diff --git a/README.md b/README.md
index c5fe2b67bebabf27386ac7271b66be7f12701267..cabdf5cb47a4edd9996cb47495b47492a9def755 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
-# 12765-ViralHostRangeDB
+# ViralHostRangeDB
Running at https://viralhostrangedb.pasteur.cloud/
-Documentation at http://hub.pages.pasteur.fr/12765-viralhostrangedb/
+Documentation at http://hub.pages.pasteur.fr/viralhostrangedb/
-
+
diff --git a/doc/compatible_file.rst b/doc/compatible_file.rst
index 787f6db19e0f30f01b58ea805e52d7500afbe9d7..ee2467ec952fde737f95c2736b51136fe7704405 100644
--- a/doc/compatible_file.rst
+++ b/doc/compatible_file.rst
@@ -17,7 +17,7 @@ A compatible file is an Excel spreadsheet (.xlsx) in which :term:`hosts` are ind
| MyVirus | 2 | 1 |
+---------------------------+-------------------------------+------------------------------+
-User can also download the xlsx version `here <https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/blob/master/src/viralhostrange/viralhostrangedb/static/media/example.xlsx>`_.
+User can also download the xlsx version `here <https://gitlab.pasteur.fr/hub/viralhostrangedb/blob/master/src/viralhostrange/viralhostrangedb/static/media/example.xlsx>`_.
Detailed version
-------
@@ -82,6 +82,6 @@ Variants in the file disposition
Robustness of file import
~~~~~~~~~~~~~~~~~~~~~~~~~
-The resilience of the importation module to read and interpret the file is of a paramount importance, we generated multiple configuration in which a file could be written and how we should read it. At each change in the programme we test that each file is still read as expected. The file collection can be browsed at https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/tree/master/src/viralhostrange/test_data, where for an input file ``<filename>.xlsx`` the data we extract from it is ``<filename>.xlsx.json``.
+The resilience of the importation module to read and interpret the file is of a paramount importance, we generated multiple configuration in which a file could be written and how we should read it. At each change in the programme we test that each file is still read as expected. The file collection can be browsed at https://gitlab.pasteur.fr/hub/viralhostrangedb/tree/master/src/viralhostrange/test_data, where for an input file ``<filename>.xlsx`` the data we extract from it is ``<filename>.xlsx.json``.
-If you tried to import a file which should work but did not, please to not hesitate to submit an issue at https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/issues with the file cleaned of its private data. You can also e-mail the file and steps to reproduce the bug at viralhostrangedb@pasteur.fr. We will either correct the importation module so that the file can now be imported, or return a error message clear enough so users understand what is wrong with their file.
+If you tried to import a file which should work but did not, please to not hesitate to submit an issue at https://gitlab.pasteur.fr/hub/viralhostrangedb/issues with the file cleaned of its private data. You can also e-mail the file and steps to reproduce the bug at viralhostrangedb@pasteur.fr. We will either correct the importation module so that the file can now be imported, or return a error message clear enough so users understand what is wrong with their file.
diff --git a/doc/conf.py b/doc/conf.py
index 6341d41c6a475d571621e4ce00d2573fd6c46c17..2be89b6f3c3506f167e4734846ac2c9706323d62 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -74,7 +74,7 @@ html_context = {
"display_gitlab": True, # Integrate Gitlab
"gitlab_user": "hub", # Username
"gitlab_host": "gitlab.pasteur.fr",
- "gitlab_repo": "12765-viralhostrangedb", # Repo name
+ "gitlab_repo": "viralhostrangedb", # Repo name
"gitlab_version": "master", # Version
"conf_py_path": "/doc/", # Path in the checkout to the docs root
}
@@ -85,4 +85,4 @@ html_theme_options = {
html_css_files = [
'theme_overrides.css',
-]
\ No newline at end of file
+]
diff --git a/doc/data_import.rst b/doc/data_import.rst
index 1f1b55d2db72cd3b62c1ef8d39658985d899b7ff..32ac7f582733264fc6efe807ceae6db9ea724064 100644
--- a/doc/data_import.rst
+++ b/doc/data_import.rst
@@ -151,7 +151,7 @@ Example
Computing details about the mapping tresholds
~~~~~~~~~~~~~~~~~~~~~~
-To compute the thresholds, a clustering algorithm is run on the original :term:`responses` of the :term:`data source` with three clusters :math:`c_1`, :math:`c_2` and :math:`c_3`, then the threshold between :math:`c_k` and :math:`c_{k+1}` is the mean of the centroid of the these two clusters. Implementation code can be found in the `RangeMappingForm implementation <https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/blob/master/src/viralhostrange/viralhostrangedb/forms.py#L296-308>`_.
+To compute the thresholds, a clustering algorithm is run on the original :term:`responses` of the :term:`data source` with three clusters :math:`c_1`, :math:`c_2` and :math:`c_3`, then the threshold between :math:`c_k` and :math:`c_{k+1}` is the mean of the centroid of the these two clusters. Implementation code can be found in the `RangeMappingForm implementation <https://gitlab.pasteur.fr/hub/viralhostrangedb/blob/master/src/viralhostrange/viralhostrangedb/forms.py#L296-308>`_.
diff --git a/doc/index.rst b/doc/index.rst
index 783982f8a1e1c63ba1e84303f8e82514b8224059..3848bc2208305f170834f763c9eb607bb33fb163 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -6,7 +6,7 @@
VHRdb documentation
===================
-You found a bug ? Please submit an issue in the `issue tracking system <https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/issues>`_
+You found a bug ? Please submit an issue in the `issue tracking system <https://gitlab.pasteur.fr/hub/viralhostrangedb/issues>`_
You have a question ? Please send us an email at viralhostrangedb at pasteur.fr.
diff --git a/joss/paper.md b/joss/paper.md
index 6fdd8db58d4d36d39acd63e9665f3aaad55f411d..14a7f8a75a0cd6d1614d2b0586b4fcb4f147b038 100644
--- a/joss/paper.md
+++ b/joss/paper.md
@@ -51,7 +51,7 @@ Data source can be public, but also private with the ability to share it with na
## Sharing data with the community
-Easing the process of sharing a data source is crucial for the adoption of VHRdb by the virology community. We decomposed the submission of a new data source into multiple step (i.e a *wizard form* pattern). First, the user provide general information and indicate if the data source is public, if not the next step let him/her specify the list of user granted to see the data source. Then, the user is encourage to given an extensive description of the experiment (lab, experimenter, scoring method, ...). To import the data, they have to be stored in spreadsheet file (Excel, LibreOffice) following a specific, yet simple, format documented [here](http://hub.pages.pasteur.fr/12765-viralhostrangedb/compatible_file.html). The user can either indicate that she/he has a file following the format, or can generate a tailored template file. To generate the template he/she provides the list of hosts and viruses for which she/he has responses. At the last step the template can be downloaded, filled by the user and re-uploaded.
+Easing the process of sharing a data source is crucial for the adoption of VHRdb by the virology community. We decomposed the submission of a new data source into multiple step (i.e a *wizard form* pattern). First, the user provide general information and indicate if the data source is public, if not the next step let him/her specify the list of user granted to see the data source. Then, the user is encourage to given an extensive description of the experiment (lab, experimenter, scoring method, ...). To import the data, they have to be stored in spreadsheet file (Excel, LibreOffice) following a specific, yet simple, format documented [here](http://hub.pages.pasteur.fr/viralhostrangedb/compatible_file.html). The user can either indicate that she/he has a file following the format, or can generate a tailored template file. To generate the template he/she provides the list of hosts and viruses for which she/he has responses. At the last step the template can be downloaded, filled by the user and re-uploaded.
Each data source can have different standard in recording the response of the infection of an host by a virus. For example one can use a two-state scheme (0/1), while the other one would use a continuous scale from 0 to 4 (as in the following example). In order to compare a data source to the others, the data source owner have to map the dedicated scheme of its data source to the global scheme.
@@ -72,4 +72,4 @@ https://www.phage.ulaval.ca/fr/accueil/
We acknowledge Thomas Menard and the Direction des Service de l'Information of the Institut Pasteur in hosting the Kubernetes cluster, and their training in using this cluster.
-# References
\ No newline at end of file
+# References
diff --git a/src/viralhostrange/locale/en/LC_MESSAGES/django.po b/src/viralhostrange/locale/en/LC_MESSAGES/django.po
index d187380dfcc3bb0fdb4237bf6741b205468446b2..ede4c44ef703dd7d5f84df8b841d7bae3edb86de 100644
--- a/src/viralhostrange/locale/en/LC_MESSAGES/django.po
+++ b/src/viralhostrange/locale/en/LC_MESSAGES/django.po
@@ -8,7 +8,7 @@ msgid ""
msgstr ""
"Project-Id-Version: PACKAGE VERSION\n"
"Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2020-05-27 12:10+0200\n"
+"POT-Creation-Date: 2020-06-11 10:03+0200\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
"Language-Team: LANGUAGE <LL@li.org>\n"
@@ -787,8 +787,8 @@ msgid "curators_explanation_text"
msgstr ""
"Curators help maintaining a coherent naming scheme among the public data "
"sources. For more information on what a curator can and cannot do or see, "
-"please check the <a target=\"_blank\" href=\"http://hub.pages.pasteur."
-"fr/12765-viralhostrangedb/permissions.html#curator\">documentation</a>."
+"please check the <a target=\"_blank\" href=\"http://hub.pages.pasteur.fr/"
+"viralhostrangedb/permissions.html#curator\">documentation</a>."
msgid "Team"
msgstr ""
@@ -1168,9 +1168,9 @@ msgstr ""
"be mapped to the global scheme. Please provide the thresholds values "
"allowing to distribute each original response to one of the accepted "
"responses. More help and example can be found in the <a href=\"http://hub."
-"pages.pasteur.fr/12765-viralhostrangedb/data_import.html#mapping-responses-"
-"to-the-global-scheme\" target=\"blank\">documentation</a>.</p><p>If the "
-"original response do not follow an ascending order (i.e responses are to be "
+"pages.pasteur.fr/viralhostrangedb/data_import.html#mapping-responses-to-the-"
+"global-scheme\" target=\"blank\">documentation</a>.</p><p>If the original "
+"response do not follow an ascending order (i.e responses are to be "
"considered as labels, not numbers), you can <a href=\"%(url_label_edit)s"
"\">go here</a> and assign manually each response.</p>"
@@ -1308,8 +1308,8 @@ msgstr ""
"is entered as a number. The recommended values to use are: %(scheme)s, but "
"you will later be able to map any value used to this global scheme. </"
"p><p>More information can be found in the <a target=\"_blank\" href=\"http://"
-"hub.pages.pasteur.fr/12765-viralhostrangedb/compatible_file.html"
-"\">documentation</a>.</p>"
+"hub.pages.pasteur.fr/viralhostrangedb/compatible_file.html\">documentation</"
+"a>.</p>"
msgid "Editing a data source"
msgstr ""
@@ -1565,8 +1565,8 @@ msgstr ""
"status is entered as a number. The recommended values to use are: "
"%(scheme)s, but you will later be able to map any value used to this global "
"scheme. </p><p>More information on a <i>compatible file</i> can be found in "
-"the <a target=\"_blank\" href=\"http://hub.pages.pasteur.fr/12765-"
-"viralhostrangedb/compatible_file.html\">documentation</a>.</p>"
+"the <a target=\"_blank\" href=\"http://hub.pages.pasteur.fr/viralhostrangedb/"
+"compatible_file.html\">documentation</a>.</p>"
#, python-format
msgid "step_message_Upload%(scheme)s"
@@ -1581,14 +1581,14 @@ msgstr ""
"later in the data source page by editing hosts/viruses.</p><p>Note that "
"colors only are not be taken into account during import. </p><p>More "
"information can be found in the <a target=\"_blank\" href=\"http://hub.pages."
-"pasteur.fr/12765-viralhostrangedb/compatible_file.html\">documentation</a>.</"
+"pasteur.fr/viralhostrangedb/compatible_file.html\">documentation</a>.</"
"p><p><i>‡ Only for bacterial viruses</i></p>"
msgid "step_message_LiveInput when is_bound"
msgstr ""
"You can now provide the list of viruses and hosts you want to add to your "
"data source. <br/>If you have your elements along with their identifiers "
-"(see <a target=\"_blank\" href=\"http://hub.pages.pasteur.fr/12765-"
+"(see <a target=\"_blank\" href=\"http://hub.pages.pasteur.fr/"
"viralhostrangedb/virus_host_identifiers.html\">documentation</a>), you can "
"copy/paste them from a spreadsheet in a format with two column where the "
"first column is the name, and the second column is the identifier. <br/>If "
@@ -1602,7 +1602,7 @@ msgid "step_message_LiveInput when not is_bound"
msgstr ""
"You can now provide the list of viruses and hosts you want to add to your "
"data source. <br/>If you have your elements along with their identifiers "
-"(see <a target=\"_blank\" href=\"http://hub.pages.pasteur.fr/12765-"
+"(see <a target=\"_blank\" href=\"http://hub.pages.pasteur.fr/"
"viralhostrangedb/virus_host_identifiers.html\">documentation</a>), you can "
"copy/paste them from a spreadsheet in a format with two column where the "
"first column is the name, and the second column is the identifier."
@@ -1622,7 +1622,7 @@ msgstr ""
"\"Identifier\" class=\"border border-secondary\">id of Virus 1</span>;<span "
"title=\"Identifier\" class=\"border border-secondary\">HER:27</span>)</"
"code></p><p>More information can be found in the <a target=\"_blank\" href="
-"\"http://hub.pages.pasteur.fr/12765-viralhostrangedb/compatible_file.html"
+"\"http://hub.pages.pasteur.fr/viralhostrangedb/compatible_file.html"
"\">documentation</a>.</p><p><i>‡ Only for bacterial viruses</i></p>"
msgid "Fig 1: A (subset of) your template<br/>"
diff --git a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/base.html b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/base.html
index 145580f3f9105a6a0f3e14e91aa6dab1cfbdeefb..557b122a2bf7565382d1748c6a8efed0a1c6e9b9 100644
--- a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/base.html
+++ b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/base.html
@@ -18,7 +18,7 @@
{% block upper_nav_bar_right_before_form %}
-<li class="nav-item"><a class="nav-link" href="http://hub.pages.pasteur.fr/12765-viralhostrangedb/" target="_blank"><i class="fa fa-book"></i> {%trans "Documentation"%}</a></li>
+<li class="nav-item"><a class="nav-link" href="http://hub.pages.pasteur.fr/viralhostrangedb/" target="_blank"><i class="fa fa-book"></i> {%trans "Documentation"%}</a></li>
{% endblock %}
{% block upper_nav_bar_right_form %}
diff --git a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/datasource_detail.html b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/datasource_detail.html
index 977af00b7c2df1b82a7c3d79461751220cff4c53..940fcb2879556cc27bd14059b79bc7ff060df0d0 100644
--- a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/datasource_detail.html
+++ b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/datasource_detail.html
@@ -154,7 +154,7 @@
class="float-right btn btn-outline-primary">
<i class="fa fa-download"></i> {%trans "Download it" %}
</a>
- <a href="http://hub.pages.pasteur.fr/12765-viralhostrangedb/compatible_file.html" target="_blank" style="flex-grow:0"
+ <a href="http://hub.pages.pasteur.fr/viralhostrangedb/compatible_file.html" target="_blank" style="flex-grow:0"
class="float-right btn btn-outline-primary">
<i class="fa fa-question-circle"></i>
</a>
diff --git a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/datasource_history.html b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/datasource_history.html
index da963f5a0ee1f11c96df8b3d7865cfda5f12587f..9124b45f04744d2b7e237a7d9a9d62634685d716 100644
--- a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/datasource_history.html
+++ b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/datasource_history.html
@@ -46,7 +46,7 @@
{%endif%}
{% else %}
<i>{%trans 'Backup missing' %}</i>
- <a href="http://hub.pages.pasteur.fr/12765-viralhostrangedb/history.html#life-cycle-of-a-backup"
+ <a href="http://hub.pages.pasteur.fr/viralhostrangedb/history.html#life-cycle-of-a-backup"
title="{%trans 'See life cycle of a backup'%}"
target="_blank">
<i class="fa fa-question-circle"></i>
@@ -65,7 +65,7 @@
<th class="dt-combobox">{%trans "Change By"%}</th>
<th class="dt-column-filter">{%trans "Changes"%}</th>
<th class="text-center pt-3">
- <a href="http://hub.pages.pasteur.fr/12765-viralhostrangedb/history.html" target="_blank">
+ <a href="http://hub.pages.pasteur.fr/viralhostrangedb/history.html" target="_blank">
<i class="fa fa-book"></i>
{%trans "See backup strategy"%}
</a>
diff --git a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/login_menu.html b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/login_menu.html
index b22b9bbe4eab3db408d60cfc3aafb98b6db8fa55..ff7ac9f9d1dbf2acfb2ab63991fd8c9deba11695 100644
--- a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/login_menu.html
+++ b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/login_menu.html
@@ -1,5 +1,5 @@
{% extends "basetheme_bootstrap/login_menu.html" %}
{% block login_menu_staff_dropdown_items %}
{{block.super}}
-<a class="dropdown-item" href="https://gitlab.pasteur.fr/hub/12765-viralhostrangedb" target="_blank"><i class="fa fa-bug"></i> Issue tracking</a>
+<a class="dropdown-item" href="https://gitlab.pasteur.fr/hub/viralhostrangedb" target="_blank"><i class="fa fa-bug"></i> Issue tracking</a>
{% endblock %}
\ No newline at end of file
diff --git a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/nav_bar.html b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/nav_bar.html
index 3e84f469a4bfc60c606c9d555dc2cab6535576c0..0a0e9d197c0c1470bdb12819902b7331c0d4b1ad 100644
--- a/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/nav_bar.html
+++ b/src/viralhostrange/viralhostrangedb/templates/viralhostrangedb/nav_bar.html
@@ -11,7 +11,7 @@
<span class="btf-virus"></span> {%trans "Viruses"%}</a></li>
<li class="nav-item hidden-in-header"><a class="nav-link" href="{% url 'viralhostrangedb:host-list'%}"><span class="btf-host"></span> {%trans "Hosts"%}</a></li>
<li class="nav-item"><a class="nav-link" href="{% url 'viralhostrangedb:search'%}"><i class="fa fa-search"></i> {%trans "Search"%}</a></li>
-<li class="nav-item hidden-in-header"><a class="nav-link" href="http://hub.pages.pasteur.fr/12765-viralhostrangedb/"><i class="fa fa-book"></i> {%trans "Documentation"%}</a></li>
+<li class="nav-item hidden-in-header"><a class="nav-link" href="http://hub.pages.pasteur.fr/viralhostrangedb/"><i class="fa fa-book"></i> {%trans "Documentation"%}</a></li>
<li class="nav-item {{ request|is_active_or_desc:'basetheme_bootstrap:about_page'}}"><a class="nav-link" href="{% url 'basetheme_bootstrap:about_page'%}">{%trans "About"%}</a></li>
<form class="form-inline d-sm-none d-md-none d-lg-none d-xl-none" action="{% url 'viralhostrangedb:search' %}" method="post">{% csrf_token %}
<input class="form-control" name="search" type="text" value="{{search_bar_value}}" placeholder="{%trans 'Type your search here'%}" aria-label="Search">