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@LucaCilibrasi
LucaCilibrasi committed Nov 24, 2021
1 parent 173925a commit 0f6600a
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Showing 10 changed files with 349 additions and 87 deletions.
8 changes: 6 additions & 2 deletions backend/apis/analyze.py
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Expand Up @@ -20,7 +20,8 @@
client = MongoClient(uri)
db = client.gcm_gisaid

collection_db = db.seq_2021_08_26_2
# collection_db = db.seq_2021_08_26_2
collection_db = db.viruclust_db_0
collection_update_date = db.db_meta

########################################################################################################
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class FieldList(Resource):
@api.doc('update_date')
def get(self):
results = collection_update_date.find({}, {"date": {"$toString": '$date_of_import'}})
# results = collection_update_date.find({"collection_name": "seq_2021_08_26_2"},
# {"date": {"$toString": '$date_of_import'}})
results = collection_update_date.find({"collection_name": "viruclust_db_0"},
{"date": {"$toString": '$date_of_import'}})
result_to_return = results[0]['date'].split('T')[0]
return result_to_return

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2 changes: 1 addition & 1 deletion backend/app.py
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Expand Up @@ -8,7 +8,7 @@

from apis import api_blueprint

base_url = '/viruclust_gisaid/'
base_url = '/viruclust/'
api_url = base_url + 'api'
repo_static_url = base_url + 'repo_static'

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26 changes: 13 additions & 13 deletions frontend/src/components/AnalyzeProvinceRegion.vue
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Expand Up @@ -7,33 +7,33 @@
<h1>EVOLUTION IN SPACE</h1>
</v-card-title>
<v-card-text>
<v-layout row wrap justify-center style="padding: 30px;">
<v-layout row wrap justify-space-between style="padding: 30px;">
<v-flex class="no-horizontal-padding xs12 d-flex" style="justify-content: center; margin-top: 10px">
<h2>PICK A LINEAGE, PLACE AND INTERVAL OF TIME</h2>
</v-flex>
<v-flex class="no-horizontal-padding xs12 lg6 xl3 d-flex" style="justify-content: center;">
<v-flex class="no-horizontal-padding xs12 lg12 xl12 d-flex" style="justify-content: center;">
<SelectorsQueryGeo
field = 'lineage'>
</SelectorsQueryGeo>
</v-flex>
<v-flex class="no-horizontal-padding xs12 d-flex" style="justify-content: center;">
</v-flex>
<v-flex class="no-horizontal-padding xs12 lg6 xl3 d-flex" style="justify-content: center;">
<v-flex class="no-horizontal-padding xs12 md6 lg2 d-flex" style="justify-content: center;">
<SelectorsQueryGeo
field = 'geo_group'>
</SelectorsQueryGeo>
</v-flex>
<v-flex class="no-horizontal-padding xs12 lg6 xl3 d-flex" style="justify-content: center;">
<v-flex class="no-horizontal-padding xs12 md6 lg2 d-flex" style="justify-content: center;">
<SelectorsQueryGeo
field = 'country'>
</SelectorsQueryGeo>
</v-flex>
<v-flex class="no-horizontal-padding xs12 lg6 xl3 d-flex" style="justify-content: center;">
<v-flex class="no-horizontal-padding xs12 md6 lg2 d-flex" style="justify-content: center;">
<SelectorsQueryGeo
field = 'region'>
</SelectorsQueryGeo>
</v-flex>
<v-flex class="no-horizontal-padding xs12 lg6 xl3 d-flex" style="justify-content: center;">
<v-flex class="no-horizontal-padding xs12 md6 lg2 d-flex" style="justify-content: center;">
<SelectorsQueryGeo
field = 'province'>
</SelectorsQueryGeo>
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% BACKGROUND
</v-card-title>
<v-card-text>
...
This filter allows to reduce the number of mutations shown in the results, based on the percentage of appearance of each mutation in the background population.
</v-card-text>
</v-card>
</v-dialog>
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# SEQUENCES IN BACKGROUND
</v-card-title>
<v-card-text>
...
This filter allows to reduce the number of mutations shown in the results, based on the appearance (in absolute numbers) of each mutation in the background population.
</v-card-text>
</v-card>
</v-dialog>
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% TARGET
</v-card-title>
<v-card-text>
...
This filter allows to reduce the number of mutations shown in the results, based on the percentage of appearance of each mutation in the target population.
</v-card-text>
</v-card>
</v-dialog>
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# SEQUENCES IN TARGET
</v-card-title>
<v-card-text>
...
This filter allows to reduce the number of mutations shown in the results, based on the appearance (in absolute numbers) of each mutation in the target population.
</v-card-text>
</v-card>
</v-dialog>
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P-VALUE
</v-card-title>
<v-card-text>
...
This filter allows to reduce the number of mutations shown in the results, based on their p-values. The p-value is calculated through a chi-squared test.
</v-card-text>
</v-card>
</v-dialog>
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ODDS RATIO
</v-card-title>
<v-card-text>
...
This filter allows to reduce the number of mutations shown in the results, based on their odds ratio. The odds ratio is calculated as: (percentage in target + epsilon) / (percentage in background + epsilon)
</v-card-text>
</v-card>
</v-dialog>
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FILTER PROTEIN
</v-card-title>
<v-card-text>
...
This filter allows to reduce the number of mutations shown in the results, based on their protein.
</v-card-text>
</v-card>
</v-dialog>
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