From 27b31be1c8cf721f3b8b78d20839a4ac51f99ebc Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Thu, 11 Jun 2020 10:04:26 +0200
Subject: [PATCH] renaming gitlab project, remove project number
---
README.md | 6 ++--
doc/compatible_file.rst | 6 ++--
doc/conf.py | 4 +--
doc/data_import.rst | 2 +-
doc/index.rst | 2 +-
joss/paper.md | 4 +--
.../locale/en/LC_MESSAGES/django.po | 28 +++++++++----------
.../templates/viralhostrangedb/base.html | 2 +-
.../viralhostrangedb/datasource_detail.html | 2 +-
.../viralhostrangedb/datasource_history.html | 4 +--
.../viralhostrangedb/login_menu.html | 2 +-
.../templates/viralhostrangedb/nav_bar.html | 2 +-
12 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/README.md b/README.md
index c5fe2b67..cabdf5cb 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 787f6db1..ee2467ec 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 6341d41c..2be89b6f 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 1f1b55d2..32ac7f58 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 783982f8..3848bc22 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 6fdd8db5..14a7f8a7 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 d187380d..ede4c44e 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 145580f3..557b122a 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 977af00b..940fcb28 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 da963f5a..9124b45f 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 b22b9bbe..ff7ac9f9 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 3e84f469..0a0e9d19 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">
--
GitLab