Internal report fixes (#20)

* fix csv output if a field is missing from a pub

* make abstract hidden by default

* fix flake8

* fix tests

pubs/__init__.py

@@ -33,3 +33,16 @@
     'ara': 'ARA',
     'wipac': 'WIPAC',
 }
+
+FIELDS = [
+    '_id',
+    'title',
+    'authors',
+    'type',
+    'citation',
+    'date',
+    'abstract',
+    'downloads',
+    'projects',
+    'sites',
+]

pubs/__main__.py

@@ -1,7 +1,7 @@
 import asyncio
 import logging
 
-from  wipac_dev_tools import from_environment
+from wipac_dev_tools import from_environment
 
 from .server import create_server
 

pubs/server.py

@@ -20,7 +20,7 @@
 from bson.objectid import ObjectId
 
 from . import __version__ as version
-from . import PUBLICATION_TYPES, PROJECTS, SITES
+from . import PUBLICATION_TYPES, PROJECTS, SITES, FIELDS
 from .utils import create_indexes, date_format, add_pub, edit_pub, try_import_file
 
 logger = logging.getLogger('server')
@@ -182,12 +182,14 @@ async def get(self):
         pubs = await self.get_pubs()
 
         f = StringIO()
-        writer = csv.DictWriter(f, fieldnames=list(pubs['publications'][0].keys()))
+        writer = csv.DictWriter(f, fieldnames=FIELDS)
         writer.writeheader()
         for p in pubs['publications']:
             data = {}
-            for k in p:
-                if isinstance(p[k], list):
+            for k in FIELDS:
+                if k not in p:
+                    data[k] = ''
+                elif isinstance(p[k], list):
                     data[k] = ','.join(p[k])
                 else:
                     data[k] = p[k]

pubs/static/external.css

@@ -56,6 +56,14 @@ article.publication {
     content: "and";
     padding: 0 .4rem;
 }
+.publication .abstract_div button {
+    line-height: .9rem;
+}
+.publication .abstract {
+    padding: .5rem;
+    margin: .5rem;
+    border: 1px solid #ccc;
+}
 .publication .downloads .download:not(:first-child)::before {
     content: "|";
     padding: 0 .4rem;

pubs/static/external.js

@@ -141,6 +141,11 @@ async function Pubs(id, baseurl = 'https://publications.icecube.aq', filters = {
   let pubsCount = await pubs_count_fut;
 
   Vue.component('pub', {
+    data: function() {
+      return {
+        show_abstract: false
+      }
+    },
     props: {
       title: String,
       authors: String,
@@ -182,15 +187,19 @@ async function Pubs(id, baseurl = 'https://publications.icecube.aq', filters = {
   <div><span class="type">({{ type }})</span>
   <span class="citation">{{ citation }}</span>
   <span v-if="show_date" class="date">{{ day_month_year }}</span></div>
-  <div class="abstract_div" v-if="abstract">Abstract: <span class="abstract">{{ abstract }}</span></div>
   <div>
-    <span class="downloads" v-if="downloads">Download:
+    <span class="downloads" v-if="downloads.length">Download:
       <span class="download" v-for="link in downloads"><a :href="link" target="_blank">{{ getDomain(link) }}</a></span>
     </span>
-    <span class="projects" v-if="projects && !filters.hide_projects">Project:
+    <span class="projects" v-if="projects.length && !filters.hide_projects">Project:
       <span class="project" v-for="project in projects">{{ project_labels[project] }}</span>
     </span>
   </div>
+  <div class="abstract_div" v-if="abstract">Abstract:
+    <button v-if="show_abstract" v-on:click="show_abstract = false">Hide</button>
+    <button v-else v-on:click="show_abstract = true">Show</button>
+    <div class="abstract" v-if="show_abstract">{{ abstract }}</div>
+  </div>
 </article>`
   });
 

pubs/templates/main.html

@@ -43,9 +43,6 @@ <h2>Selected Publications:</h2>
   <div><span class="type">({{ PUBLICATION_TYPES[pub['type']] }})</span>
   <span class="citation">{{ pub['citation'] }}</span>
   <span class="date">{{ date_format(pub['date']) }}</span></div>
-  {% if pub.get('abstract', '') %}
-  <div class="abstract_div">Abstract: <span class="abstract">{{ pub['abstract'] }}</span></div>
-  {% end %}
   <div>
     {% if pub['downloads'] %}
     <span class="downloads">Download:
@@ -58,6 +55,9 @@ <h2>Selected Publications:</h2>
     {% end %}
     </span>
   </div>
+  {% if pub.get('abstract', '') %}
+  <div class="abstract_div">Abstract: <div class="abstract">{{ pub['abstract'] }}</div></div>
+  {% end %}
 </article>
 {% end %}
 </div>

pubs/templates/manage.html

@@ -102,9 +102,6 @@ <h2>Existing Publications:</h2>
   <div><span class="type">({{ PUBLICATION_TYPES[pub['type']] }})</span>
   <span class="citation">{{ pub['citation'] }}</span>
   <span class="date">{{ date_format(pub['date']) }}</span></div>
-  {% if pub.get('abstract', '') %}
-  <div class="abstract_div">Abstract: <span class="abstract">{{ pub['abstract'] }}</span></div>
-  {% end %}
   <div>
     {% if pub['downloads'] %}
     <span class="downloads">Download:
@@ -121,21 +118,24 @@ <h2>Existing Publications:</h2>
       {% for site in pub['sites'] %}<span class="site">{{ SITES[site] }}</span>{% end %}
       </span>
     {% end %}
-    <div class="actions">
-      <button class="edit">Edit</button>
-      <form class="delete" action="{{ request.path }}" method="post">
-        {% module xsrf_form_html() %}
-        {% if search %}<input type="hidden" name="search" value="{{ search }}" />{% end %}
-        {% if start_date %}<input type="hidden" name="start_date" value="{{ start_date }}" />{% end %}
-        {% if end_date %}<input type="hidden" name="end_date" value="{{ end_date }}" />{% end %}
-        {% for t in type %}<input type="hidden" name="type" value="{{ t }}" />{% end %}
-        {% for p in projects %}<input type="hidden" name="projects" value="{{ p }}" />{% end %}
-        {% for s in sites %}<input type="hidden" name="sites" value="{{ s }}" />{% end %}
-        <input type="hidden" name="pub_id" value="{{ pub['_id'] }}" />
-        <input type="hidden" name="action" value="delete" />
-        <input type="submit" value="Delete" />
-      </form>
-    </div>
+  </div>
+  {% if pub.get('abstract', '') %}
+  <div class="abstract_div">Abstract: <div class="abstract">{{ pub['abstract'] }}</div></div>
+  {% end %}
+  <div class="actions">
+    <button class="edit">Edit</button>
+    <form class="delete" action="{{ request.path }}" method="post">
+      {% module xsrf_form_html() %}
+      {% if search %}<input type="hidden" name="search" value="{{ search }}" />{% end %}
+      {% if start_date %}<input type="hidden" name="start_date" value="{{ start_date }}" />{% end %}
+      {% if end_date %}<input type="hidden" name="end_date" value="{{ end_date }}" />{% end %}
+      {% for t in type %}<input type="hidden" name="type" value="{{ t }}" />{% end %}
+      {% for p in projects %}<input type="hidden" name="projects" value="{{ p }}" />{% end %}
+      {% for s in sites %}<input type="hidden" name="sites" value="{{ s }}" />{% end %}
+      <input type="hidden" name="pub_id" value="{{ pub['_id'] }}" />
+      <input type="hidden" name="action" value="delete" />
+      <input type="submit" value="Delete" />
+    </form>
   </div>
 </article>
 {% end %}

pubs/utils.py

@@ -77,38 +77,38 @@ async def add_pub(db, title, authors, pub_type, abstract, citation, date, downlo
 async def edit_pub(db, mongo_id, title=None, authors=None, pub_type=None, abstract=None, citation=None, date=None, downloads=None, projects=None, sites=None):
     match = {'_id': ObjectId(mongo_id)}
     update = {}
-    if title:
+    if title is not None:
         assert isinstance(title, str)
         update['title'] = title
-    if authors:
+    if authors is not None:
         assert isinstance(authors, list)
         for a in authors:
             assert isinstance(a, str)
         update['authors'] = authors
-    if pub_type:
+    if pub_type is not None:
         assert pub_type in PUBLICATION_TYPES
         update['type'] = pub_type
-    if abstract:
+    if abstract is not None:
         assert isinstance(abstract, str)
         update['abstract'] = abstract
-    if citation:
+    if citation is not None:
         assert isinstance(citation, str)
         update['citation'] = citation
-    if date:
+    if date is not None:
         assert isinstance(date, str)
         date_format(date)
         update['date'] = date
-    if downloads:
+    if downloads is not None:
         assert isinstance(downloads, list)
         for d in downloads:
             assert isinstance(d, str)
         update['downloads'] = downloads
-    if projects:
+    if projects is not None:
         assert isinstance(projects, list)
         for p in projects:
             assert p in PROJECTS
         update['projects'] = projects
-    if sites:
+    if sites is not None:
         assert isinstance(sites, list)
         for s in sites:
             assert s in SITES

tests/test_main.py

@@ -241,3 +241,29 @@ async def test_authors(server):
 
     pubs = await get_pubs(url, params={'authors': 'auth4'})
     assert len(pubs) == 0
+
+
+@pytest.mark.asyncio
+async def test_csv(server):
+    db, url = server
+
+    await add_pub(db, title='Test Title1', authors=['auth1'], abstract='',
+                  pub_type="journal", citation="TestJournal", date=nowstr(),
+                  downloads=[], projects=['icecube'])
+
+    await add_pub(db, title='Test Title2', authors=['auth2'], abstract='',
+                  pub_type="proceeding", citation="TestJournal", date=nowstr(),
+                  downloads=[], projects=['icecube'])
+
+    await add_pub(db, title='Test Title3', authors=['auth1', 'auth3'], abstract='',
+                  pub_type="thesis", citation="TestJournal", date=nowstr(),
+                  downloads=[], projects=['icecube'])
+
+    await add_pub(db, title='Test Title4', authors=['auth1', 'auth4'], abstract='the abstract',
+                  pub_type="internal", citation="TestReport", date=nowstr(),
+                  downloads=[], projects=['icecube'])
+
+    s = AsyncSession(retries=0, backoff_factor=1)
+    r = await asyncio.wrap_future(s.get(url+'/csv'))
+    r.raise_for_status()
+

tests/test_util.py

@@ -76,30 +76,30 @@ async def test_add_pub_err(mocker, title, authors, pub_type, abstract, citation,
 @pytest.mark.parametrize('abstract', ['This is an abstract', '', None])
 @pytest.mark.parametrize('citation', ['citation', None])
 @pytest.mark.parametrize('date', ['2020-11-03T00:00:00', None])
-@pytest.mark.parametrize('downloads', [['down1', 'down2'], None])
-@pytest.mark.parametrize('projects', [['icecube','hawc'], None])
-@pytest.mark.parametrize('sites', [['icecube', 'wipac'], None])
+@pytest.mark.parametrize('downloads', [['down1', 'down2'], [], None])
+@pytest.mark.parametrize('projects', [['icecube','hawc'], [], None])
+@pytest.mark.parametrize('sites', [['icecube', 'wipac'], [], None])
 @pytest.mark.asyncio
 async def test_edit_pub(mocker, title, authors, pub_type, abstract, citation, date, downloads, projects, sites):
     mongo_id = ObjectId()
     args = {}
-    if title:
+    if title is not None:
         args['title'] = title
-    if authors:
+    if authors is not None:
         args['authors'] = authors
-    if pub_type:
+    if pub_type is not None:
         args['type'] = pub_type
-    if abstract:
+    if abstract is not None:
         args['abstract'] = abstract
-    if citation:
+    if citation is not None:
         args['citation'] = citation
-    if date:
+    if date is not None:
         args['date'] = date
-    if downloads:
+    if downloads is not None:
         args['downloads'] = downloads
-    if projects:
+    if projects is not None:
         args['projects'] = projects
-    if sites:
+    if sites is not None:
         args['sites'] = sites
 
     db = mocker.AsyncMock()