From ef54b46265442bbc865fd78bd68915a78de3e53a Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 31 Jan 2024 16:28:06 +0100
Subject: [PATCH 1/3] fixed Omnicrobe API base URL
---
static/files/omnicrobe.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/static/files/omnicrobe.py b/static/files/omnicrobe.py
index adb8d1d..e349598 100644
--- a/static/files/omnicrobe.py
+++ b/static/files/omnicrobe.py
@@ -27,7 +27,9 @@ Variables:
import requests
-BASE_URL = 'http://omnicrobe.migale.inrae.fr/api'
+
+BASE_URL = 'https://omnicrobe.migale.inrae.fr/api'
+
class OmnicrobeError(Exception):
def __init__(self, *args, **kwargs):
--
GitLab
From 2fdadce8754060ef44635463eabb751deff35e23 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 31 Jan 2024 16:28:30 +0100
Subject: [PATCH 2/3] Python code style
---
static/files/omnicrobe.py | 44 ++++++++++++++++++++-------------------
1 file changed, 23 insertions(+), 21 deletions(-)
diff --git a/static/files/omnicrobe.py b/static/files/omnicrobe.py
index e349598..5999c53 100644
--- a/static/files/omnicrobe.py
+++ b/static/files/omnicrobe.py
@@ -1,3 +1,6 @@
+#!/usr/bin/env python3.6
+
+
# Copyright 2022 Robert Bossy (INRAE)
#
# Licensed under the Apache License, Version 2.0 (the "License");
@@ -12,7 +15,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-#!/usr/bin/env python3.6
'''Wrapper objects and functions for the Omnicrobe REST API. See: http://omnicrobe.migale.inrae.fr/api.
@@ -202,6 +204,7 @@ class OBTType(object):
return obt_type.name
return str(obt_type)
+
HABITAT = OBTType('habitat')
PHENOTYPE = OBTType('phenotype')
USE = OBTType('use')
@@ -332,42 +335,41 @@ class Relation:
)
-
if __name__ == '__main__':
- print ('Version')
- print (version())
- print ('\n')
+ print('Version')
+ print(version())
+ print('\n')
- print ('taxon info by id')
+ print('taxon info by id')
bs = Taxon('ncbi:1423')
- print (bs)
+ print(bs)
print('\n')
- print ('obt info by id')
+ print('obt info by id')
soil = OBT('OBT:000427')
- print (soil)
+ print(soil)
print('\n')
- print ('search taxon descendants')
+ print('search taxon descendants')
for t in Taxon.search(root=bs):
- print (t.identifier)
+ print(t.identifier)
print('\n')
- print ('search taxon name')
+ print('search taxon name')
for t in Taxon.search('propionibacterium'):
- print (t.identifier)
+ print(t.identifier)
print('\n')
- print ('search obt descendants')
+ print('search obt descendants')
for o in OBT.search(root=soil):
- print (o.identifier)
- print ('\n')
+ print(o.identifier)
+ print('\n')
- print ('search obt name')
+ print('search obt name')
for o in OBT.search('food'):
- print (o.identifier)
- print ('\n')
+ print(o.identifier)
+ print('\n')
- print ('search relations')
+ print('search relations')
for r in Relation.search(taxon=bs, obt=soil, qps=True, sources='GenBank'):
- print (r)
+ print(r)
--
GitLab
From 394e206416a6266834742142340de20f64372dcb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sandra=20D=C3=A9rozier?= <sandra.derozier@inra.fr>
Date: Mon, 6 May 2024 10:04:53 +0200
Subject: [PATCH 3/3] Release April 2024
---
templates/release.html | 106 ++++++++++++++++++++++++++++++++++++-----
1 file changed, 95 insertions(+), 11 deletions(-)
diff --git a/templates/release.html b/templates/release.html
index 58c81d1..4ff9589 100644
--- a/templates/release.html
+++ b/templates/release.html
@@ -27,8 +27,103 @@
<div style="margin-left: 5%;margin-right: 5%;">
<h2><span style="color: #21517A;">Release Notes</span></h2><br/>
+ <div class="alert alert-info" role="alert">
+ To keep users of the application informed of new features, we’ve set up a dedicated mailing list: <a class="text-info" href="mailto:omnicrobe-users-request@groupes.renater.fr">omnicrobe-users-request@groupes.renater.fr</a>, which you can subscribe to by <a href="https://groupes.renater.fr/sympa/subscribe/omnicrobe-users?previous_action=edit_list_request" target="_blank" class="text-info">clicking here</a>.
+ </div>
+
<p><h4 class="text-info">Current release</h4></p>
+ <div class="card" style="border-color: #21517A;">
+ <div class="card-header text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ Omnicrobe 1.4 (<i>current release</i>)
+ </div>
+ <div class="card-body">
+ <p align='justify'>
+ <h5 class="text-info">Information about the data</h5>
+ <ul>
+ <li>Ontologies used: <a href="http://agroportal.lirmm.fr/ontologies/ONTOBIOTOPE" target="_blank">OntoBiotope</a> version 2022-04-28 & <a href="https://forgemia.inra.fr/omnicrobe/extended-microorganisms-taxonomy" target="_blank">Taxonomy</a> version 2024-04-18.</li>
+ </ul>
+ <div style="margin-left: 15%;margin-right: 15%;">
+ <table class="table table-sm table-striped">
+ <caption class="text-center">Versions and number of relationships per source</caption>
+ <thead>
+ <tr>
+ <th scope="col"></th>
+ <th class="text-right" scope="col">PubMed</th>
+ <th class="text-right" scope="col">GenBank</th>
+ <th class="text-right" scope="col">DSMZ</th>
+ <th class="text-right" scope="col">CIRM-BIA</th>
+ <th class="text-right" scope="col">CIRM-CFBP</th>
+ <th class="text-right" scope="col">CIRM-Levures</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <th scope="row">Version</th>
+ <td class="text-right">2024-04-18</td>
+ <td class="text-right">2024-04-18</td>
+ <td class="text-right">2024-04-18</td>
+ <td class="text-right">2023-03-09</td>
+ <td class="text-right">2023-03-16</td>
+ <td class="text-right">2022-10-14</td>
+ </tr>
+ <tr>
+ <th scope="row">Taxa - Habitat relations</th>
+ <td class="text-right">628,173</td>
+ <td class="text-right">296,517</td>
+ <td class="text-right">53,616</td>
+ <td class="text-right">707</td>
+ <td class="text-right">1,125</td>
+ <td class="text-right">936</td>
+ </tr>
+ <tr>
+ <th scope="row">Taxa - Phenotype relations</th>
+ <td class="text-right">45,408</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ </tr>
+ <tr>
+ <th scope="row">Taxa - Use relations</th>
+ <td class="text-right">14,169</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+
+ <h5 class="text-info">New features and improvements in this release</h5>
+ <ul>
+ <li>improved extraction quality</li>
+ <li>improved taxon name disambiguation</li>
+ <li>fixed bugs</li>
+ <li>updated taxonomy</li>
+ <li>updated PubMed, GenBank and DSMZ data</li>
+ </ul>
+ <!-- <h5 class="text-info">Fixed in this release</h5>
+ <ul>
+ <li>...</li>
+ </ul> -->
+ <!--h5 class="text-info">Source code</h5>
+ <ul>
+ <li>Text-mining workflow: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
+ <li>Web interface: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
+ </ul-->
+ </p>
+ </div>
+ <div class="card-footer text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ 22 April 2024
+ </div>
+ </div>
+ <br/>
+ <p><h4 class="text-info">Previous releases</h4></p>
+
<div class="card" style="border-color: #21517A;">
<div class="card-header text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
Omnicrobe 1.3 (<i>current release</i>)
@@ -100,23 +195,12 @@
<li>fixed bugs</li>
<li>updated taxonomy</li>
</ul>
- <!-- <h5 class="text-info">Fixed in this release</h5>
- <ul>
- <li>...</li>
- </ul> -->
- <!--h5 class="text-info">Source code</h5>
- <ul>
- <li>Text-mining workflow: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
- <li>Web interface: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
- </ul-->
</p>
</div>
<div class="card-footer text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
19 October 2023
</div>
</div>
- <br/>
- <p><h4 class="text-info">Previous releases</h4></p>
<div class="card" style="border-color: #21517A;">
<div class="card-header text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
--
GitLab