diff --git a/uploader/publications/views.py b/uploader/publications/views.py
index 4ec832f..f0ec95a 100644
--- a/uploader/publications/views.py
+++ b/uploader/publications/views.py
@@ -10,6 +10,8 @@ from flask import (
render_template,
current_app as app)
+from uploader.sui import sui_template
+
from uploader.flask_extensions import url_for
from uploader.authorisation import require_login
from uploader.route_utils import redirect_to_next
@@ -30,7 +32,7 @@ pubbp = Blueprint("publications", __name__)
@require_login
def index():
"""Index page for publications."""
- return render_template("publications/index.html")
+ return render_template(sui_template("publications/index.html"))
@pubbp.route("/list", methods=["GET"])
@@ -72,7 +74,7 @@ def view_publication(publication_id: int):
return redirect(url_for('publications.index'))
return render_template(
- "publications/view-publication.html",
+ sui_template("publications/view-publication.html"),
publication=publication,
linked_phenotypes=tuple(fetch_publication_phenotypes(
conn, publication_id)))
@@ -82,13 +84,21 @@ def view_publication(publication_id: int):
@require_login
def create_publication():
"""Create a new publication."""
+ _get_args = {
+ key: request.args[key]
+ for key in ("species_id", "population_id", "dataset_id", "return_to")
+ if bool(request.args.get(key))
+ }
+
if request.method == "GET":
- return render_template("publications/create-publication.html")
+ return render_template(
+ sui_template("publications/create-publication.html"),
+ get_args=_get_args)
form = request.form
authors = form.get("publication-authors").encode("utf8")
if authors is None or authors == "":
flash("The publication's author(s) MUST be provided!", "alert alert-danger")
- return redirect(url_for("publications.create", **request.args))
+ return redirect(url_for("publications.create"))
with database_connection(app.config["SQL_URI"]) as conn:
publications = create_new_publications(conn, ({
@@ -106,7 +116,7 @@ def create_publication():
return redirect(url_for(
request.args.get("return_to") or "publications.view_publication",
publication_id=publications[0]["publication_id"],
- **request.args))
+ **_get_args))
flash("Publication creation failed!", "alert alert-danger")
app.logger.debug("Failed to create the new publication.", exc_info=True)
@@ -120,7 +130,7 @@ def edit_publication(publication_id: int):
with database_connection(app.config["SQL_URI"]) as conn:
if request.method == "GET":
return render_template(
- "publications/edit-publication.html",
+ sui_template("publications/edit-publication.html"),
publication=fetch_publication_by_id(conn, publication_id),
linked_phenotypes=tuple(fetch_publication_phenotypes(
conn, publication_id)),
@@ -171,15 +181,16 @@ def delete_publication(publication_id: int):
flash("Cannot delete publication with linked phenotypes!",
"alert-warning")
return redirect(url_for(
- "publications.view_publication", publication_id=publication_id))
+ sui_template("publications.view_publication"),
+ publication_id=publication_id))
if request.method == "GET":
return render_template(
- "publications/delete-publication.html",
+ sui_template("publications/delete-publication.html"),
publication=publication,
linked_phenotypes=linked_phenotypes,
publication_id=publication_id)
delete_publications(conn, (publication,))
flash("Deleted the publication successfully.", "alert-success")
- return render_template("publications/delete-publication-success.html")
+ return redirect(url_for("publications.index"))
diff --git a/uploader/route_utils.py b/uploader/route_utils.py
index 4449475..fa63233 100644
--- a/uploader/route_utils.py
+++ b/uploader/route_utils.py
@@ -56,15 +56,17 @@ def generic_select_population(
def redirect_to_next(default: dict):
"""Redirect to the next uri if specified, else redirect to default."""
assert "uri" in default, "You must provide at least the 'uri' value."
- try:
- next_page = base64_decode_to_dict(request.args.get("next"))
- _uri = next_page["uri"]
- next_page.pop("uri")
- return redirect(url_for(_uri, **next_page))
- except (TypeError, JSONDecodeError) as _err:
- logger.debug("We could not decode the next value '%s'",
- next_page,
- exc_info=True)
+ _next = request.args.get("next")
+ if bool(_next):
+ try:
+ next_page = base64_decode_to_dict(_next)
+ _uri = next_page["uri"]
+ next_page.pop("uri")
+ return redirect(url_for(_uri, **next_page))
+ except (TypeError, JSONDecodeError) as _err:
+ logger.debug("We could not decode the next value '%s'",
+ next_page,
+ exc_info=True)
return redirect(url_for(
default["uri"],
diff --git a/uploader/static/css/theme.css b/uploader/static/css/theme.css
index 99b7af3..bdac745 100644
--- a/uploader/static/css/theme.css
+++ b/uploader/static/css/theme.css
@@ -83,3 +83,8 @@ table.dataTable tbody tr.selected td {
padding-bottom: 0.2em;
border-bottom: solid gray 1px;
}
+
+
+.breadcrumb-item {
+ text-transform: Capitalize;
+}
diff --git a/uploader/templates/phenotypes/sui-view-dataset.html b/uploader/templates/phenotypes/sui-view-dataset.html
index 6a26004..f858c4e 100644
--- a/uploader/templates/phenotypes/sui-view-dataset.html
+++ b/uploader/templates/phenotypes/sui-view-dataset.html
@@ -53,14 +53,6 @@
title="Add a bunch of phenotypes"
class="btn btn-primary">Add phenotypes</a>
</div>
-
- <div class="col">
- <a href="#"
- title="List all existing publications for this population."
- class="btn btn-primary not-implemented">view publications</a>
- <!-- Maybe, actually filter publications by population? -->
- <!-- Provide other features for publications on loaded page. -->
- </div>
<div class="col">
<form id="frm-recompute-phenotype-means"
diff --git a/uploader/templates/publications/sui-base.html b/uploader/templates/publications/sui-base.html
new file mode 100644
index 0000000..64e41ef
--- /dev/null
+++ b/uploader/templates/publications/sui-base.html
@@ -0,0 +1,9 @@
+{%extends "sui-base.html"%}
+
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
+ <a href="{{url_for('publications.index')}}"
+ title="Manage publications">Publications</a>
+</li>
+{%endblock%}
diff --git a/uploader/templates/publications/sui-create-publication.html b/uploader/templates/publications/sui-create-publication.html
new file mode 100644
index 0000000..81edca6
--- /dev/null
+++ b/uploader/templates/publications/sui-create-publication.html
@@ -0,0 +1,200 @@
+{%extends "publications/sui-base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}View Publication{%endblock%}
+
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
+ <a href="{{url_for('publications.create_publication', **get_args)}}"
+ title="Manage publications">create publication</a>
+</li>
+{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <form id="frm-create-publication"
+ method="POST"
+ action="{{url_for('publications.create_publication', **get_args)}}"
+ class="form-horizontal">
+
+ <div class="row mb-3">
+ <label for="txt-pubmed-id" class="col-sm-2 col-form-label">
+ PubMed ID</label>
+ <div class="col-sm-10">
+ <div class="input-group">
+ <input type="text"
+ id="txt-pubmed-id"
+ name="pubmed-id"
+ class="form-control"/>
+ <div class="input-group-text">
+ <button class="btn btn-outline-primary"
+ id="btn-search-pubmed-id">search</button>
+ </div>
+ </div>
+ <span id="search-pubmed-id-error"
+ class="form-text text-muted text-danger visually-hidden">
+ </span>
+ <span class="form-text text-muted">This is the publication's ID on
+ <a href="https://pubmed.ncbi.nlm.nih.gov/"
+ title="Link to NCBI's PubMed service">NCBI's Pubmed Service</a>
+ </span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-title" class="col-sm-2 col-form-label">
+ Title</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-title"
+ name="publication-title"
+ class="form-control" />
+ <span class="form-text text-muted">Provide the publication's title here.</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-authors" class="col-sm-2 col-form-label">
+ Authors</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-authors"
+ name="publication-authors"
+ required="required"
+ class="form-control" />
+ <span class="form-text text-muted">
+ A publication <strong>MUST</strong> have an author. You <em>must</em>
+ provide a value for the authors field.
+ </span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-journal" class="col-sm-2 col-form-label">
+ Journal</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-journal"
+ name="publication-journal"
+ class="form-control" />
+ <span class="form-text text-muted">Provide the name journal where the
+ publication was done, here.</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="select-publication-month"
+ class="col-sm-2 col-form-label">
+ Month</label>
+ <div class="col-sm-4">
+ <select class="form-control"
+ id="select-publication-month"
+ name="publication-month">
+ <option value="">Select a month</option>
+ <option value="january">January</option>
+ <option value="february">February</option>
+ <option value="march">March</option>
+ <option value="april">April</option>
+ <option value="may">May</option>
+ <option value="june">June</option>
+ <option value="july">July</option>
+ <option value="august">August</option>
+ <option value="september">September</option>
+ <option value="october">October</option>
+ <option value="november">November</option>
+ <option value="december">December</option>
+ </select>
+ <span class="form-text text-muted">Month of publication</span>
+ </div>
+
+ <label for="txt-publication-year"
+ class="col-sm-2 col-form-label">
+ Year</label>
+ <div class="col-sm-4">
+ <input type="number"
+ id="txt-publication-year"
+ name="publication-year"
+ class="form-control"
+ min="1960" />
+ <span class="form-text text-muted">Year of publication</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-volume"
+ class="col-sm-2 col-form-label">
+ Volume</label>
+ <div class="col-sm-4">
+ <input type="text"
+ id="txt-publication-volume"
+ name="publication-volume"
+ class="form-control">
+ <span class="form-text text-muted">Journal volume</span>
+ </div>
+
+ <label for="txt-publication-pages"
+ class="col-sm-2 col-form-label">
+ Pages</label>
+ <div class="col-sm-4">
+ <input type="text"
+ id="txt-publication-pages"
+ name="publication-pages"
+ class="form-control" />
+ <span class="form-text text-muted">Journal pages for the publication</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-abstract" class="col-sm-2 col-form-label">Abstract</label>
+ <div class="col-sm-10">
+ <textarea id="txt-publication-abstract"
+ name="publication-abstract"
+ class="form-control"
+ rows="7"></textarea>
+ </div>
+ </div>
+
+ <div class="row">
+ <div class="col">
+ <input type="submit"
+ class="btn btn-primary"
+ value="create publication" />
+ </div>
+ <div class="col">
+ <input type="reset" class="btn btn-danger" value="reset form" />
+ </div>
+ </div>
+
+</form>
+</div>
+
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/pubmed.js"></script>
+<script type="text/javascript">
+ $(function() {
+ $("#btn-search-pubmed-id").on("click", (event) => {
+ event.preventDefault();
+ var search_button = event.target;
+ var pubmed_id = $("#txt-pubmed-id").val().trim();
+ remove_class($("#txt-pubmed-id").parent(), "has-error");
+ if(pubmed_id == "") {
+ add_class($("#txt-pubmed-id").parent(), "has-error");
+ return false;
+ }
+
+ search_button.disabled = true;
+ // Fetch publication details
+ fetch_publication_details(pubmed_id,
+ [() => {search_button.disabled = false;}]);
+ return false;
+ });
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/publications/sui-delete-publication.html b/uploader/templates/publications/sui-delete-publication.html
new file mode 100644
index 0000000..436f2c1
--- /dev/null
+++ b/uploader/templates/publications/sui-delete-publication.html
@@ -0,0 +1,95 @@
+{%extends "publications/sui-base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Delete Publication{%endblock%}
+
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
+ <a href="{{url_for('publications.delete_publication',
+ publication_id=publication.Id)}}"
+ title="Manage publications">delete publication</a>
+</li>
+{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+<div class="row">
+ <p>You are about to delete the publication with the following details:</p>
+</div>
+
+<div class="row">
+ <table class="table">
+ <tr>
+ <th>Linked Phenotypes</th>
+ <td>{{linked_phenotypes | count}}</td>
+ </tr>
+ <tr>
+ <th>PubMed</th>
+ <td>
+ {%if publication.PubMed_ID%}
+ <a href="https://pubmed.ncbi.nlm.nih.gov/{{publication.PubMed_ID}}/"
+ target="_blank">{{publication.PubMed_ID}}</a>
+ {%else%}
+ —
+ {%endif%}
+ </td>
+ </tr>
+ <tr>
+ <th>Title</th>
+ <td>{{publication.Title or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Authors</th>
+ <td>{{publication.Authors or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Journal</th>
+ <td>{{publication.Journal or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Published</th>
+ <td>{{publication.Month or ""}} {{publication.Year or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Volume</th>
+ <td>{{publication.Volume or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Pages</th>
+ <td>{{publication.Pages or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Abstract</th>
+ <td>
+ {%for line in (publication.Abstract or "—").replace("\r\n", "<br />").replace("\n", "<br />").split("<br />")%}
+ <p>{{line}}</p>
+ {%endfor%}
+ </td>
+ </tr>
+ </table>
+</div>
+
+<div class="row">
+ <p>If you are sure that is what you want, click the button below to delete the
+ publication</p>
+ <p class="form-text text-small">
+ <small>You will not be able to recover the data if you click
+ delete below.</small></p>
+
+ <form action="{{url_for('publications.delete_publication', publication_id=publication_id)}}"
+ method="POST">
+ <div class="form-group">
+ <input type="submit" value="delete" class="btn btn-danger" />
+ </div>
+ </form>
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+ $(function() {});
+</script>
+{%endblock%}
diff --git a/uploader/templates/publications/sui-edit-publication.html b/uploader/templates/publications/sui-edit-publication.html
new file mode 100644
index 0000000..847b020
--- /dev/null
+++ b/uploader/templates/publications/sui-edit-publication.html
@@ -0,0 +1,203 @@
+{%extends "publications/sui-base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Edit Publication{%endblock%}
+
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
+ <a href="{{url_for('publications.edit_publication',
+ publication_id=publication.Id)}}"
+ title="Edit the publication's details">edit publication</a>
+</li>
+{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <form id="frm-create-publication"
+ method="POST"
+ action="{{url_for('publications.edit_publication',
+ publication_id=publication_id,
+ next=request.args.get('next', ''))}}"
+ class="form-horizontal">
+
+ <div class="row mb-3">
+ <label for="txt-pubmed-id" class="col-sm-2 col-form-label">
+ PubMed ID</label>
+ <div class="col-sm-10">
+ <div class="input-group">
+ <input type="text"
+ id="txt-pubmed-id"
+ name="pubmed-id"
+ value="{{publication.PubMed_ID or ''}}"
+ class="form-control" />
+ <div class="input-group-text">
+ <button class="btn btn-outline-primary"
+ id="btn-search-pubmed-id">search</button>
+ </div>
+ </div>
+ <span id="search-pubmed-id-error"
+ class="form-text text-muted text-danger visually-hidden">
+ </span>
+ <span class="form-text text-muted">This is the publication's ID on
+ <a href="https://pubmed.ncbi.nlm.nih.gov/"
+ title="Link to NCBI's PubMed service">NCBI's Pubmed Service</a>
+ </span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-title" class="col-sm-2 col-form-label">
+ Title</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-title"
+ name="publication-title"
+ value="{{publication.Title}}"
+ class="form-control" />
+ <span class="form-text text-muted">Provide the publication's title here.</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-authors" class="col-sm-2 col-form-label">
+ Authors</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-authors"
+ name="publication-authors"
+ value="{{publication.Authors}}"
+ required="required"
+ class="form-control" />
+ <span class="form-text text-muted">
+ A publication <strong>MUST</strong> have an author. You <em>must</em>
+ provide a value for the authors field.
+ </span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-journal" class="col-sm-2 col-form-label">
+ Journal</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-journal"
+ name="publication-journal"
+ value="{{publication.Journal}}"
+ class="form-control" />
+ <span class="form-text text-muted">Provide the name journal where the
+ publication was done, here.</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="select-publication-month"
+ class="col-sm-2 col-form-label">
+ Month</label>
+ <div class="col-sm-4">
+ <select class="form-control"
+ id="select-publication-month"
+ name="publication-month">
+ <option value="">Select a month</option>
+ {%for month in ("january", "february", "march", "april", "may", "june", "july", "august", "september", "october", "november", "december"):%}
+ <option value="{{month}}"
+ {%if publication.Month | lower == month %}
+ selected="selected"
+ {%endif%}>
+ {{month | title}}
+ </option>
+ {%endfor%}
+ </select>
+ <span class="form-text text-muted">Month of publication</span>
+ </div>
+
+ <label for="txt-publication-year"
+ class="col-sm-2 col-form-label">
+ Year</label>
+ <div class="col-sm-4">
+ <input type="number"
+ id="txt-publication-year"
+ name="publication-year"
+ value="{{publication.Year}}"
+ class="form-control"
+ min="1960" />
+ <span class="form-text text-muted">Year of publication</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-volume"
+ class="col-sm-2 col-form-label">
+ Volume</label>
+ <div class="col-sm-4">
+ <input type="text"
+ id="txt-publication-volume"
+ name="publication-volume"
+ value="{{publication.Volume}}"
+ class="form-control">
+ <span class="form-text text-muted">Journal volume</span>
+ </div>
+
+ <label for="txt-publication-pages"
+ class="col-sm-2 col-form-label">
+ Pages</label>
+ <div class="col-sm-4">
+ <input type="text"
+ id="txt-publication-pages"
+ name="publication-pages"
+ value="{{publication.Pages}}"
+ class="form-control" />
+ <span class="form-text text-muted">Journal pages for the publication</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-abstract" class="col-sm-2 col-form-label">Abstract</label>
+ <div class="col-sm-10">
+ <textarea id="txt-publication-abstract"
+ name="publication-abstract"
+ class="form-control"
+ rows="7">{{publication.Abstract or ""}}</textarea>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <div class="col-sm-2"></div>
+ <div class="col-sm-8">
+ <input type="submit" class="btn btn-primary" value="Save" />
+ <input type="reset" class="btn btn-danger" />
+ </div>
+ </div>
+
+</form>
+</div>
+
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/pubmed.js"></script>
+<script type="text/javascript">
+ $(function() {
+ $("#btn-search-pubmed-id").on("click", (event) => {
+ event.preventDefault();
+ var search_button = event.target;
+ var pubmed_id = $("#txt-pubmed-id").val().trim();
+ remove_class($("#txt-pubmed-id").parent(), "has-error");
+ if(pubmed_id == "") {
+ add_class($("#txt-pubmed-id").parent(), "has-error");
+ return false;
+ }
+
+ search_button.disabled = true;
+ // Fetch publication details
+ fetch_publication_details(pubmed_id,
+ [() => {search_button.disabled = false;}]);
+ return false;
+ });
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/publications/sui-index.html b/uploader/templates/publications/sui-index.html
new file mode 100644
index 0000000..e405dd1
--- /dev/null
+++ b/uploader/templates/publications/sui-index.html
@@ -0,0 +1,109 @@
+{%extends "publications/sui-base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Publications{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row" style="padding-bottom: 1em;">
+ <div class="col">
+ <a href="{{url_for('publications.create_publication')}}"
+ class="btn btn-primary"
+ title="Create a new publication.">
+ add new publication</a>
+ </div>
+</div>
+
+<div class="row">
+ <p>Click on title to view more details and to edit details for that
+ publication.</p>
+</div>
+
+<div class="row">
+ <table id="tbl-list-publications" class="table compact stripe">
+ <thead>
+ <tr>
+ <th>#</th>
+ <th>PubMed ID</th>
+ <th>Title</th>
+ <th>Authors</th>
+ </tr>
+ </thead>
+
+ <tbody></tbody>
+ </table>
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/urls.js"></script>
+
+<script type="text/javascript">
+ $(function() {
+ var publicationsDataTable = buildDataTable(
+ "#tbl-list-publications",
+ [],
+ [
+ {data: "index"},
+ {
+ searchable: true,
+ data: (pub) => {
+ if(pub.PubMed_ID) {
+ return `<a href="https://pubmed.ncbi.nlm.nih.gov/` +
+ `${pub.PubMed_ID}/" target="_blank" ` +
+ `title="Link to publication on NCBI.">` +
+ `${pub.PubMed_ID}</a>`;
+ }
+ return "";
+ }
+ },
+ {
+ searchable: true,
+ data: (pub) => {
+ var title = "⸻";
+ if(pub.Title) {
+ title = pub.Title
+ }
+ url=buildURLFromCurrentURL(
+ `/publications/view/${pub.Id}`);
+ return `<a href="${url}" target="_blank" ` +
+ `title="Link to view publication details">` +
+ `${title}</a>`;
+ }
+ },
+ {
+ searchable: true,
+ data: (pub) => {
+ authors = pub.Authors.split(",").map(
+ (item) => {return item.trim();});
+ if(authors.length > 1) {
+ return authors[0] + ", et. al.";
+ }
+ return authors[0];
+ }
+ }
+ ],
+ {
+ serverSide: true,
+ ajax: {
+ url: "/publications/list",
+ dataSrc: "publications"
+ },
+ scrollY: 700,
+ scroller: true,
+ scrollCollapse: true,
+ paging: true,
+ deferRender: true,
+ layout: {
+ topStart: "info",
+ topEnd: "search",
+ bottomStart: "pageLength",
+ bottomEnd: false
+ }
+ });
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/publications/sui-view-publication.html b/uploader/templates/publications/sui-view-publication.html
new file mode 100644
index 0000000..740fc37
--- /dev/null
+++ b/uploader/templates/publications/sui-view-publication.html
@@ -0,0 +1,80 @@
+{%extends "publications/sui-base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}View Publication{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <table class="table">
+ <tr>
+ <th>Linked Phenotypes</th>
+ <td>{{linked_phenotypes | count}}</td>
+ </tr>
+ <tr>
+ <th>PubMed</th>
+ <td>
+ {%if publication.PubMed_ID%}
+ <a href="https://pubmed.ncbi.nlm.nih.gov/{{publication.PubMed_ID}}/"
+ target="_blank">{{publication.PubMed_ID}}</a>
+ {%else%}
+ —
+ {%endif%}
+ </td>
+ </tr>
+ <tr>
+ <th>Title</th>
+ <td>{{publication.Title or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Authors</th>
+ <td>{{publication.Authors or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Journal</th>
+ <td>{{publication.Journal or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Published</th>
+ <td>{{publication.Month or ""}} {{publication.Year or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Volume</th>
+ <td>{{publication.Volume or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Pages</th>
+ <td>{{publication.Pages or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Abstract</th>
+ <td>
+ {%for line in (publication.Abstract or "—").replace("\r\n", "<br />").replace("\n", "<br />").split("<br />")%}
+ <p>{{line}}</p>
+ {%endfor%}
+ </td>
+ </tr>
+ </table>
+</div>
+
+<div class="row">
+ <div>
+ <a href="{{url_for('publications.edit_publication', publication_id=publication.Id)}}"
+ title="Edit details for this publication."
+ class="btn btn-primary">Edit</a>
+ {%if linked_phenotypes | length == 0%}
+ <a href="{{url_for('publications.delete_publication', publication_id=publication.Id)}}"
+ class="btn btn-danger">delete</a>
+ {%endif%}
+ </div>
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+ $(function() {});
+</script>
+{%endblock%}
diff --git a/uploader/templates/sui-index.html b/uploader/templates/sui-index.html
index 888823f..b93bf40 100644
--- a/uploader/templates/sui-index.html
+++ b/uploader/templates/sui-index.html
@@ -13,16 +13,16 @@
{%macro add_form_buttons()%}
<div class="row form-buttons">
- <div class="col">
- <input type="submit"
- class="btn btn-primary"
- value="use selected species" />
- </div>
- <div class="col">
- <a href="{{url_for('species.create_species', return_to='base.index')}}"
- class="btn btn-outline-primary"
- title="Create a new species.">Create a new Species</a>
- </div>
+ <div class="col">
+ <input type="submit"
+ class="btn btn-primary"
+ value="use selected species" />
+ </div>
+ <div class="col">
+ <a href="{{url_for('species.create_species', return_to='base.index')}}"
+ class="btn btn-outline-primary"
+ title="Create a new species.">Create a new Species</a>
+ </div>
</div>
{%endmacro%}
@@ -31,93 +31,131 @@
{%if user_logged_in()%}
<div class="row">
- <div class="row">
- <h2 class="heading">Species</h2>
-
- <p>Select the species you want to work with.</p>
- </div>
+ <ul class="nav nav-tabs" id="index-actions">
+ <li class="nav-item presentation">
+ <button class="nav-link active"
+ id="upload-data-tab"
+ data-bs-toggle="tab"
+ data-bs-target="#upload-data-content"
+ type="button"
+ role="tab"
+ aria-controls="upload-data-content"
+ aria-selected="false">Upload Data</button></li>
+ <li class="nav-item presentation">
+ <button class="nav-link"
+ id="publications-tab"
+ data-bs-toggle="tab"
+ data-bs-target="#publications-content"
+ type="button"
+ role="tab"
+ aria-controls="publications-content"
+ aria-selected="true">Publications</button></li>
+ </ul>
</div>
<div class="row">
- <form method="GET" action="{{url_for('base.index')}}" class="form-horizontal">
- {{add_http_feature_flags()}}
-
- {{add_form_buttons()}}
-
- {%if species | length != 0%}
- <div style="margin-top:1em;">
- <table id="tbl-select-species" class="table compact stripe"
- data-species-list='{{species | tojson}}'>
- <thead>
- <tr>
- <th></th>
- <th>Species Name</th>
- </tr>
- </thead>
-
- <tbody></tbody>
- </table>
- </div>
+ <div class="tab-content" id="upload-data-tabs-content">
+ <div class="tab-pane fade show active"
+ id="upload-data-content"
+ role="tabpanel"
+ aria-labelledby="upload-data-content-tab">
+ <h2 class="heading">Species</h2>
- {%else%}
+ <p>Select the species you want to work with.</p>
- <label class="control-label" for="rdo-cant-find-species">
- <input id="rdo-cant-find-species" type="radio" name="species_id"
- value="CREATE-SPECIES" />
- There are no species to select from. Create the first one.</label>
+ <form method="GET" action="{{url_for('base.index')}}" class="form-horizontal">
+ {{add_http_feature_flags()}}
- <div class="col-sm-offset-10 col-sm-2">
- <input type="submit"
- class="btn btn-primary col-sm-offset-1"
- value="continue" />
- </div>
+ {{add_form_buttons()}}
- {%endif%}
+ {%if species | length != 0%}
+ <div style="margin-top:1em;">
+ <table id="tbl-select-species" class="table compact stripe"
+ data-species-list='{{species | tojson}}'>
+ <thead>
+ <tr>
+ <th></th>
+ <th>Species Name</th>
+ </tr>
+ </thead>
- {{add_form_buttons()}}
+ <tbody></tbody>
+ </table>
+ </div>
- </form>
-</div>
+ {%else%}
-{%else%}
+ <label class="control-label" for="rdo-cant-find-species">
+ <input id="rdo-cant-find-species" type="radio" name="species_id"
+ value="CREATE-SPECIES" />
+ There are no species to select from. Create the first one.</label>
-<div class="row">
- <p>The Genenetwork Uploader (<em>gn-uploader</em>) enables upload of new data
- into the Genenetwork System. It provides Quality Control over data, and
- guidance in case you data does not meet the standards for acceptance.</p>
- <p>
- <a href="{{authserver_authorise_uri()}}"
- title="Sign in to the system"
- class="btn btn-primary">Sign in</a>
- to get started.</p>
-</div>
-{%endif%}
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit"
+ class="btn btn-primary col-sm-offset-1"
+ value="continue" />
+ </div>
-{%endblock%}
+ {%endif%}
+ {{add_form_buttons()}}
+ </form>
+ </div>
-{%block sidebarcontents%}
-<div class="row">
- <p>The data in Genenetwork is related to one species or another. Use the form
- provided to select from existing species, or click on the
- "Create a New Species" button if you cannot find the species you want to
- work with.</p>
-</div>
-<div class="row">
- <form id="frm-quick-navigation">
- <legend>Quick Navigation</legend>
- <div class="form-group">
- <label for="fqn-species-id">Species</label>
- <select name="species_id">
- <option value="">Select species</option>
- </select>
+ <div class="tab-pane fade"
+ id="publications-content"
+ role="tabpanel"
+ aria-labelledby="publications-content-tab">
+ <p>View, edit and delete existing publications, and add new
+ publications by clicking on the button below.</p>
+
+ <a href="{{url_for('publications.index')}}"
+ title="Manage publications."
+ class="btn btn-primary">manage publications</a>
</div>
- </form>
+ </div>
</div>
-{%endblock%}
+
+ {%else%}
+
+ <div class="row">
+ <p>The Genenetwork Uploader (<em>gn-uploader</em>) enables upload of new data
+ into the Genenetwork System. It provides Quality Control over data, and
+ guidance in case you data does not meet the standards for acceptance.</p>
+ <p>
+ <a href="{{authserver_authorise_uri()}}"
+ title="Sign in to the system"
+ class="btn btn-primary">Sign in</a>
+ to get started.</p>
+ </div>
+ {%endif%}
+
+ {%endblock%}
+
+
+
+ {%block sidebarcontents%}
+ <div class="row">
+ <p>The data in Genenetwork is related to one species or another. Use the form
+ provided to select from existing species, or click on the
+ "Create a New Species" button if you cannot find the species you want to
+ work with.</p>
+ </div>
+ <div class="row">
+ <form id="frm-quick-navigation">
+ <legend>Quick Navigation</legend>
+ <div class="form-group">
+ <label for="fqn-species-id">Species</label>
+ <select name="species_id">
+ <option value="">Select species</option>
+ </select>
+ </div>
+ </form>
+ </div>
+ {%endblock%}
-{%block javascript%}
-<script type="text/javascript" src="/static/js/species.js"></script>
-{%endblock%}
+ {%block javascript%}
+ <script type="text/javascript" src="/static/js/species.js"></script>
+ {%endblock%}
|
