 143 | 148 |
gene = None |
@@ -146,16 +151,16 @@ def populate(path="gwascatalog.txt", limit=100): |
||
| 146 | 151 |
|
| 147 | 152 |
# The retards at GWAS use 1 == intergenic, 2 == not intergenic |
| 148 | 153 |
# ... no seriously, _retards_ |
| 149 |
- intergenic = rel["Intergenic"].strip() == "2"
|
|
| 154 |
+ intergenic = line["Intergenic"].strip() == "2"
|
|
| 150 | 155 |
|
| 151 | 156 |
if not intergenic: |
| 152 |
- geneid = rel["Snp_gene_ids"].strip()
|
|
| 157 |
+ geneid = line["Snp_gene_ids"].strip()
|
|
| 153 | 158 |
if geneid != "": |
| 154 | 159 |
# not intergenic => one direct gene |
| 155 |
- names = rel["Mapped_gene"].split(" - ")
|
|
| 160 |
+ names = line["Mapped_gene"].split(" - ")
|
|
| 156 | 161 |
if len(names) == 1: |
| 157 | 162 |
gene = Gene.get_or_insert(geneid, |
| 158 |
- name = rel["Mapped_gene"],
|
|
| 163 |
+ name = line["Mapped_gene"],
|
|
| 159 | 164 |
geneid = geneid) |
| 160 | 165 |
if not study.key() in gene.studies: |
| 161 | 166 |
gene.studies.append(study.key()) |
@@ -165,11 +170,11 @@ def populate(path="gwascatalog.txt", limit=100): |
||
| 165 | 170 |
AddGeneDocument(gene) |
| 166 | 171 |
else: |
| 167 | 172 |
# up and downstream genes must be set |
| 168 |
- down_id = rel["Downstream_gene_id"].strip() |
|
| 169 |
- up_id = rel["Upstream_gene_id"].strip() |
|
| 173 |
+ down_id = line["Downstream_gene_id"].strip() |
|
| 174 |
+ up_id = line["Upstream_gene_id"].strip() |
|
| 170 | 175 |
|
| 171 | 176 |
if up_id != "" and down_id != "": |
| 172 |
- up_down_names = rel["Mapped_gene"].split(" - ")
|
|
| 177 |
+ up_down_names = line["Mapped_gene"].split(" - ")
|
|
| 173 | 178 |
if len(up_down_names) < 2: |
| 174 | 179 |
# gene = NR / NS or whatever.. |
| 175 | 180 |
up_down_names = ["N/A", "N/A"] |
@@ -195,12 +200,12 @@ def populate(path="gwascatalog.txt", limit=100): |
||
| 195 | 200 |
|
| 196 | 201 |
# init snps.. |
| 197 | 202 |
snp = None |
| 198 |
- snpid = rel["Snp_id_current"].strip()
|
|
| 203 |
+ snpid = line["Snp_id_current"].strip()
|
|
| 199 | 204 |
|
| 200 | 205 |
if snpid != "": |
| 201 | 206 |
# non=blank snp |
| 202 | 207 |
try: |
| 203 |
- # create relation only if a 'single' snp is in the gwas
|
|
| 208 |
+ # create lineation only if a 'single' snp is in the gwas
|
|
| 204 | 209 |
int(snpid) |
| 205 | 210 |
snp = Snp.get_or_insert(snpid, |
| 206 | 211 |
snpid=snpid) |
@@ -215,7 +220,7 @@ def populate(path="gwascatalog.txt", limit=100): |
||
| 215 | 220 |
except: |
| 216 | 221 |
# haplotype? |
| 217 | 222 |
snpid = "N/A" |
| 218 |
- # if no gene or snp relation is mentioned - ignore and just insert study
|
|
| 223 |
+ # if no gene or snp lineation is mentioned - ignore and just insert study
|
|
| 219 | 224 |
if (gene is None or up_gene is None) and snp is None: |
| 220 | 225 |
print "skipping gwas" |
| 221 | 226 |
continue |
@@ -235,25 +240,25 @@ def populate(path="gwascatalog.txt", limit=100): |
||
| 235 | 240 |
gwas.gene = gene |
| 236 | 241 |
|
| 237 | 242 |
# parse remaining gwas information |
| 238 |
- gwas.p_string = rel["p-Value"].strip()
|
|
| 243 |
+ gwas.p_string = line["p-Value"].strip()
|
|
| 239 | 244 |
# could be none |
| 240 | 245 |
gwas.snps = snpid |
| 241 | 246 |
|
| 242 | 247 |
# parse out the exponent: 6E-8 => -8 |
| 243 | 248 |
try: |
| 244 | 249 |
# test that p-Value is actually a float before parsing out |
| 245 |
- float(rel["p-Value"]) |
|
| 246 |
- gwas.p_val = int(rel["p-Value"].split("E-")[1])
|
|
| 250 |
+ float(line["p-Value"]) |
|
| 251 |
+ gwas.p_val = int(line["p-Value"].split("E-")[1])
|
|
| 247 | 252 |
except Exception, e: |
| 248 | 253 |
# forces the filter to downgrade this gwas wrt. p-value |
| 249 | 254 |
gwas.p_val = 0 |
| 250 | 255 |
# could be interesting |
| 251 | 256 |
gwas.strongest_snp_risk_allele = \ |
| 252 |
- rel["Strongest SNP-Risk Allele"].strip() |
|
| 253 |
- # gwas.CI = rel["95% CI (text)"].strip() |
|
| 254 |
- gwas.OR_beta = rel["OR or beta"].strip() |
|
| 257 |
+ line["Strongest SNP-Risk Allele"].strip() |
|
| 258 |
+ # gwas.CI = line["95% CI (text)"].strip() |
|
| 259 |
+ gwas.OR_beta = line["OR or beta"].strip() |
|
| 255 | 260 |
gwas.riscAlleleFrequency = \ |
| 256 |
- rel["Risk Allele Frequency"].strip()
|
|
| 261 |
+ line["Risk Allele Frequency"].strip()
|
|
| 257 | 262 |
gwas.put() |
| 258 | 263 |
|
| 259 | 264 |
memcache.flush_all() |
@@ -26,7 +26,7 @@ def get(self): |
||
| 26 | 26 |
rendered = memcache.get("diseaselist_0:50")
|
| 27 | 27 |
if rendered is None: |
| 28 | 28 |
# make large query, to check for speed when cached |
| 29 |
- diseases = Disease.all() |
|
| 29 |
+ diseases = Disease.all().fetch(100)
|
|
| 30 | 30 |
# generate only the bare-bones list of diseases, ignore everything from base.html etc. |
| 31 | 31 |
rendered = self.render("diseaselistrender.html", diseases=diseases, filter=filter)
|
| 32 | 32 |
|
@@ -51,9 +51,14 @@ def get(self, name): |
||
| 51 | 51 |
if rendered is None: |
| 52 | 52 |
# make large query, to check for speed when cached |
| 53 | 53 |
disease = db.get(db.Key.from_path("Disease", name))
|
| 54 |
+ studies = db.get(disease.studies) |
|
| 55 |
+ if studies is None: |
|
| 56 |
+ logging.info("ERRRRRRROR: no studies!")
|
|
| 57 |
+ else: |
|
| 58 |
+ logging.info("%s" % studies)
|
|
| 54 | 59 |
|
| 55 | 60 |
# generate only the bare-bones list of diseases, ignore everything from base.html etc. |
| 56 |
- rendered = self.render("diseaseview.html", disease=disease)
|
|
| 61 |
+ rendered = self.render("diseaseview.html", disease=disease, studies=studies)
|
|
| 57 | 62 |
|
| 58 | 63 |
# add to memchache |
| 59 | 64 |
if not memcache.set(name, rendered, namespace="disease"): |
@@ -77,7 +82,7 @@ def get(self): |
||
| 77 | 82 |
rendered = memcache.get("studylist_0:50")
|
| 78 | 83 |
if rendered is None: |
| 79 | 84 |
# make large query, to check for speed when cached |
| 80 |
- studies = Study.all().fetch(50)
|
|
| 85 |
+ studies = Study.all().fetch(100)
|
|
| 81 | 86 |
rendered = self.render("studylistrender.html",studies=studies, filter=filter)
|
| 82 | 87 |
# logging.debug(rendered ) |
| 83 | 88 |
# add to memchache |
@@ -90,15 +95,21 @@ def get(self): |
||
| 90 | 95 |
|
| 91 | 96 |
class studyView(AppRequestHandler): |
| 92 | 97 |
"""View a particular study""" |
| 93 |
- def get(self, i):
|
|
| 98 |
+ def get(self, pubmed_id):
|
|
| 94 | 99 |
self.setTemplate('studyview.html')
|
| 95 |
- study = Study.gql("WHERE pubmed_id = :1", i).get()
|
|
| 100 |
+ study = Study.get_by_key_name(pubmed_id) |
|
| 101 |
+ if study is None: |
|
| 102 |
+ self.redirect('/studies/')
|
|
| 103 |
+ return |
|
| 96 | 104 |
self.out(study=study) |
| 97 | 105 |
|
| 98 | 106 |
# Comment on a study via POST |
| 99 |
- def post(self, i):
|
|
| 107 |
+ def post(self, pubmed_id):
|
|
| 100 | 108 |
self.setTemplate('studyview.html')
|
| 101 |
- study = Study.gql("WHERE pubmed_id = :1", i).get()
|
|
| 109 |
+ study = Study.get_by_key_name(pubmed_id) |
|
| 110 |
+ if study is None: |
|
| 111 |
+ self.redirect('/studies/')
|
|
| 112 |
+ return |
|
| 102 | 113 |
|
| 103 | 114 |
comment = Comment() |
| 104 | 115 |
comment.study = study.key() |
@@ -133,7 +144,6 @@ class genePresenter(AppRequestHandler): |
||
| 133 | 144 |
_template = 'gene.html' |
| 134 | 145 |
def get(self, gene): |
| 135 | 146 |
gene = Gene.gql("WHERE name = :1", gene).get()
|
| 136 |
- |
|
| 137 | 147 |
self.out(gene=gene) |
| 138 | 148 |
|
| 139 | 149 |
# Comment on a gene via POST |
@@ -4,9 +4,16 @@ |
||
| 4 | 4 |
class Disease(AppModel): |
| 5 | 5 |
"""For viewing a unique list of diseases, we need a disease to be a relation and not just a textfield""" |
| 6 | 6 |
name = db.StringProperty(required=True) |
| 7 |
+ studies = db.ListProperty(db.Key) |
|
| 8 |
+ _index = 'Diseases' |
|
| 7 | 9 |
|
| 10 |
+ # @property |
|
| 11 |
+ def add_study(self, study_key): |
|
| 12 |
+ # add study as relation only if it's not already in the list |
|
| 13 |
+ if study_key not in self.studies: |
|
| 14 |
+ self.studies.append(study_key) |
|
| 15 |
+ self.put() |
|
| 8 | 16 |
|
| 9 |
- _index = 'Diseases' |
|
| 10 | 17 |
|
| 11 | 18 |
# PK = pubmed_id |
| 12 | 19 |
class Study(AppModel): |
@@ -20,9 +27,10 @@ class Study(AppModel): |
||
| 20 | 27 |
# 6 - description of study |
| 21 | 28 |
name = db.StringProperty(required=True) |
| 22 | 29 |
# 7 disease or trait researched |
| 23 |
- disease_ref = db.ReferenceProperty(Disease, required=True, collection_name="studies") |
|
| 30 |
+ # disease_ref = db.ReferenceProperty(Disease, required=True, collection_name="studies") |
|
| 31 |
+ diseases = db.ListProperty(db.Key) # keys to diseases |
|
| 24 | 32 |
# to prevent relation traversal |
| 25 |
- disease_trait = db.StringProperty(required=True) |
|
| 33 |
+ # disease_trait = db.StringProperty(required=True)
|
|
| 26 | 34 |
|
| 27 | 35 |
abstract = db.StringProperty() |
| 28 | 36 |
# 8 - antal forsogspersoner |
@@ -31,6 +39,16 @@ class Study(AppModel): |
||
| 31 | 39 |
repl_sample = db.StringProperty() |
| 32 | 40 |
platform = db.StringProperty() |
| 33 | 41 |
|
| 42 |
+ # @property |
|
| 43 |
+ def add_disease(self, disease): |
|
| 44 |
+ # realation between disease and study is a many_to_many |
|
| 45 |
+ # - this helps make sure that is kept when importing |
|
| 46 |
+ # add disease to diseases attribute and add this study to the disease |
|
| 47 |
+ if disease.key() not in self.diseases: |
|
| 48 |
+ self.diseases.append(disease.key()) |
|
| 49 |
+ self.put() |
|
| 50 |
+ disease.add_study(self.key()) |
|
| 51 |
+ |
|
| 34 | 52 |
@property |
| 35 | 53 |
def genes(self): |
| 36 | 54 |
return Gene.gql("WHERE studies = :1", self.key())
|
| ... | ... |
@@ -1,4 +1,6 @@ |
| 1 |
-<h2>Diseases</h2> |
|
| 1 |
+<div class="page-header"> |
|
| 2 |
+ <h2>Diseases</h2> |
|
| 3 |
+</div> |
|
| 2 | 4 |
{% for disease in diseases %}
|
| 3 | 5 |
<article class="row"> |
| 4 | 6 |
<div class="span10"> |
| ... | ... |
@@ -1,5 +1,18 @@ |
| 1 |
-<h2>Disease: {{disease.name}}</h2>
|
|
| 2 |
-{% for study in disease.studies %}
|
|
| 1 |
+<ul class="breadcrumb"> |
|
| 2 |
+ <li> |
|
| 3 |
+ <a href="/diseases/">Diseases</a> <span class="divider">/</span> |
|
| 4 |
+ </li> |
|
| 5 |
+ <li> |
|
| 6 |
+ <a href="/disease/{{disease.name}}">{{disease.name}}</a>
|
|
| 7 |
+ </li> |
|
| 8 |
+</ul> |
|
| 9 |
+ |
|
| 10 |
+<div class="page-header"> |
|
| 11 |
+ <h2>{{disease.name}}</h2>
|
|
| 12 |
+</div> |
|
| 13 |
+ |
|
| 14 |
+{% for study in studies %}
|
|
| 15 |
+<h3>{{study}}</h3>
|
|
| 3 | 16 |
<article class="row"> |
| 4 | 17 |
<time class="span1">{{study.date}}</time>
|
| 5 | 18 |
<div class="span10"> |
@@ -6,14 +6,13 @@ |
||
| 6 | 6 |
{% block content %}
|
| 7 | 7 |
{% if gene %}
|
| 8 | 8 |
<h1>{{gene.name}}</h1>
|
| 9 |
- |
|
| 10 | 9 |
<table class="table table-striped"> |
| 11 | 10 |
<thead><th><h1><small>Referenced by</small></h1></th><th><h1><small>Correlated with</small></h1></th></thead> |
| 12 | 11 |
<tbody> |
| 13 | 12 |
{% for gwas in gene.gwas %}
|
| 14 | 13 |
<tr> |
| 15 | 14 |
<td><a href="/study/{{gwas.study.pubmed_id}}">{{gwas.study.name}}</a></td>
|
| 16 |
- <td>{{gwas.study.disease_trait}}</td>
|
|
| 15 |
+ <td>{{gwas.disease.name}}</td>
|
|
| 17 | 16 |
</tr> |
| 18 | 17 |
{% endfor %}
|
| 19 | 18 |
</tbody> |
| ... | ... |
@@ -1,22 +1,27 @@ |
| 1 | 1 |
<h2>Studies</h2> |
| 2 | 2 |
{% for study in studies %}
|
| 3 |
-<article class="row"> |
|
| 4 |
- <time class="span1">{{study.date}}</time>
|
|
| 5 |
- <div class="span10"> |
|
| 6 |
- <h3>{{study.disease_trait}}</h3>
|
|
| 7 |
- <h3><small>{{study.name}}</small></h3>
|
|
| 8 |
- <dl class="dl-horizontal"> |
|
| 9 |
- <dt>Sample size(s):</dt> |
|
| 10 |
- <dd>{{study.init_sample}}</dd>
|
|
| 11 |
- <dt>Replication sample:</dt> |
|
| 12 |
- <dd>{{study.repl_sample}}</dd>
|
|
| 13 |
- <dt>Platform</dt> |
|
| 14 |
- <dd> {{study.platform}}</dd>
|
|
| 15 |
- </dl> |
|
| 16 |
- <p><a href="/study/{{study.pubmed_id}}" class="btn btn-mini">
|
|
| 17 |
- Study #{{study.pubmed_id}}</a>
|
|
| 18 |
- <a href="{{study.pubmed_url}}" class="btn btn-mini">View on pubmed</a>
|
|
| 19 |
- </p> |
|
| 3 |
+<article class="row-fluid"> |
|
| 4 |
+ <p class="span1">{{study.date}}</p>
|
|
| 5 |
+ <div class="span11"> |
|
| 6 |
+ <h3><small>{{study.name}}</small></h3>
|
|
| 7 |
+ <h4>Disease(s):</h4> |
|
| 8 |
+ <ul> |
|
| 9 |
+ {% for disease in study.diseases %}
|
|
| 10 |
+ <li> <h4><a href="/disease/{{disease.name()}}">{{disease.name()}}</a></h4> </li>
|
|
| 11 |
+ {% endfor %}
|
|
| 12 |
+ </ul> |
|
| 13 |
+ <dl class="dl-horizontal"> |
|
| 14 |
+ <dt>Sample size(s):</dt> |
|
| 15 |
+ <dd>{{study.init_sample}}</dd>
|
|
| 16 |
+ <dt>Replication sample:</dt> |
|
| 17 |
+ <dd>{{study.repl_sample}}</dd>
|
|
| 18 |
+ <dt>Platform</dt> |
|
| 19 |
+ <dd> {{study.platform}}</dd>
|
|
| 20 |
+ </dl> |
|
| 21 |
+ <p><a href="/study/{{study.pubmed_id}}" class="btn btn-mini">
|
|
| 22 |
+ Study #{{study.pubmed_id}}</a>
|
|
| 23 |
+ <a href="{{study.pubmed_url}}" class="btn btn-mini">View on pubmed</a>
|
|
| 24 |
+ </p> |
|
| 20 | 25 |
</div> |
| 21 | 26 |
</article> |
| 22 | 27 |
{% else %}
|
| ... | ... |
@@ -1,14 +1,29 @@ |
| 1 | 1 |
{% extends "base.html" %}
|
| 2 | 2 |
{% block title %}
|
| 3 |
-Study Details: {{study.name}}
|
|
| 3 |
+Study - {{study.name}}
|
|
| 4 | 4 |
{% endblock %}
|
| 5 | 5 |
|
| 6 | 6 |
{% block content %}
|
| 7 |
- <article class="row"> |
|
| 8 |
- <time class="span1">{{study.date}}</time>
|
|
| 9 |
- <div class="span10"> |
|
| 10 |
- <h3>{{study.disease_trait}}</h3>
|
|
| 11 |
- <h3><small>{{study.name}}</small></h3>
|
|
| 7 |
+<ul class="breadcrumb"> |
|
| 8 |
+ <li> |
|
| 9 |
+ <a href="/studies/">Studies</a> <span class="divider">/</span> |
|
| 10 |
+ </li> |
|
| 11 |
+ <li> |
|
| 12 |
+ <a href="/study/{{study.key().name()}}">{{study.name}}</a>
|
|
| 13 |
+ </li> |
|
| 14 |
+</ul> |
|
| 15 |
+<article class="row-fluid"> |
|
| 16 |
+ <!-- <time class="span1">{{study.date}}</time> -->
|
|
| 17 |
+ <div class="span12"> |
|
| 18 |
+ <div class="page-header"> |
|
| 19 |
+ <h3>{{study.name}}</h3>
|
|
| 20 |
+ </div> |
|
| 21 |
+ <h3>Disease(s):</h3> |
|
| 22 |
+ <ul> |
|
| 23 |
+ {% for disease in study.diseases %}
|
|
| 24 |
+ <li> <h4><a href="/disease/{{disease.name()}}">{{disease.name()}}</a></h4> </li>
|
|
| 25 |
+ {% endfor %}
|
|
| 26 |
+ </ul> |
|
| 12 | 27 |
<dl class="dl-horizontal"> |
| 13 | 28 |
<dt>Sample size(s):</dt> |
| 14 | 29 |
<dd>{{study.init_sample}}</dd>
|
@@ -56,8 +71,7 @@ |
||
| 56 | 71 |
</table> |
| 57 | 72 |
{% endif %}
|
| 58 | 73 |
</div> |
| 59 |
- </article> |
|
| 60 |
- |
|
| 74 |
+</article> |
|
| 61 | 75 |
{% block comments %}
|
| 62 | 76 |
{% set comments = study.comments %}
|
| 63 | 77 |
{% include 'comments.html' %}
|
Tip: You can add notes to lines in a file. Hover to the left of a line to make a note
I've been having fevery dreams these last couple of weeks, and I suddenly realized why. The import used one idiotic assumption when loading the GWAS. That each study only references a single disease. This, in retrospect, is obviously not the case, given that multiple GWAS correlations could possibly be identified in a study.
This means that each study now has a list of diseases they reference, instead of just one, and each disease now has many more studies to reference (possibly).
In other words, there is actually a many-to-many relationship between disease and study, whereas the old model only had a one disease to many studies relation.
study.disease_refbut an array of keysSince this fix obviously has implications on how we search for studies, I wanted to give @wejendorp a heads up. Since the "disease_trait" field is no longer there, replaced by an array of disease_keys (I could add an additional disease_names string-array if that would simplify things?), you can no longer index the disease-field of the study. For now I've simply commented out that field in your indexing, and I couldn't figure out how to add indexing for arrays.