From c3c2c55e9fcf15027fb389e70817a8cf4c08e2de Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Thu, 28 Mar 2019 11:09:17 +1100 Subject: [PATCH 001/154] Initial commit --- README.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..c4063c6 --- /dev/null +++ b/README.md @@ -0,0 +1 @@ +# Gnosis-dev \ No newline at end of file From 90e480e8e3c82044a4c59de7d841811a878ffb56 Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Thu, 28 Mar 2019 11:35:09 +1100 Subject: [PATCH 002/154] add files --- stellar-gnosis | 1 + 1 file changed, 1 insertion(+) create mode 160000 stellar-gnosis diff --git a/stellar-gnosis b/stellar-gnosis new file mode 160000 index 0000000..9ac34e9 --- /dev/null +++ b/stellar-gnosis @@ -0,0 +1 @@ +Subproject commit 9ac34e9003bd6088251fdf6d02395a7fc7ad7413 From 6c6b17b74f812941baa128cd3be40a43cf147311 Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Thu, 28 Mar 2019 11:40:51 +1100 Subject: [PATCH 003/154] add files --- .gitignore | 4 + LICENSE | 201 +++ gnosis/catalog/__init__.py | 1 + gnosis/catalog/admin.py | 3 + gnosis/catalog/apps.py | 5 + gnosis/catalog/forms.py | 332 ++++ gnosis/catalog/migrations/__init__.py | 0 gnosis/catalog/models.py | 197 +++ .../static/catalog/csiro-data61-logos.png | Bin 0 -> 11940 bytes .../static/catalog/csiro-data61-logos.xcf | Bin 0 -> 23457 bytes .../static/catalog/csiro-logo-black.png | Bin 0 -> 5065 bytes gnosis/catalog/static/catalog/data61-logo.png | Bin 0 -> 3785 bytes gnosis/catalog/templates/build.html | 9 + gnosis/catalog/templates/code_detail.html | 24 + gnosis/catalog/templates/code_find.html | 16 + gnosis/catalog/templates/code_form.html | 17 + gnosis/catalog/templates/code_update.html | 16 + gnosis/catalog/templates/codes.html | 31 + gnosis/catalog/templates/comment_detail.html | 12 + gnosis/catalog/templates/comment_form.html | 11 + gnosis/catalog/templates/comment_update.html | 14 + gnosis/catalog/templates/comments.html | 15 + gnosis/catalog/templates/dataset_detail.html | 33 + gnosis/catalog/templates/dataset_find.html | 16 + gnosis/catalog/templates/dataset_form.html | 17 + gnosis/catalog/templates/dataset_update.html | 16 + gnosis/catalog/templates/datasets.html | 30 + gnosis/catalog/templates/paper_authors.html | 27 + .../templates/paper_connect_author.html | 35 + .../catalog/templates/paper_connect_code.html | 35 + .../templates/paper_connect_dataset.html | 26 + .../templates/paper_connect_paper.html | 27 + .../templates/paper_connect_venue.html | 29 + gnosis/catalog/templates/paper_detail.html | 121 ++ gnosis/catalog/templates/paper_find.html | 17 + gnosis/catalog/templates/paper_form.html | 22 + gnosis/catalog/templates/paper_results.html | 18 + gnosis/catalog/templates/paper_update.html | 16 + gnosis/catalog/templates/papers.html | 29 + gnosis/catalog/templates/people.html | 35 + gnosis/catalog/templates/people_results.html | 25 + gnosis/catalog/templates/person_detail.html | 32 + gnosis/catalog/templates/person_find.html | 16 + gnosis/catalog/templates/person_form.html | 16 + gnosis/catalog/templates/person_update.html | 16 + gnosis/catalog/templates/persons.html | 14 + gnosis/catalog/templates/venue_detail.html | 34 + gnosis/catalog/templates/venue_find.html | 16 + gnosis/catalog/templates/venue_form.html | 15 + gnosis/catalog/templates/venue_update.html | 16 + gnosis/catalog/templates/venues.html | 36 + gnosis/catalog/tests.py | 3 + gnosis/catalog/urls.py | 70 + gnosis/catalog/views/__init__.py | 3 + gnosis/catalog/views/views.py | 1377 +++++++++++++++++ gnosis/catalog/views/views_codes.py | 147 ++ gnosis/catalog/views/views_people.py | 154 ++ gnosis/gnosis/__init__.py | 0 gnosis/gnosis/settings.py | 137 ++ gnosis/gnosis/urls.py | 39 + gnosis/gnosis/wsgi.py | 16 + gnosis/home/__init__.py | 0 gnosis/home/admin.py | 3 + gnosis/home/apps.py | 5 + gnosis/home/migrations/__init__.py | 0 gnosis/home/models.py | 3 + gnosis/home/templates/home.html | 34 + gnosis/home/tests.py | 3 + gnosis/home/urls.py | 6 + gnosis/home/views.py | 31 + gnosis/manage.py | 15 + .../registration_complete.html | 11 + .../registration_form.html | 17 + gnosis/templates/gnosis_theme.html | 190 +++ gnosis/templates/registration/logged_out.html | 9 + gnosis/templates/registration/login.html | 48 + .../registration/password_reset_complete.html | 9 + .../registration/password_reset_confirm.html | 33 + .../registration/password_reset_done.html | 8 + .../registration/password_reset_email.html | 8 + .../registration/password_reset_form.html | 11 + requirements.txt | 29 + setup.py | 26 + stellar-gnosis | 1 - 84 files changed, 4138 insertions(+), 1 deletion(-) create mode 100644 .gitignore create mode 100644 LICENSE create mode 100644 gnosis/catalog/__init__.py create mode 100644 gnosis/catalog/admin.py create mode 100644 gnosis/catalog/apps.py create mode 100644 gnosis/catalog/forms.py create mode 100644 gnosis/catalog/migrations/__init__.py create mode 100644 gnosis/catalog/models.py create mode 100644 gnosis/catalog/static/catalog/csiro-data61-logos.png create mode 100644 gnosis/catalog/static/catalog/csiro-data61-logos.xcf create mode 100644 gnosis/catalog/static/catalog/csiro-logo-black.png create mode 100644 gnosis/catalog/static/catalog/data61-logo.png create mode 100644 gnosis/catalog/templates/build.html create mode 100644 gnosis/catalog/templates/code_detail.html create mode 100644 gnosis/catalog/templates/code_find.html create mode 100644 gnosis/catalog/templates/code_form.html create mode 100644 gnosis/catalog/templates/code_update.html create mode 100644 gnosis/catalog/templates/codes.html create mode 100644 gnosis/catalog/templates/comment_detail.html create mode 100644 gnosis/catalog/templates/comment_form.html create mode 100644 gnosis/catalog/templates/comment_update.html create mode 100644 gnosis/catalog/templates/comments.html create mode 100644 gnosis/catalog/templates/dataset_detail.html create mode 100644 gnosis/catalog/templates/dataset_find.html create mode 100644 gnosis/catalog/templates/dataset_form.html create mode 100644 gnosis/catalog/templates/dataset_update.html create mode 100644 gnosis/catalog/templates/datasets.html create mode 100644 gnosis/catalog/templates/paper_authors.html create mode 100644 gnosis/catalog/templates/paper_connect_author.html create mode 100644 gnosis/catalog/templates/paper_connect_code.html create mode 100644 gnosis/catalog/templates/paper_connect_dataset.html create mode 100644 gnosis/catalog/templates/paper_connect_paper.html create mode 100644 gnosis/catalog/templates/paper_connect_venue.html create mode 100644 gnosis/catalog/templates/paper_detail.html create mode 100644 gnosis/catalog/templates/paper_find.html create mode 100644 gnosis/catalog/templates/paper_form.html create mode 100644 gnosis/catalog/templates/paper_results.html create mode 100644 gnosis/catalog/templates/paper_update.html create mode 100644 gnosis/catalog/templates/papers.html create mode 100644 gnosis/catalog/templates/people.html create mode 100644 gnosis/catalog/templates/people_results.html create mode 100644 gnosis/catalog/templates/person_detail.html create mode 100644 gnosis/catalog/templates/person_find.html create mode 100644 gnosis/catalog/templates/person_form.html create mode 100644 gnosis/catalog/templates/person_update.html create mode 100644 gnosis/catalog/templates/persons.html create mode 100644 gnosis/catalog/templates/venue_detail.html create mode 100644 gnosis/catalog/templates/venue_find.html create mode 100644 gnosis/catalog/templates/venue_form.html create mode 100644 gnosis/catalog/templates/venue_update.html create mode 100644 gnosis/catalog/templates/venues.html create mode 100644 gnosis/catalog/tests.py create mode 100644 gnosis/catalog/urls.py create mode 100644 gnosis/catalog/views/__init__.py create mode 100644 gnosis/catalog/views/views.py create mode 100644 gnosis/catalog/views/views_codes.py create mode 100644 gnosis/catalog/views/views_people.py create mode 100644 gnosis/gnosis/__init__.py create mode 100644 gnosis/gnosis/settings.py create mode 100644 gnosis/gnosis/urls.py create mode 100644 gnosis/gnosis/wsgi.py create mode 100644 gnosis/home/__init__.py create mode 100644 gnosis/home/admin.py create mode 100644 gnosis/home/apps.py create mode 100644 gnosis/home/migrations/__init__.py create mode 100644 gnosis/home/models.py create mode 100644 gnosis/home/templates/home.html create mode 100644 gnosis/home/tests.py create mode 100644 gnosis/home/urls.py create mode 100644 gnosis/home/views.py create mode 100644 gnosis/manage.py create mode 100644 gnosis/templates/django_registration/registration_complete.html create mode 100644 gnosis/templates/django_registration/registration_form.html create mode 100644 gnosis/templates/gnosis_theme.html create mode 100644 gnosis/templates/registration/logged_out.html create mode 100644 gnosis/templates/registration/login.html create mode 100644 gnosis/templates/registration/password_reset_complete.html create mode 100644 gnosis/templates/registration/password_reset_confirm.html create mode 100644 gnosis/templates/registration/password_reset_done.html create mode 100644 gnosis/templates/registration/password_reset_email.html create mode 100644 gnosis/templates/registration/password_reset_form.html create mode 100644 requirements.txt create mode 100644 setup.py delete mode 160000 stellar-gnosis diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..01294de --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +.idea/ +.DS_Store +*.sqlite3 +__pycache__/ diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/gnosis/catalog/__init__.py b/gnosis/catalog/__init__.py new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/gnosis/catalog/__init__.py @@ -0,0 +1 @@ + diff --git a/gnosis/catalog/admin.py b/gnosis/catalog/admin.py new file mode 100644 index 0000000..8c38f3f --- /dev/null +++ b/gnosis/catalog/admin.py @@ -0,0 +1,3 @@ +from django.contrib import admin + +# Register your models here. diff --git a/gnosis/catalog/apps.py b/gnosis/catalog/apps.py new file mode 100644 index 0000000..ac42aa1 --- /dev/null +++ b/gnosis/catalog/apps.py @@ -0,0 +1,5 @@ +from django.apps import AppConfig + + +class CatalogConfig(AppConfig): + name = 'catalog' diff --git a/gnosis/catalog/forms.py b/gnosis/catalog/forms.py new file mode 100644 index 0000000..1a402aa --- /dev/null +++ b/gnosis/catalog/forms.py @@ -0,0 +1,332 @@ +from django import forms +from django.forms import ModelForm, Form +from .models import Paper, Person, Dataset, Venue, Comment, Code + + +# +# Search forms +# +class SearchVenuesForm(Form): + + def __init__(self, *args, **kwargs): + super(Form, self).__init__(*args, **kwargs) + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + + def clean_venue_name(self): + return self.cleaned_data['venue_name'] + + def clean_venue_publication_year(self): + return self.cleaned_data['venue_publication_year'] + + venue_name = forms.CharField(required=True) + venue_publication_year = forms.CharField(required=True) + + +class SearchDatasetsForm(Form): + + def __init__(self, *args, **kwargs): + super(Form, self).__init__(*args, **kwargs) + + self.fields['name'].label = 'Name' + self.fields['keywords'].label = 'Keyword (single keyword, e.g. network, computer vision)' + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + + def clean_name(self): + return self.cleaned_data['name'] + + def clean_keywords(self): + return self.cleaned_data['keywords'] + + # one of them is required but we are going to enforce this in the + # view code because we don't know at this stage which one of the + # two the user will specify and we want to give her the option to + # search by dataset name or keywords or both. + name = forms.CharField(required=False) + keywords = forms.CharField(required=False) + + +class SearchPapersForm(Form): + + def __init__(self, *args, **kwargs): + super(Form, self).__init__(*args, **kwargs) + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + + def clean_paper_title(self): + return self.cleaned_data['paper_title'] + + paper_title = forms.CharField(required=True) + + +class SearchPeopleForm(Form): + + def __init__(self, *args, **kwargs): + super(Form, self).__init__(*args, **kwargs) + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + + def clean_person_name(self): + return self.cleaned_data['person_name'] + + person_name = forms.CharField(required=True) + + +class SearchCodesForm(Form): + + def __init__(self, *args, **kwargs): + super(Form, self).__init__(*args, **kwargs) + + self.fields['keywords'].label = 'Keywords (e.g. GCN, network, computer vision)' + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + + def clean_keywords(self): + return self.cleaned_data['keywords'] + + keywords = forms.CharField(required=False) + + +# +# Model forms +# +class PaperForm(ModelForm): + + def __init__(self, *args, **kwargs): + super(ModelForm, self).__init__(*args, **kwargs) + + self.fields['abstract'].widget = forms.Textarea() + self.fields['abstract'].widget.attrs.update({'rows': '8'}) + self.fields['title'].label = 'Title*' + self.fields['abstract'].label = 'Abstract*' + self.fields['keywords'].label = 'Keywords' + self.fields['download_link'].label = 'Download Link*' + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + + def clean_title(self): + return self.cleaned_data['title'] + + def clean_abstract(self): + return self.cleaned_data['abstract'] + + def clean_keywords(self): + return self.cleaned_data['keywords'] + + def clean_download_link(self): + return self.cleaned_data['download_link'] + + class Meta: + model = Paper + fields = ['title', 'abstract', 'keywords', 'download_link'] + + +class PaperImportForm(Form): + """ + A form for importing a paper from a website such as arXiv.org. + The form only present the user with a field to enter a url. + """ + def __init__(self, *args, **kwargs): + super(Form, self).__init__(*args, **kwargs) + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + + def clean_url(self): + return self.cleaned_data['url'] + + url = forms.CharField(label='Source URL, e.g., https://arxiv.org/abs/1607.00653*', max_length=200) + + +class PersonForm(ModelForm): + + def __init__(self, *args, **kwargs): + super(ModelForm, self).__init__(*args, **kwargs) + + self.fields['first_name'].label = 'First Name*' + self.fields['middle_name'].label = 'Middle Name' + self.fields['last_name'].label = 'Last Name*' + self.fields['affiliation'].label = 'Affiliation' + self.fields['website'].label = 'Website' + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + visible.field.widget.attrs.update({'style': 'width:25em'}) + print(visible.field.widget.attrs.items()) + + def clean_first_name(self): + return self.cleaned_data['first_name'] + + def clean_middle_name(self): + return self.cleaned_data['middle_name'] + + def clean_last_name(self): + return self.cleaned_data['last_name'] + + def clean_affiliation(self): + return self.cleaned_data['affiliation'] + + def clean_website(self): + return self.cleaned_data['website'] + + class Meta: + model = Person + fields = ['first_name', 'middle_name', 'last_name', 'affiliation', 'website'] + + +class DatasetForm(ModelForm): + + def __init__(self, *args, **kwargs): + super(ModelForm, self).__init__(*args, **kwargs) + # The default for the description field widget is text input. Buy we want to display + # more than one rows so we replace it with a Textarea widget. + self.fields['description'].widget = forms.Textarea() + self.fields['description'].widget.attrs.update({'rows': '5'}) + + self.fields['name'].label = 'Name*' + self.fields['keywords'].label = 'Keywords*' + self.fields['description'].label = 'Description*' + self.fields['source_type'].label = 'Type*' + self.fields['publication_date'].label = 'Publication Date (yyyy-mm-dd)' + self.fields['website'].label = 'Website' + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + visible.field.widget.attrs.update({'style': 'width:25em'}) + + print(type(self.fields['description'].widget)) + print(self.fields['description'].widget.attrs.items()) + + def clean_name(self): + return self.cleaned_data['name'] + + def clean_keywords(self): + return self.cleaned_data['keywords'] + + def clean_description(self): + return self.cleaned_data['description'] + + def clean_source_type(self): + return self.cleaned_data['source_type'] + + def clean_publication_date(self): + return self.cleaned_data['publication_date'] + + def clean_website(self): + return self.cleaned_data['website'] + + class Meta: + model = Dataset + fields = ['name', 'keywords', 'description', 'source_type', 'publication_date', 'website'] + + +class VenueForm(ModelForm): + + def __init__(self, *args, **kwargs): + super(ModelForm, self).__init__(*args, **kwargs) + + self.fields['name'].label = 'Name*' + self.fields['publisher'].label = 'Publisher*' + # self.fields['publication_date'].help_text = 'YYYY-MM-DD' + self.fields['publication_date'].label = 'Publication Date (yyyy-mm-dd)*' + self.fields['type'].label = 'Type*' + self.fields['peer_reviewed'].label = 'Peer Reviewed*' + self.fields['keywords'].label = 'Keywords*' + self.fields['website'].label = 'Website' + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + visible.field.widget.attrs.update({'style': 'width:25em'}) + print(visible.field.widget.attrs.items()) + + def clean_name(self): + return self.cleaned_data['name'] + + def clean_publisher(self): + return self.cleaned_data['publisher'] + + def clean_publication_date(self): + return self.cleaned_data['publication_date'] + + def clean_type(self): + return self.cleaned_data['type'] + + def clean_peer_reviewed(self): + return self.cleaned_data['peer_reviewed'] + + def clean_keywords(self): + return self.cleaned_data['keywords'] + + def clean_website(self): + return self.cleaned_data['website'] + + class Meta: + model = Venue + fields = ['name', 'publisher', 'publication_date', 'type', 'peer_reviewed', 'keywords', 'website'] + + +class CommentForm(ModelForm): + + def __init__(self, *args, **kwargs): + super(ModelForm, self).__init__(*args, **kwargs) + + self.fields['text'].widget = forms.Textarea() + self.fields['text'].widget.attrs.update({'rows': '5'}) + self.fields['text'].label = '' + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + visible.field.widget.attrs.update({'style': 'width:35em'}) + print(visible.field.widget.attrs.items()) + + def clean_text(self): + return self.cleaned_data['text'] + + def clean_publication_date(self): + return self.cleaned_data['publication_date'] + + # def clean_author(self): + # return self.cleaned_data['author'] + + class Meta: + model = Comment + fields = ['text'] + + +class CodeForm(ModelForm): + + def __init__(self, *args, **kwargs): + super(ModelForm, self).__init__(*args, **kwargs) + # The default for the description field widget is text input. Buy we want to display + # more than one rows so we replace it with a Textarea widget. + self.fields['description'].widget = forms.Textarea() + self.fields['description'].widget.attrs.update({'rows': '5'}) + + self.fields['website'].label = 'Website*' + self.fields['keywords'].label = 'Keywords*' + self.fields['description'].label = 'Description*' + + for visible in self.visible_fields(): + visible.field.widget.attrs['class'] = 'form-control' + visible.field.widget.attrs.update({'style': 'width:25em'}) + + # print(type(self.fields['description'].widget)) + # print(self.fields['description'].widget.attrs.items()) + + def clean_keywords(self): + return self.cleaned_data['keywords'] + + def clean_description(self): + return self.cleaned_data['description'] + + def clean_website(self): + return self.cleaned_data['website'] + + class Meta: + model = Code + fields = ['website', 'keywords', 'description'] + diff --git a/gnosis/catalog/migrations/__init__.py b/gnosis/catalog/migrations/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/gnosis/catalog/models.py b/gnosis/catalog/models.py new file mode 100644 index 0000000..fafd42b --- /dev/null +++ b/gnosis/catalog/models.py @@ -0,0 +1,197 @@ +from datetime import datetime +from django_neomodel import DjangoNode +from django.urls import reverse +from neomodel import StringProperty, DateTimeProperty, DateProperty, UniqueIdProperty, \ + IntegerProperty, RelationshipTo + + +# Create your models here. +class Paper(DjangoNode): + + uid = UniqueIdProperty() + + created = DateTimeProperty(default=datetime.now()) + created_by = IntegerProperty() # The uid of the user who created this node + + # These are always required + title = StringProperty(required=True) + abstract = StringProperty(required=True) + keywords = StringProperty(required=False) + download_link = StringProperty(required=True) + + # Links + cites = RelationshipTo("Paper", "cites") + uses = RelationshipTo("Paper", "uses") + extends = RelationshipTo("Paper", "extends") + evaluates_on = RelationshipTo("Dataset", "evaluates_on") + was_published_at = RelationshipTo("Venue", "was_published_at") + published = RelationshipTo("Dataset", "published") + + class Meta: + app_label = 'catalog' + ordering = ["title", "-published"] # title is A-Z and published is from newest to oldest + + def __str__(self): + """ + String for representing the Paper object, e.g., in Admin site. + :return: The paper's title + """ + return self.title + + def get_absolute_url(self): + return reverse('paper_detail', args=[self.id]) + + +class Person(DjangoNode): + + uid = UniqueIdProperty() + created = DateTimeProperty(default=datetime.now()) + created_by = IntegerProperty() # The uid of the user who created this node + + # These are always required + first_name = StringProperty(required=True) + last_name = StringProperty(required=True) + middle_name = StringProperty() + affiliation = StringProperty() + website = StringProperty() + + authors = RelationshipTo("Paper", "authors") + co_authors_with = RelationshipTo("Person", "co_authors_with") + advisor_of = RelationshipTo("Person", "advisor_of") + + class Meta: + app_label = 'catalog' + ordering = ['last_name', 'first_name', 'affiliation'] + + def __str__(self): + if self.middle_name is not None or len(self.middle_name) > 0: + return '{} {} {}'.format(self.first_name, self.middle_name, self.last_name) + return '{} {}'.format(self.first_name, self.last_name) + + def get_absolute_url(self): + return reverse('person_detail', args=[self.id]) + + +class Dataset(DjangoNode): + + uid = UniqueIdProperty() + created = DateTimeProperty(default=datetime.now()) + created_by = IntegerProperty() # The uid of the user who created this node + + # These are always required + name = StringProperty(required=True) + # keywords that describe the dataset + keywords = StringProperty(required=True) + # A brief description of the dataset + description = StringProperty(required=True) + # The date of publication. + publication_date = DateProperty(required=False) + + # data_types = {'N': 'Network', 'I': 'Image(s)', 'V': 'Video(s)', 'M': 'Mix'} + data_types = (('N', 'Network'), + ('I', 'Image(s)'), + ('V', 'Video(s)'), + ('M', 'Mix'),) + source_type = StringProperty(choices=data_types) + website = StringProperty() + + # We should be able to link a dataset to a paper if the dataset was + # published as part of the evaluation for a new algorithm. We note + # that the Paper model already includes a link of type 'published' + # so a dataset list or detail view should provide a link to add a + # 'published' edge between a dataset and a paper. + + class Meta: + app_label = 'catalog' + ordering = ['name', 'type'] + + def __str__(self): + return '{}'.format(self.name) + + def get_absolute_url(self): + return reverse('dataset_detail', args=[self.id]) + + +class Venue(DjangoNode): + + venue_types = (('J', 'Journal'), + ('C', 'Conference'), + ('W', 'Workshop'), + ('O', 'Open Source'), + ('R', 'Tech Report'), + ('O', 'Other'),) + + review_types = (('Y', 'Yes'), + ('N', 'No'),) + + uid = UniqueIdProperty() + created = DateTimeProperty(default=datetime.now()) + created_by = IntegerProperty() # The uid of the user who created this node + + # These are always required + name = StringProperty(required=True) + publication_date = DateProperty(required=True) + type = StringProperty(required=True, choices=venue_types) # journal, tech report, open source, conference, workshop + publisher = StringProperty(required=True) + keywords = StringProperty(required=True) + + peer_reviewed = StringProperty(required=True, choices=review_types) # Yes or no + website = StringProperty() + + class Meta: + app_label = 'catalog' + ordering = ['name', 'publisher', 'publication_date', 'type'] + + def __str__(self): + return '{} by {} on {}'.format(self.name, self.publisher, self.publication_date) + + def get_absolute_url(self): + return reverse('venue_detail', args=[self.id]) + + +class Comment(DjangoNode): + + uid = UniqueIdProperty() + created = DateTimeProperty(default=datetime.now()) + created_by = IntegerProperty() # The uid of the user who created this node + + # These are always required + author = StringProperty() # required but should be able to get it from user object + text = StringProperty(required=True) + + publication_date = DateTimeProperty(default_now=True) + + discusses = RelationshipTo("Paper", "discusses") + + class Meta: + app_label = 'catalog' + ordering = ['publication_date'] + + def __str__(self): + return '{%s}'.format(self.author) + + def get_absolute_url(self): + return reverse('comment_detail', args=[self.id]) + + +class Code(DjangoNode): + + uid = UniqueIdProperty() + created = DateTimeProperty(default=datetime.now()) + created_by = IntegerProperty() # The uid of the user who created this node + + description = StringProperty(required=True) + website = StringProperty(required=True) + keywords = StringProperty(required=True) + + implements = RelationshipTo("Paper", "implements") + + class Meta: + app_label = 'catalog' + ordering = ['website', 'description', 'keywords'] + + def __str__(self): + return '{}'.format(self.website) + + def get_absolute_url(self): + return reverse('code_detail', args=[self.id]) diff --git a/gnosis/catalog/static/catalog/csiro-data61-logos.png b/gnosis/catalog/static/catalog/csiro-data61-logos.png new file mode 100644 index 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?WT;Z`uKFgEujf`2>p=BBypk=>&i^3DUzXrl~aqW#*&#Ww$ zw1oOhWtIznu7k6G_`(neF64`#+{ZViG|-PRA#}{u_lKsBQ%^2dz*QlXv@xqDw($PF zRa?JV>uQ;;rA^Me7!JMzQeY`oAu@TCKP!}ZY(6=cb;_Q^vZKMZPSkW_lG@cWx6U@U zdl9Kzci{&|flZ+7^zzAfQ8+CtXhJz(tdy@g@W-nDMF=NOEPD=Lso>1|OF`Ztk{5#) zfro>I!0EG0_%oFn^u}z65FtW@2vK=NQu+~U+PYX-+%&9rJH{dq7N1n#VP3!$)x4rI z5RdPwI*AL^jQNt**|Jr2j5TW7yp5}!do^}i)Y?tQC>g62BfdVZGr2`|lS`u+qpWGZ zav<}p{Dg=65CRUoLUXJUd7Zb~z%L+S)c13(!&)tt)W+s2S*eTK?$&)3 zTYpXr%VpxpF>-73yGdBMxj;+p9N)6ylKQaN??Qv8Xl(gww2FlnZDU?}Lbt{DgwTs) zPu>&wF@)Uey4FVglGCE?7GLunlc>+=C&Oynn0O2N0urq{XVJP|b}|lQ_M_EK>j7Bu z2Vyzn?beIV367JjRBZDmuFmT-FuQ=1un zph0=xlyS{YHPuvXO{n1moxwZpzYe8<177RBCclnrRCq~DY=r{z$1>FGuyi&Lm zL?iwSr+e`%V=MgkgNVOty`~iheXHV_?ZO?fa~0V?R&)l`D-hmSr)+oz7x zI?NVa{DwgPO~Fx){cqq8xg*k^80<~f5reY8IvVF}g*({9YYXzjxlf)Luc|5ImfCq$ zkZOp!<|**q^M$aqngP8x+zH(bE!?$wVPTg~Z2R;c`9zi_4#2hCijM3};fLwQ`~r(F zAi*d)k{eZ9zlUQ7uW6M4{#&sV7eVBwweA9+7TM;%|I8&Oy_O?`czjnxMwel9+e?9k zANGH+Qk-A7vyagk&Q}+k`O_b&3&+hj_EX&C?XZ~FggeRa*%mPV*3hnZXF+Sgq4~ zHo7DiPWgoq9aPUO&YD`IxPyzLI*A{OcsS>C2M8?6(Ldmab2QiFG8a1^>J~H}g7`bG zI{KP?|IOPRE@WLPU%H2{ji1naubAuhNqhWw6q&ghxUB1#Eb^-FyofALL=b{K!i1E# z?ID=3!nEGU=W<@Pf{V^6h;%o;@&gAO;j7BO)Xe@w4h2npQkr-92vDCig);5x47 zBQView Catalog.

+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/code_detail.html b/gnosis/catalog/templates/code_detail.html new file mode 100644 index 0000000..c7960a6 --- /dev/null +++ b/gnosis/catalog/templates/code_detail.html @@ -0,0 +1,24 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + + +
+

+ {{ code.website }} + {% if user.is_authenticated %} + {% if user.is_superuser or user.id == code.created_by %} + + + + + + {% endif %} + {% endif %} +

+

+

{{ code.description }}

+

Keywords: {{ code.keywords }}

+
+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/code_find.html b/gnosis/catalog/templates/code_find.html new file mode 100644 index 0000000..c4b0055 --- /dev/null +++ b/gnosis/catalog/templates/code_find.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find Code

+ +{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/code_form.html b/gnosis/catalog/templates/code_form.html new file mode 100644 index 0000000..f0bd156 --- /dev/null +++ b/gnosis/catalog/templates/code_form.html @@ -0,0 +1,17 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

New Code

+ +
+ {% csrf_token %} + + {{ form.as_table }} +
+ + +
+ +

*required
+
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/code_update.html b/gnosis/catalog/templates/code_update.html new file mode 100644 index 0000000..0f01814 --- /dev/null +++ b/gnosis/catalog/templates/code_update.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

Update {{ code.name }}

+ + +
+ {% csrf_token %} + + {{ form }} +
+ +
+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/codes.html b/gnosis/catalog/templates/codes.html new file mode 100644 index 0000000..054ab48 --- /dev/null +++ b/gnosis/catalog/templates/codes.html @@ -0,0 +1,31 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

+

+ + Search Codes + +

+ +{% load el_pagination_tags %} + +{% paginate codes %} + +{% for code in codes %} +
+

{{ code.website }}

+

{{ code.description|truncatewords:25 }}

+

Keywords: {{ code.keywords }}

+
+{% endfor %} + +{% get_pages %} +Showing entries +{{ pages.current_start_index }}-{{ pages.current_end_index }} of +{{ pages.total_count }}. +{# Just print pages to render the Digg-style pagination. #} +{{ pages.get_rendered }} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/comment_detail.html b/gnosis/catalog/templates/comment_detail.html new file mode 100644 index 0000000..a26f2af --- /dev/null +++ b/gnosis/catalog/templates/comment_detail.html @@ -0,0 +1,12 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +{% if user.is_authenticated %} +

!! You have Permission !!

+{% else %} +

No permission

+{% endif %} +

Dataset Detail

+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/comment_form.html b/gnosis/catalog/templates/comment_form.html new file mode 100644 index 0000000..2f83334 --- /dev/null +++ b/gnosis/catalog/templates/comment_form.html @@ -0,0 +1,11 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Share your thoughts!

+ +
+ {% csrf_token %} + {{ form }} + +
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/comment_update.html b/gnosis/catalog/templates/comment_update.html new file mode 100644 index 0000000..cfd6ad8 --- /dev/null +++ b/gnosis/catalog/templates/comment_update.html @@ -0,0 +1,14 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

Revise your thoughts {{ comment.author }}

+ + +
+ {% csrf_token %} + {{ form }} + +
+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/comments.html b/gnosis/catalog/templates/comments.html new file mode 100644 index 0000000..80b6578 --- /dev/null +++ b/gnosis/catalog/templates/comments.html @@ -0,0 +1,15 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

User Comments in our DB

+
    +{% for comment in comments %} +
  • {{ comment.author }} + {% if user.is_authenticated %}|| Edit{% endif %}
    • +{% endfor %} +
+

Number of comments {{ num_comments }}

+

Home|Papers

+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/dataset_detail.html b/gnosis/catalog/templates/dataset_detail.html new file mode 100644 index 0000000..05bdd3a --- /dev/null +++ b/gnosis/catalog/templates/dataset_detail.html @@ -0,0 +1,33 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + + +
+

+

{{ dataset.name}}

+ {% if dataset.website %} + + + + {% endif %} + {% if user.is_authenticated %} + {% if user.is_superuser or user.id == dataset.created_by %} + + + + + + {% endif %} + {% endif %} +

+
+ +

Keywords: {{ dataset.keywords }}

+

Publication Date: {{ dataset.publication_date }}

+ +

Description: {{ dataset.description }}

+ +

Type: {{dataset.source_type}}

+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/dataset_find.html b/gnosis/catalog/templates/dataset_find.html new file mode 100644 index 0000000..8560fb9 --- /dev/null +++ b/gnosis/catalog/templates/dataset_find.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a dataset

+ +{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/dataset_form.html b/gnosis/catalog/templates/dataset_form.html new file mode 100644 index 0000000..707f2d5 --- /dev/null +++ b/gnosis/catalog/templates/dataset_form.html @@ -0,0 +1,17 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

New Dataset

+ +
+ {% csrf_token %} + + {{ form.as_table }} +
+ + +
+ +

*required
+
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/dataset_update.html b/gnosis/catalog/templates/dataset_update.html new file mode 100644 index 0000000..bf4c08d --- /dev/null +++ b/gnosis/catalog/templates/dataset_update.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

Update {{ dataset.name }}

+ + +
+ {% csrf_token %} + + {{ form }} +
+ +
+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/datasets.html b/gnosis/catalog/templates/datasets.html new file mode 100644 index 0000000..7099503 --- /dev/null +++ b/gnosis/catalog/templates/datasets.html @@ -0,0 +1,30 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

+

+ + Search Datasets + +

+ +{% load el_pagination_tags %} + +{% paginate datasets %} + +{% for dataset in datasets %} +
+

{{ dataset.name }}

+

{{ dataset.description|truncatewords:25 }}

+
+{% endfor %} + +{% get_pages %} +Showing entries +{{ pages.current_start_index }}-{{ pages.current_end_index }} of +{{ pages.total_count }}. +{# Just print pages to render the Digg-style pagination. #} +{{ pages.get_rendered }} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_authors.html b/gnosis/catalog/templates/paper_authors.html new file mode 100644 index 0000000..9cf04d3 --- /dev/null +++ b/gnosis/catalog/templates/paper_authors.html @@ -0,0 +1,27 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

+ +

{{ paper.title }}

+ +{% for author, author_url in authors %} + +{% endfor %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_connect_author.html b/gnosis/catalog/templates/paper_connect_author.html new file mode 100644 index 0000000..47905a7 --- /dev/null +++ b/gnosis/catalog/templates/paper_connect_author.html @@ -0,0 +1,35 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a person

+ +
+{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+
+ +{% if people %} +
+

These are the people that matched your query

+ +
+{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_connect_code.html b/gnosis/catalog/templates/paper_connect_code.html new file mode 100644 index 0000000..adae618 --- /dev/null +++ b/gnosis/catalog/templates/paper_connect_code.html @@ -0,0 +1,35 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a code repo

+ +
+{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+
+ +{% if codes %} +
+

These are the code repos that matched your query

+
    + {% for code, code_connect_url in codes %} +
  • + {{ code.website }} + {% if user.is_authenticated and user.is_superuser %} + Connect + {% endif %} +
    • + {% endfor %} +
+
+{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_connect_dataset.html b/gnosis/catalog/templates/paper_connect_dataset.html new file mode 100644 index 0000000..3e4db1d --- /dev/null +++ b/gnosis/catalog/templates/paper_connect_dataset.html @@ -0,0 +1,26 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a dataset

+ +{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+ +{% if people %} +

These are the datasets that matched your query

+ +{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_connect_paper.html b/gnosis/catalog/templates/paper_connect_paper.html new file mode 100644 index 0000000..1b3bf03 --- /dev/null +++ b/gnosis/catalog/templates/paper_connect_paper.html @@ -0,0 +1,27 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a Paper

+ +{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+ + +{% if papers %} +

These are the papers that matched your query

+ +{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_connect_venue.html b/gnosis/catalog/templates/paper_connect_venue.html new file mode 100644 index 0000000..066f181 --- /dev/null +++ b/gnosis/catalog/templates/paper_connect_venue.html @@ -0,0 +1,29 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a Venue

+ +{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+ + +

+ Venue

+ +{% if venues %} +

These are the venues that matched your query

+ +{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_detail.html b/gnosis/catalog/templates/paper_detail.html new file mode 100644 index 0000000..69ff534 --- /dev/null +++ b/gnosis/catalog/templates/paper_detail.html @@ -0,0 +1,121 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

{{ paper.title }}

+ +

+ + {% if user.is_authenticated %} + + {% endif %} +

+ +
+ {{ authors }} {% if user.is_authenticated %}{% endif %} +
+ +
+ keywords: {{ paper.keywords }} +
+ +

Abstract: {{ paper.abstract }}

+{% if venue %} +

+ Venue: {{ venue }} +

+{% endif%} + +{% if messages %} +{% for message in messages %} +

{{ message }}

+{% endfor %} +{% endif %} + +

{% if user.is_authenticated %} Connect with: Paper + || Venue || + Author || + Dataset || + Code Repo{% endif %}

+ +{% if codes %} +

Code

+ +{% endif %} + +
+ +

{% if user.is_authenticated %} + Comment

+{% else %} +

Login to comment

+{% endif %} +{% if num_comments > 0 %} +

{{ num_comments }} Comments

+{% for comment in comments %} +
+

{{comment.author }} says:

+

+ {{ comment.publication_date }} +

+

{{ comment.text }}

+ {% if comment.created_by == user.id %} + Edit + {% endif %} +
+{% endfor %} +{% endif %} + + + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_find.html b/gnosis/catalog/templates/paper_find.html new file mode 100644 index 0000000..0f3e0a9 --- /dev/null +++ b/gnosis/catalog/templates/paper_find.html @@ -0,0 +1,17 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a paper

+ +{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ + +
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_form.html b/gnosis/catalog/templates/paper_form.html new file mode 100644 index 0000000..95aceca --- /dev/null +++ b/gnosis/catalog/templates/paper_form.html @@ -0,0 +1,22 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

New Paper

+ +
+ {% csrf_token %} + {{ form }} +

+ +
+ +
+

{{ message }}

+
+ +{% if message %} +

{{ message }}

+{% endif %} +

*required
+
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_results.html b/gnosis/catalog/templates/paper_results.html new file mode 100644 index 0000000..a7de9a4 --- /dev/null +++ b/gnosis/catalog/templates/paper_results.html @@ -0,0 +1,18 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

Papers that match your query

+ +{% for paper in papers %} +
+ {{ paper.title }} +
+{% endfor %} + + +{% if message %} +

{{ message }}

+{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/paper_update.html b/gnosis/catalog/templates/paper_update.html new file mode 100644 index 0000000..4e9fb48 --- /dev/null +++ b/gnosis/catalog/templates/paper_update.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

{{ paper.title }}

+ + +
+ {% csrf_token %} + {{ form }} +
+ +
+
+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/papers.html b/gnosis/catalog/templates/papers.html new file mode 100644 index 0000000..3a43f76 --- /dev/null +++ b/gnosis/catalog/templates/papers.html @@ -0,0 +1,29 @@ +{% extends "gnosis_theme.html" %} +{% block content %} +

+

+ + Search Papers + +

+ +{% load el_pagination_tags %} + +{% paginate papers %} +{% for paper, authors, venue in papers %} +
+

{{ paper.title }}

+

{{ authors }}

+

{{ venue }}

+ {{ paper.abstract|truncatewords:50 }} +
+{% endfor %} + +{% get_pages %} +Showing entries +{{ pages.current_start_index }}-{{ pages.current_end_index }} of +{{ pages.total_count }}. +{# Just print pages to render the Digg-style pagination. #} +{{ pages.get_rendered }} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/people.html b/gnosis/catalog/templates/people.html new file mode 100644 index 0000000..595660a --- /dev/null +++ b/gnosis/catalog/templates/people.html @@ -0,0 +1,35 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

+

+ + Search People + +

+ +{% load el_pagination_tags %} + +{% paginate people %} + +{% for person in people %} +
+ {% if person.middel_name %} +

{{person.first_name}} {{person.middle_name}} {{ person.last_name }} +

+ {% else %} +

{{person.first_name}} {{ person.last_name }}

+ {% endif %} + {% if person.affiliation %}

Affiliation: {{ person.affiliation }}

{% endif %} +
+{% endfor %} + +{% get_pages %} +Showing entries +{{ pages.current_start_index }}-{{ pages.current_end_index }} of +{{ pages.total_count }}. +{# Just print pages to render the Digg-style pagination. #} +{{ pages.get_rendered }} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/people_results.html b/gnosis/catalog/templates/people_results.html new file mode 100644 index 0000000..14c8d89 --- /dev/null +++ b/gnosis/catalog/templates/people_results.html @@ -0,0 +1,25 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

People that match your query

+ +{% load el_pagination_tags %} + +{% paginate people %} + +{% for person in people %} +
+ {{ person.first_name }} {{ person.middle_name }} {{ person.last_name }} +
+{% endfor %} + + +{% get_pages %} +Showing entries +{{ pages.current_start_index }}-{{ pages.current_end_index }} of +{{ pages.total_count }}. +{# Just print pages to render the Digg-style pagination. #} +{{ pages.get_rendered }} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/person_detail.html b/gnosis/catalog/templates/person_detail.html new file mode 100644 index 0000000..2fed18a --- /dev/null +++ b/gnosis/catalog/templates/person_detail.html @@ -0,0 +1,32 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +
+

+ {% if person.middle_name %} +

{{ person.first_name}} {{person.middle_name}} {{person.last_name}}

+ {% else %} +

{{ person.first_name}} {{person.last_name}}

+ {% endif %} + {% if user.is_authenticated %} + {% if user.is_superuser or user.id == person.created_by %} +

+ +

+ {% endif %} + {% endif %} +

+
+ +{% if person.website %} +

Website:

+{% endif %} + +{% if person.affiliation %} +

Affiliation: {{ person.affiliation }}

+{% else %} +

Affiliation: Unknown

+{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/person_find.html b/gnosis/catalog/templates/person_find.html new file mode 100644 index 0000000..b6e460a --- /dev/null +++ b/gnosis/catalog/templates/person_find.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a person

+ +{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/person_form.html b/gnosis/catalog/templates/person_form.html new file mode 100644 index 0000000..2a6107b --- /dev/null +++ b/gnosis/catalog/templates/person_form.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

New Person/Author

+ +
+ {% csrf_token %} + + {{ form.as_table }} +
+ + +
+

*required
+
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/person_update.html b/gnosis/catalog/templates/person_update.html new file mode 100644 index 0000000..0503b73 --- /dev/null +++ b/gnosis/catalog/templates/person_update.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

Update {{ person.last_name }}

+ + +
+ {% csrf_token %} + + {{ form }} +
+ +
+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/persons.html b/gnosis/catalog/templates/persons.html new file mode 100644 index 0000000..1976938 --- /dev/null +++ b/gnosis/catalog/templates/persons.html @@ -0,0 +1,14 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

People in our DB

+
    +{% for person in persons %} +
  • {{ person.first_name }} {{ person.last_name }}
    • +{% endfor %} +
+

Number of people {{ num_people }}

+

Home|Papers

+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/venue_detail.html b/gnosis/catalog/templates/venue_detail.html new file mode 100644 index 0000000..1d26995 --- /dev/null +++ b/gnosis/catalog/templates/venue_detail.html @@ -0,0 +1,34 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + + +
+

+

{{ venue.name}}

+ {% if user.is_authenticated %} + {% if user.is_superuser or user.id == venue.created_by %} +

+ + + +

+ {% endif %} + {% endif %} +

+
+ +{% if venue.website %} +

Website

+{% endif %} + +

Publication Date: {{ venue.publication_date }}

+{% if venue.keywords %} +

Keywords: {{ venue.keywords }}

+{% endif %} + +

Publisher: {{venue.publisher}}

+

Type: {{venue.type}}

+

+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/venue_find.html b/gnosis/catalog/templates/venue_find.html new file mode 100644 index 0000000..8664143 --- /dev/null +++ b/gnosis/catalog/templates/venue_find.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Find a venue

+ +{% if message %} +

{{ message }}

+{% endif %} + +
+ {% csrf_token %} + {{ form }} +

+ +
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/venue_form.html b/gnosis/catalog/templates/venue_form.html new file mode 100644 index 0000000..c11a02c --- /dev/null +++ b/gnosis/catalog/templates/venue_form.html @@ -0,0 +1,15 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

New Venue

+ +
+ {% csrf_token %} + + {{ form.as_table }} +
+ + +
+
*required
+{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/venue_update.html b/gnosis/catalog/templates/venue_update.html new file mode 100644 index 0000000..76c6c50 --- /dev/null +++ b/gnosis/catalog/templates/venue_update.html @@ -0,0 +1,16 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

Update {{ venue.name }}

+ + +
+ {% csrf_token %} + + {{ form }} +
+ +
+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/templates/venues.html b/gnosis/catalog/templates/venues.html new file mode 100644 index 0000000..f694690 --- /dev/null +++ b/gnosis/catalog/templates/venues.html @@ -0,0 +1,36 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

+

+ + Search Venues + +

+ +{% load el_pagination_tags %} + +{% paginate venues %} + +{% for venue in venues %} +
+

{{ venue.name }}

+

Published on {{ venue.publication_date }} by {{ venue.publisher }}

+
+{% endfor %} + +{% get_pages %} +Showing entries +{{ pages.current_start_index }}-{{ pages.current_end_index }} of +{{ pages.total_count }}. +{# Just print pages to render the Digg-style pagination. #} +{{ pages.get_rendered }} + +{% comment %} +{{ pages.previous }} {{ pages.next }} +{% show_pages %} +{% endcomment %} + + +{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/tests.py b/gnosis/catalog/tests.py new file mode 100644 index 0000000..7ce503c --- /dev/null +++ b/gnosis/catalog/tests.py @@ -0,0 +1,3 @@ +from django.test import TestCase + +# Create your tests here. diff --git a/gnosis/catalog/urls.py b/gnosis/catalog/urls.py new file mode 100644 index 0000000..3daa60f --- /dev/null +++ b/gnosis/catalog/urls.py @@ -0,0 +1,70 @@ +from django.urls import path +from . import views + +urlpatterns = [ + path('', views.papers), + path('papers/', views.papers, name='papers_index'), + path('persons/', views.persons, name='persons_index'), + path('paper//', views.paper_detail, name='paper_detail'), + path('build', views.build, name='build_db'), +] + +# for updating/creating a new Paper node +urlpatterns += [ + path('paper//update', views.paper_update, name='paper_update'), + path('paper//connect/venue', views.paper_connect_venue, name='paper_connect_venue'), + path('paper//connect/author', views.paper_connect_author, name='paper_connect_author'), + path('paper//connect/author/', views.paper_connect_author_selected, name='paper_connect_author_selected'), + path('paper//connect/paper', views.paper_connect_paper, name='paper_connect_paper'), + path('paper//connect/dataset', views.paper_connect_dataset, name='paper_connect_dataset'), + path('paper//connect/code', views.paper_connect_code, name='paper_connect_code'), + path('paper//connect/code/', views.paper_connect_code_selected, name='paper_connect_code_selected'), + path('paper//authors', views.paper_authors, name='paper_authors'), + path('paper//remove/author/', views.paper_remove_author, name='paper_remove_author'), + path('paper/create/', views.paper_create, name='paper_create'), + path('paper/import/', views.paper_create_from_arxiv, name='paper_create_from_arxiv'), + path('paper/find/', views.paper_find, name='paper_find'), +] + +# for updating/creating a new Person node +urlpatterns += [ + path('person/create/', views.person_create, name='person_create'), + path('person//', views.person_detail, name='person_detail'), + path('person//update', views.person_update, name='person_update'), + path('person/find/', views.person_find, name='person_find'), +] + +# for updating/creating a new Dataset node +urlpatterns += [ + path('datasets/', views.datasets, name='datasets_index'), + path('dataset/create/', views.dataset_create, name='dataset_create'), + path('dataset/find/', views.dataset_find, name='dataset_find'), + path('dataset//', views.dataset_detail, name='dataset_detail'), + path('dataset//update', views.dataset_update, name='dataset_update'), +] + +# for updating/creating a new Venue node +urlpatterns += [ + path('venues/', views.venues, name='venues_index'), + path('venue/create/', views.venue_create, name='venue_create'), + path('venue/find/', views.venue_find, name='venue_find'), + path('venue//', views.venue_detail, name='venue_detail'), + path('venue//update', views.venue_update, name='venue_update'), +] + +# for updating/creating a new Comment node +urlpatterns += [ + path('comments/', views.comments, name='comments_index'), + path('comment/create/', views.comment_create, name='comment_create'), + path('comment//', views.comment_detail, name='comment_detail'), + path('comment//update', views.comment_update, name='comment_update'), +] + +# for updating/creating a new Code node +urlpatterns += [ + path('codes/', views.codes, name='codes_index'), + path('code/create/', views.code_create, name='code_create'), + path('code/find/', views.code_find, name='code_find'), + path('code//', views.code_detail, name='code_detail'), + path('code//update', views.code_update, name='code_update'), +] \ No newline at end of file diff --git a/gnosis/catalog/views/__init__.py b/gnosis/catalog/views/__init__.py new file mode 100644 index 0000000..cda4e2e --- /dev/null +++ b/gnosis/catalog/views/__init__.py @@ -0,0 +1,3 @@ +from catalog.views.views import * +from catalog.views.views_people import * +from catalog.views.views_codes import * \ No newline at end of file diff --git a/gnosis/catalog/views/views.py b/gnosis/catalog/views/views.py new file mode 100644 index 0000000..9867c04 --- /dev/null +++ b/gnosis/catalog/views/views.py @@ -0,0 +1,1377 @@ +from django.contrib.auth.decorators import login_required +from django.contrib.admin.views.decorators import staff_member_required +from django.shortcuts import render, redirect +from catalog.models import Paper, Person, Dataset, Venue, Comment, Code +from catalog.forms import PaperForm, DatasetForm, VenueForm, CommentForm, PaperImportForm +from catalog.forms import SearchVenuesForm, SearchPapersForm, SearchPeopleForm, SearchDatasetsForm, SearchCodesForm +from django.urls import reverse +from django.http import HttpResponseRedirect +from neomodel import db +from datetime import date +from nltk.corpus import stopwords +from urllib.request import urlopen +from urllib.error import HTTPError, URLError +from bs4 import BeautifulSoup +from django.contrib import messages + +from catalog.views.views_codes import _code_find + + +# +# Paper Views +# +def get_paper_authors(paper): + query = "MATCH (:Paper {title: {paper_title}})<--(a:Person) RETURN a" + results, meta = db.cypher_query(query, dict(paper_title=paper.title)) + if len(results) > 0: + authors = [Person.inflate(row[0]) for row in results] + else: + authors = [] + # pdb.set_trace() + authors = ['{}. {}'.format(author.first_name[0], author.last_name) for author in authors] + + return authors + + +def _get_paper_codes(paper): + query = "MATCH (:Paper {title: {paper_title}})<--(c:Code) RETURN c" + results, meta = db.cypher_query(query, dict(paper_title=paper.title)) + if len(results) > 0: + codes = [Code.inflate(row[0]) for row in results] + else: + codes = [] + # pdb.set_trace() + #authors = ['{}. {}'.format(author.first_name[0], author.last_name) for author in authors] + + return codes + + +def get_paper_venue(paper): + query = "MATCH (:Paper {title: {paper_title}})--(v:Venue) RETURN v" + results, meta = db.cypher_query(query, dict(paper_title=paper.title)) + if len(results) == 1: # there should only be one venue associated with a paper + venue = [Venue.inflate(row[0]) for row in results][0] + else: + venue = None + # pdb.set_trace() + if venue is not None: + return '{}, {}'.format(venue.name, venue.publication_date) + else: + return '' + + +def papers(request): + # Retrieve the papers ordered by newest addition to DB first. + # limit to maximum 50 papers until we get pagination to work. + # However, even with pagination, we are going to want to limit + # the number of papers retrieved for speed, especially when the + # the DB grows large. + all_papers = Paper.nodes.order_by('-created')[:50] + # Retrieve all comments about this paper. + all_authors = [', '.join(get_paper_authors(paper)) for paper in all_papers] + all_venues = [get_paper_venue(paper) for paper in all_papers] + + papers = list(zip(all_papers, all_authors, all_venues)) + + return render(request, + 'papers.html', + {'papers': papers, + 'papers_only': all_papers, + 'num_papers': len(Paper.nodes.all())}) + + +def paper_authors(request, id): + """Displays the list of authors associated with this paper""" + paper = _get_paper_by_id(id) + print("Retrieved paper with title {}".format(paper.title)) + + query = "MATCH (p:Paper)<-[r]-(a:Person) WHERE ID(p)={id} RETURN a, ID(r)" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + authors = [Person.inflate(row[0]) for row in results] + relationship_ids = [row[1] for row in results] + else: + authors = [] + print("paper author link ids {}".format(relationship_ids)) + print("Found {} authors for paper with id {}".format(len(authors), id)) + + # for rid in relationship_ids: + delete_urls = [reverse('paper_remove_author', kwargs={'id': id, 'rid': rid}) for rid in relationship_ids] + print("author remove urls") + print(delete_urls) + + authors = zip(authors, delete_urls) + + return render(request, + 'paper_authors.html', + {'authors': authors, + 'paper': paper, }) + + +# should limit access to admin users only!! +@staff_member_required +def paper_remove_author(request, id, rid): + print("Paper id {} and edge id {}".format(id, rid)) + + # Cypher query to delete edge of type authors with id equal to rid + query = "MATCH ()-[r:authors]-() WHERE ID(r)={id} DELETE r" + results, meta = db.cypher_query(query, dict(id=rid)) + + return HttpResponseRedirect(reverse("paper_authors", kwargs={'id': id})) + + +def _get_paper_by_id(id): + # Retrieve the paper from the database + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + paper = None + if len(results) > 0: + all_papers = [Paper.inflate(row[0]) for row in results] + paper = all_papers[0] + return paper + + +def paper_detail(request, id): + # Retrieve the paper from the database + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + all_papers = [Paper.inflate(row[0]) for row in results] + paper = all_papers[0] + else: # go back to the paper index page + return render(request, 'papers.html', {'papers': Paper.nodes.all(), 'num_papers': len(Paper.nodes.all())}) + + # Retrieve the paper's authors + authors = get_paper_authors(paper) + # authors is a list of strings so just concatenate the strings. + authors = ", ".join(authors) + + # Retrieve all comments about this paper. + query = "MATCH (:Paper {title: {paper_title}})<--(c:Comment) RETURN c" + results, meta = db.cypher_query(query, dict(paper_title=paper.title)) + if len(results) > 0: + comments = [Comment.inflate(row[0]) for row in results] + num_comments = len(comments) + else: + comments = [] + num_comments = 0 + + # Retrieve the code repos that implement the algorithm(s) in this paper + codes = _get_paper_codes(paper) + + # Retrieve venue where paper was published. + query = "MATCH (:Paper {title: {paper_title}})-->(v:Venue) RETURN v" + results, meta = db.cypher_query(query, dict(paper_title=paper.title)) + if len(results) > 0: + venues = [Venue.inflate(row[0]) for row in results] + venue = venues[0] + else: + venue = None + + request.session['last-viewed-paper'] = id + + ego_network_json = _get_node_ego_network(paper.id, paper.title) + + print("ego_network_json: {}".format(ego_network_json)) + return render(request, + 'paper_detail.html', + {'paper': paper, + 'venue': venue, + 'authors': authors, + 'comments': comments, + 'codes': codes, + 'num_comments': num_comments, + 'ego_network': ego_network_json}) + + +def _get_node_ego_network(id, paper_title): + ''' + Returns a json formatted string of the nodes ego network + :param id: + :return: + ''' + query = "MATCH (s:Paper {title: {paper_title}})-->(t:Paper) RETURN t" + results, meta = db.cypher_query(query, dict(paper_title=paper_title)) + ego_json = '' + if len(results) > 0: + target_papers = [Paper.inflate(row[0]) for row in results] + print("Paper cites {} other papers.".format(len(target_papers))) + ego_json = "{{data : {{id: '{}', title: '{}', href: '{}' }} }}".format(id, + paper_title, + reverse('paper_detail', + kwargs={'id': id})) + for tp in target_papers: + ego_json += ", {{data : {{id: '{}', title: '{}', href: '{}' }} }}".format(tp.id, + tp.title, + reverse('paper_detail', + kwargs={'id': tp.id})) + for tp in target_papers: + ego_json += ",{{data: {{ id: '{}{}', label: '{}', source: {}, target: {} }}}}".format(id, tp.id, 'cites', + id, tp.id) + else: + print("No cited papers found!") + + return '[' + ego_json + ']' + + +def paper_find(request): + message = None + if request.method == 'POST': + form = SearchPapersForm(request.POST) + print("Received POST request") + if form.is_valid(): + english_stopwords = stopwords.words('english') + paper_title = form.cleaned_data['paper_title'].lower() + paper_title_tokens = [w for w in paper_title.split(' ') if not w in english_stopwords] + paper_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in paper_title_tokens) + '+.*' + query = "MATCH (p:Paper) WHERE p.title =~ { paper_query } RETURN p LIMIT 25" + print("Cypher query string {}".format(query)) + results, meta = db.cypher_query(query, dict(paper_query=paper_query)) + if len(results) > 0: + print("Found {} matching papers".format(len(results))) + papers = [Paper.inflate(row[0]) for row in results] + return render(request, 'paper_results.html', {'papers': papers}) + else: + message = "No results found. Please try again!" + + elif request.method == 'GET': + print("Received GET request") + form = SearchPapersForm() + + return render(request, 'paper_find.html', {'form': form, 'message': message}) + + +@login_required +def paper_connect_venue(request, id): + if request.method == 'POST': + form = SearchVenuesForm(request.POST) + if form.is_valid(): + # search the db for the venue + # if venue found, then link with paper and go back to paper view + # if not, ask the user to create a new venue + english_stopwords = stopwords.words('english') + venue_name = form.cleaned_data['venue_name'].lower() + venue_publication_year = form.cleaned_data['venue_publication_year'] + # TO DO: should probably check that data is 4 digits... + venue_name_tokens = [w for w in venue_name.split(' ') if not w in english_stopwords] + venue_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in venue_name_tokens) + '+.*' + query = "MATCH (v:Venue) WHERE v.publication_date =~ '" + venue_publication_year[0:4] + \ + ".*' AND v.name =~ { venue_query } RETURN v" + results, meta = db.cypher_query(query, dict(venue_publication_year=venue_publication_year[0:4], + venue_query=venue_query)) + if len(results) > 0: + venues = [Venue.inflate(row[0]) for row in results] + print("Found {} venues that match".format(len(venues))) + for v in venues: + print("\t{}".format(v)) + + if len(results) > 1: + # ask the user to select one of them + return render(request, 'paper_connect_venue.html', {'form': form, + 'venues': venues, + 'message': 'Found more than one matching venues. Please narrow your search'}) + else: + venue = venues[0] + print('Selected Venue: {}'.format(venue)) + + # retrieve the paper + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + all_papers = [Paper.inflate(row[0]) for row in results] + paper = all_papers[0] + print("Found paper: {}".format(paper.title)) + # check if the paper is connect with a venue; if yes, the remove link to + # venue before adding link to the new venue + query = 'MATCH (p:Paper)-[r:was_published_at]->(v:Venue) where id(p)={id} return v' + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + venues = [Venue.inflate(row[0]) for row in results] + for v in venues: + print("Disconnecting from: {}".format(v)) + paper.was_published_at.disconnect(v) + paper.save() + else: + print("Could not find paper!") + # should not get here since we started from the actual paper...but what if we do end up here? + pass # Should raise an exception but for now just pass + # we have a venue and a paper, so connect them. + print("Citation link not found, adding it!") + messages.add_message(request, messages.INFO, "Link to venue added!") + paper.was_published_at.connect(venue) + return redirect('paper_detail', id=paper.id) + else: + # render new Venue form with the searched name as + message = 'No matching venues found' + + if request.method == 'GET': + form = SearchVenuesForm() + message = None + + return render(request, 'paper_connect_venue.html', {'form': form, 'venues': None, 'message': message}) + + +@login_required +def paper_connect_author_selected(request, id, aid): + + query = "MATCH (p:Paper), (a:Person) WHERE ID(p)={id} AND ID(a)={aid} MERGE (a)-[r:authors]->(p) RETURN r" + results, meta = db.cypher_query(query, dict(id=id, aid=aid)) + + if len(results) > 0: + messages.add_message(request, messages.INFO, "Linked with author.") + else: + messages.add_message(request, messages.INFO, "Link to author failed!") + + return HttpResponseRedirect(reverse("paper_detail", kwargs={'id': id})) + +@login_required +def paper_connect_author(request, id): + if request.method == 'POST': + form = SearchPeopleForm(request.POST) + if form.is_valid(): + # search the db for the person + # if the person is found, then link with paper and go back to paper view + # if not, ask the user to create a new person + name = form.cleaned_data['person_name'] + people_found = _person_find(name) + + if people_found is not None: + print("Found {} people that match".format(len(people_found))) + for person in people_found: + print("\t{} {} {}".format(person.first_name, person.middle_name, person.last_name)) + + if len(people_found) > 0: + # for rid in relationship_ids: + author_connect_urls = [reverse('paper_connect_author_selected', kwargs={'id': id, 'aid': person.id}) for person in people_found] + print("author remove urls") + print(author_connect_urls) + + authors = zip(people_found, author_connect_urls) + + # ask the user to select one of them + return render(request, 'paper_connect_author.html', {'form': form, + 'people': authors, + 'message': ''}) + else: + message = 'No matching people found' + + if request.method == 'GET': + form = SearchPeopleForm() + message = None + + return render(request, 'paper_connect_author.html', {'form': form, 'people': None, 'message': message}) + + +@login_required +def paper_connect_paper(request, id): + """ + View function for connecting a paper with another paper. + + :param request: + :param id: + :return: + """ + message = None + if request.method == 'POST': + form = SearchPapersForm(request.POST) + if form.is_valid(): + # search the db for the person + # if the person is found, then link with paper and go back to paper view + # if not, ask the user to create a new person + paper_title_query = form.cleaned_data['paper_title'] + papers_found = _find_paper(paper_title_query) + + if len(papers_found) > 0: # found more than one matching papers + print("Found {} papers that match".format(len(papers_found))) + for paper in papers_found: + print("\t{}".format(paper.title)) + + if len(papers_found) > 1: + return render(request, 'paper_connect_paper.html', {'form': form, + 'papers': papers_found, + 'message': 'Found more than one matching papers. Please narrow your search'}) + else: + paper_target = papers_found[0] # one person found + print('Selected paper: {}'.format(paper.title)) + + # retrieve the paper + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + all_papers = [Paper.inflate(row[0]) for row in results] + paper_source = all_papers[0] # since we search by id only one paper should have been returned. + print("Found paper: {}".format(paper_source.title)) + # check if the papers are already connected with a cites link; if yes, then + # do nothing. Otherwise, add the link. + query = 'MATCH (q:Paper)<-[r:cites]-(p:Paper) where id(p)={source_id} and id(q)={target_id} return p' + results, meta = db.cypher_query(query, dict(source_id=paper_source.id, target_id=paper_target.id)) + if len(results) == 0: + # papers are not linked so add the edge + print("Citation link not found, adding it!") + paper_source.cites.connect(paper_target) + messages.add_message(request, messages.INFO, "Citation Added!") + else: + print("Citation link found not adding it!") + messages.add_message(request, messages.INFO, "Citation Already Exists!") + else: + print("Could not find paper!") + messages.add_message(request, messages.INFO, "Could not find paper!") + return redirect('paper_detail', id=id) + else: + message = 'No matching papers found' + + if request.method == 'GET': + form = SearchPapersForm() + + return render(request, 'paper_connect_paper.html', {'form': form, 'papers': None, 'message': message}) + + +@login_required +def paper_connect_dataset(request, id): + """ + View function for connecting a paper with a dataset. + + :param request: + :param id: + :return: + """ + if request.method == 'POST': + form = SearchDatasetsForm(request.POST) + if form.is_valid(): + # search the db for the dataset + # if the dataset is found, then link with paper and go back to paper view + # if not, ask the user to create a new dataset + dataset_query_name = form.cleaned_data['name'] + dataset_query_keywords = form.cleaned_data['keywords'] + datasets_found = _dataset_find(dataset_query_name, dataset_query_keywords) + + if len(datasets_found) > 0: # found more than one matching dataset + print("Found {} datasets that match".format(len(datasets_found))) + for dataset in datasets_found: + print("\t{}".format(dataset.name)) + + if len(datasets_found) > 1: + return render(request, 'paper_connect_dataset.html', {'form': form, + 'datasets': datasets_found, + 'message': 'Found more than one matching datasets. Please narrow your search'}) + else: + dataset_target = datasets_found[0] # one person found + print('Selected dataset: {}'.format(dataset_target.name)) + + # retrieve the paper + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + all_papers = [Paper.inflate(row[0]) for row in results] + paper_source = all_papers[0] # since we search by id only one paper should have been returned. + print("Found paper: {}".format(paper_source.title)) + # check if the papers are already connected with a cites link; if yes, then + # do nothing. Otherwise, add the link. + query = 'MATCH (d:Dataset)<-[r:evaluates_on]-(p:Paper) where id(p)={id} and id(d)={dataset_id} return p' + results, meta = db.cypher_query(query, dict(id=id, dataset_id=dataset_target.id)) + if len(results) == 0: + # dataset is not linked with paper so add the edge + paper_source.evaluates_on.connect(dataset_target) + messages.add_message(request, messages.INFO, "Link to dataset added!") + else: + messages.add_message(request, messages.INFO, "Link to dataset already exists!") + else: + print("Could not find paper!") + return redirect('paper_detail', id=id) + + else: + message = 'No matching datasets found' + + if request.method == 'GET': + form = SearchDatasetsForm() + message = None + + return render(request, 'paper_connect_dataset.html', {'form': form, 'datasets': None, 'message': message}) + +@login_required +def paper_connect_code_selected(request, id, cid): + + query = "MATCH (p:Paper), (c:Code) WHERE ID(p)={id} AND ID(c)={cid} MERGE (c)-[r:implements]->(p) RETURN r" + results, meta = db.cypher_query(query, dict(id=id, cid=cid)) + + if len(results) > 0: + messages.add_message(request, messages.INFO, "Linked with code repo.") + else: + messages.add_message(request, messages.INFO, "Link to code repo failed!") + + return HttpResponseRedirect(reverse("paper_detail", kwargs={'id': id})) + + +@login_required +def paper_connect_code(request, id): + """ + View function for connecting a paper with a dataset. + + :param request: + :param id: + :return: + """ + message = '' + if request.method == 'POST': + form = SearchCodesForm(request.POST) + if form.is_valid(): + # search the db for the person + # if the person is found, then link with paper and go back to paper view + # if not, ask the user to create a new person + keywords = form.cleaned_data['keywords'] + codes_found = _code_find(keywords) + + if len(codes_found) > 0: + print("Found {} codes that match".format(len(codes_found))) + for code in codes_found: + print("\t{} {}".format(code.website, code.keywords)) + + if len(codes_found) > 0: + # for rid in relationship_ids: + codes_connect_urls = [reverse('paper_connect_code_selected', kwargs={'id': id, 'cid': code.id}) for code in codes_found] + print(codes_connect_urls) + + codes = zip(codes_found, codes_connect_urls) + + # ask the user to select one of them + return render(request, 'paper_connect_code.html', {'form': form, + 'codes': codes, + 'message': ''}) + else: + message = 'No matching codes found' + + if request.method == 'GET': + form = SearchCodesForm() + message = None + + return render(request, 'paper_connect_code.html', {'form': form, 'codes': None, 'message': message}) + + +@login_required +def paper_update(request, id): + # retrieve paper by ID + # https://github.com/neo4j-contrib/neomodel/issues/199 + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + all_papers = [Paper.inflate(row[0]) for row in results] + paper_inst = all_papers[0] + else: + paper_inst = Paper() + + # if this is POST request then process the Form data + if request.method == 'POST': + + form = PaperForm(request.POST) + if form.is_valid(): + paper_inst.title = form.cleaned_data['title'] + paper_inst.abstract = form.cleaned_data['abstract'] + paper_inst.keywords = form.cleaned_data['keywords'] + paper_inst.download_link = form.cleaned_data['download_link'] + paper_inst.save() + + return HttpResponseRedirect(reverse('papers_index')) + # GET request + else: + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + all_papers = [Paper.inflate(row[0]) for row in results] + paper_inst = all_papers[0] + else: + paper_inst = Paper() + # paper_inst = Paper() + form = PaperForm(initial={'title': paper_inst.title, + 'abstract': paper_inst.abstract, + 'keywords': paper_inst.keywords, + 'download_link': paper_inst.download_link, }) + + return render(request, 'paper_update.html', {'form': form, 'paper': paper_inst}) + + +def _find_paper(query_string): + """ + Helper method to query the DB for a paper based on its title. + :param query_string: The query string, e.g., title of paper to search for + :return: List of papers that match the query or empty list if none match. + """ + papers_found = [] + + english_stopwords = stopwords.words('english') + paper_title = query_string.lower() + paper_title_tokens = [w for w in paper_title.split(' ') if not w in english_stopwords] + paper_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in paper_title_tokens) + '+.*' + query = "MATCH (p:Paper) WHERE p.title =~ { paper_query } RETURN p LIMIT 25" + print("Cypher query string {}".format(query)) + results, meta = db.cypher_query(query, dict(paper_query=paper_query)) + + if len(results) > 0: + papers_found = [Paper.inflate(row[0]) for row in results] + + return papers_found + + +def _add_author(author, paper=None): + """ + Adds author to the DB if author does not already exist and links to paper + as author if paper is not None + :param author: + :param paper: + """ + link_with_paper = False + p = None + people_found = _person_find(author, exact_match=True) + author_name = author.strip().split(' ') + if people_found is None: # not in DB + print("Author {} not in DB".format(author)) + p = Person() + p.first_name = author_name[0] + if len(author_name) > 2: # has middle name(s) + p.middle_name = author_name[1:-1] + else: + p.middle_name = None + p.last_name = author_name[-1] + p.save() # save to DB + link_with_paper = True + elif len(people_found) == 1: + # Exactly one person found. Check if name is an exact match. + p = people_found[0] + # NOTE: The problem with this simple check is that if two people have + # the same name then the wrong person will be linked to the paper. + if p.first_name == author_name[0] and p.last_name == author_name[-1]: + if len(author_name) > 2: + if p.middle_name == author_name[1:-1]: + link_with_paper = True + else: + link_with_paper = True + else: + print("Person with similar but not exactly the same name is already in DB.") + + if link_with_paper and paper is not None: + print("Adding authors link to paper {}".format(paper.title[:50])) + # link author with paper + p.authors.connect(paper) + + +@login_required +def paper_create(request): + user = request.user + print("In paper_create() view.") + message = '' + if request.method == 'POST': + print(" POST") + paper = Paper() + paper.created_by = user.id + form = PaperForm(instance=paper, data=request.POST) + if form.is_valid(): + # Check if the paper already exists in DB + matching_papers = _find_paper(form.cleaned_data['title']) + if len(matching_papers) > 0: # paper in DB already + message = "Paper already exists in Gnosis!" + return render(request, 'paper_results.html', {'papers': matching_papers, 'message': message}) + else: # the paper is not in DB yet. + form.save() # store + # Now, add the authors and link each author to the paper with an "authors" + # type edge. + if request.session.get('from_arxiv', False): + paper_authors = request.session['arxiv_authors'] + for paper_author in paper_authors.split(','): + print("Adding author {}".format(paper_author)) + _add_author(paper_author, paper) + + request.session['from_arxiv'] = False # reset + # go back to paper index page. + # Should this redirect to the page of the new paper just added? + return HttpResponseRedirect(reverse('papers_index')) + else: # GET + print(" GET") + # check if this is a redirect from paper_create_from_arxiv + # if so, then pre-populate the form with the data from arXiv, + # otherwise start with an empty form. + if request.session.get('from_arxiv', False) is True: + title = request.session['arxiv_title'] + abstract = request.session['arxiv_abstract'] + url = request.session['arxiv_url'] + + form = PaperForm(initial={'title': title, + 'abstract': abstract, + 'download_link': url}) + else: + form = PaperForm() + + return render(request, 'paper_form.html', {'form': form, 'message': message}) + + +def get_authors(bs4obj): + """ + Extract authors from arXiv.org paper page + :param bs4obj: + :return: None or a string with comma separated author names from first to last name + """ + authorList = bs4obj.findAll("div", {"class": "authors"}) + if authorList is not None: + if len(authorList) > 1: + # there should be just one but let's just take the first one + authorList = authorList[0] + + # for author in authorList: + # print("type of author {}".format(type(author))) + author_str = authorList[0].get_text() + if author_str.startswith("Authors:"): + author_str = author_str[8:] + return author_str + # authorList is None so return None + return None + + +def get_title(bs4obj): + """ + Extract paper title from arXiv.org paper page. + :param bs4obj: + :return: + """ + titleList = bs4obj.findAll("h1", {"class": "title"}) + if titleList is not None: + if len(titleList) == 0: + return None + else: + if len(titleList) > 1: + print("WARNING: Found more than one title. Returning the first one.") + # return " ".join(titleList[0].get_text().split()[1:]) + title_text = titleList[0].get_text() + if title_text.startswith('Title:'): + return title_text[6:] + else: + return title_text + return None + + +def get_abstract(bs4obj): + """ + Extract paper abstract from arXiv.org paper page. + :param bs4obj: + :return: + """ + abstract = bs4obj.find("blockquote", {"class": "abstract"}) + if abstract is not None: + abstract = " ".join(abstract.get_text().split(' ')[1:]) + return abstract + + +def get_venue(bs4obj): + """ + Extract publication venue from arXiv.org paper page. + :param bs4obj: + :return: + """ + venue = bs4obj.find("td", {"class": "tablecell comments mathjax"}) + if venue is not None: + venue = venue.get_text().split(';')[0] + return venue + + +def get_paper_info(url): + """ + Extract paper information, title, abstract, and authors, from arXiv.org + paper page. + :param url: + :return: + """ + try: + # html = urlopen("http://pythonscraping.com/pages/page1.html") + html = urlopen(url) + except HTTPError as e: + print(e) + except URLError as e: + print(e) + print("The server could not be found.") + else: + bs4obj = BeautifulSoup(html) + # Now, we can access individual element in the page + authors = get_authors(bs4obj) + title = get_title(bs4obj) + abstract = get_abstract(bs4obj) + # venue = get_venue(bs4obj) + return title, authors, abstract + + return None, None, None + + +@login_required +def paper_create_from_arxiv(request): + user = request.user + + if request.method == 'POST': + # create the paper from the extracted data and send to + # paper_form.html asking the user to verify + print("{}".format(request.POST['url'])) + # get the data from arxiv + url = request.POST['url'] + # check if url includes https, and if not add it + if not url.startswith("https://"): + url = "https://" + url + # retrieve paper info. If the information cannot be retrieved from remote + # server, then we will return an error message and redirect to paper_form.html. + title, authors, abstract = get_paper_info(url) + if title is None or authors is None or abstract is None: + form = PaperImportForm() + return render(request, 'paper_form.html', {'form': form, 'message': "Invalid source, please try again."}) + + request.session['from_arxiv'] = True + request.session['arxiv_title'] = title + request.session['arxiv_abstract'] = abstract + request.session['arxiv_url'] = url + request.session['arxiv_authors'] = authors # comma separate list of author names, first to last name + + print("Authors: {}".format(authors)) + + return HttpResponseRedirect(reverse('paper_create')) + else: # GET + request.session['from_arxiv'] = False + form = PaperImportForm() + + return render(request, 'paper_form.html', {'form': form}) + + +def _person_find(person_name, exact_match=False): + """ + Searches the DB for a person whose name matches the given name + :param person_name: + :return: + """ + person_name = person_name.lower() + person_name_tokens = [w for w in person_name.split()] + if exact_match: + if len(person_name_tokens) > 2: + query = ( + "MATCH (p:Person) WHERE LOWER(p.last_name) IN { person_tokens } AND LOWER(p.first_name) IN { person_tokens } AND LOWER(p.middle_name) IN { person_tokens } RETURN p LIMIT 20") + else: + query = ( + "MATCH (p:Person) WHERE LOWER(p.last_name) IN { person_tokens } AND LOWER(p.first_name) IN { person_tokens } RETURN p LIMIT 20") + else: + query = "MATCH (p:Person) WHERE LOWER(p.last_name) IN { person_tokens } OR LOWER(p.first_name) IN { person_tokens } OR LOWER(p.middle_name) IN { person_tokens } RETURN p LIMIT 20" + + results, meta = db.cypher_query(query, dict(person_tokens=person_name_tokens)) + + if len(results) > 0: + print("Found {} matching people".format(len(results))) + people = [Person.inflate(row[0]) for row in results] + return people + else: + return None + + +# +# Dataset Views +# +def datasets(request): + all_datasets = Dataset.nodes.order_by('-publication_date')[:50] + return render(request, 'datasets.html', {'datasets': all_datasets}) + + +def dataset_detail(request, id): + # Retrieve the paper from the database + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + # There should be only one results because ID should be unique. Here we check that at + # least one result has been returned and take the first result as the correct match. + # Now, it should not happen that len(results) > 1 since IDs are meant to be unique. + # For the MVP we are going to ignore the latter case and just continue but ultimately, + # we should be checking for > 1 and failing gracefully. + all_datasets = [Dataset.inflate(row[0]) for row in results] + dataset = all_datasets[0] + else: # go back to the paper index page + return render(request, 'datasets.html', + {'datasets': Dataset.nodes.all(), 'num_datasets': len(Dataset.nodes.all())}) + + # + # TO DO: Retrieve and list all papers that evaluate on this dataset. + # + + request.session['last-viewed-dataset'] = id + + return render(request, + 'dataset_detail.html', + {'dataset': dataset}) + + +def _dataset_find(name, keywords): + """ + Helper method for searching Neo4J DB for a dataset. + + :param name: Dataset name search query + :param keywords: Dataset keywords search query + :return: + """ + dataset_name_tokens = [w for w in name.split()] + dataset_keywords = [w for w in keywords.split()] + datasets = [] + if len(dataset_keywords) > 0 and len(dataset_name_tokens) > 0: + # Search using both the name and the keywords + keyword_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in dataset_keywords) + '+.*' + name_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in dataset_name_tokens) + '+.*' + query = "MATCH (d:Dataset) WHERE d.name =~ { name_query } AND d.keywords =~ { keyword_query} RETURN d LIMIT 25" + results, meta = db.cypher_query(query, dict(name_query=name_query, keyword_query=keyword_query)) + if len(results) > 0: + datasets = [Dataset.inflate(row[0]) for row in results] + return datasets + else: + if len(dataset_keywords) > 0: + # only keywords given + dataset_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in dataset_keywords) + '+.*' + query = "MATCH (d:Dataset) WHERE d.keywords =~ { dataset_query } RETURN d LIMIT 25" + else: + # only name or nothing (will still return all datasets if name and + # keywords fields are left empty and sumbit button is pressed. + dataset_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in dataset_name_tokens) + '+.*' + query = "MATCH (d:Dataset) WHERE d.name =~ { dataset_query } RETURN d LIMIT 25" + # results, meta = db.cypher_query(query, dict(dataset_query=dataset_query)) + + results, meta = db.cypher_query(query, dict(dataset_query=dataset_query)) + if len(results) > 0: + datasets = [Dataset.inflate(row[0]) for row in results] + return datasets + + return datasets # empty list + + +def dataset_find(request): + """ + Searching for a dataset in the DB. + + :param request: + :return: + """ + message = None + if request.method == 'POST': + form = SearchDatasetsForm(request.POST) + print("Received POST request") + if form.is_valid(): + dataset_name = form.cleaned_data['name'].lower() + dataset_keywords = form.cleaned_data['keywords'].lower() # comma separated list + + datasets = _dataset_find(dataset_name, dataset_keywords) + + if len(datasets) > 0: + return render(request, 'datasets.html', {'datasets': datasets}) + else: + message = "No results found. Please try again!" + elif request.method == 'GET': + print("Received GET request") + form = SearchDatasetsForm() + + return render(request, 'dataset_find.html', {'form': form, 'message': message}) + + +@login_required +def dataset_create(request): + user = request.user + + if request.method == 'POST': + dataset = Dataset() + dataset.created_by = user.id + form = DatasetForm(instance=dataset, data=request.POST) + if form.is_valid(): + form.save() + return HttpResponseRedirect(reverse('datasets_index')) + else: # GET + form = DatasetForm() + + return render(request, 'dataset_form.html', {'form': form}) + + +@login_required +def dataset_update(request, id): + # retrieve paper by ID + # https://github.com/neo4j-contrib/neomodel/issues/199 + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + datasets = [Dataset.inflate(row[0]) for row in results] + dataset = datasets[0] + else: + dataset = Dataset() + + # if this is POST request then process the Form data + if request.method == 'POST': + form = DatasetForm(request.POST) + if form.is_valid(): + dataset.name = form.cleaned_data['name'] + dataset.keywords = form.cleaned_data['keywords'] + dataset.description = form.cleaned_data['description'] + dataset.publication_date = form.cleaned_data['publication_date'] + dataset.source_type = form.cleaned_data['source_type'] + dataset.website = form.cleaned_data['website'] + dataset.save() + + return HttpResponseRedirect(reverse('datasets_index')) + # GET request + else: + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + datasets = [Dataset.inflate(row[0]) for row in results] + dataset = datasets[0] + else: + dataset = Dataset() + form = DatasetForm(initial={'name': dataset.name, + 'keywords': dataset.keywords, + 'description': dataset.description, + 'publication_date': dataset.publication_date, + 'source_type': dataset.source_type, + 'website': dataset.website, + } + ) + + return render(request, 'dataset_update.html', {'form': form, 'dataset': dataset}) + + +# +# Venue Views +# +def venues(request): + all_venues = Venue.nodes.order_by('-publication_date')[:50] + return render(request, 'venues.html', {'venues': all_venues}) + + +def venue_detail(request, id): + # Retrieve the paper from the database + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + # There should be only one results because ID should be unique. Here we check that at + # least one result has been returned and take the first result as the correct match. + # Now, it should not happen that len(results) > 1 since IDs are meant to be unique. + # For the MVP we are going to ignore the latter case and just continue but ultimately, + # we should be checking for > 1 and failing gracefully. + all_venues = [Venue.inflate(row[0]) for row in results] + venue = all_venues[0] + else: # go back to the paper index page + return render(request, 'venues.html', {'venues': Venue.nodes.all(), 'num_venues': len(Venue.nodes.all())}) + + # + # TO DO: Retrieve all papers published at this venue and list them + # + request.session['last-viewed-venue'] = id + return render(request, + 'venue_detail.html', + {'venue': venue}) + + +def venue_find(request): + """ + Search for venue. + :param request: + :return: + """ + if request.method == 'POST': + form = SearchVenuesForm(request.POST) + if form.is_valid(): + # search the db for the venue + # if venue found, then link with paper and go back to paper view + # if not, ask the user to create a new venue + english_stopwords = stopwords.words('english') + venue_name = form.cleaned_data['venue_name'].lower() + venue_publication_year = form.cleaned_data['venue_publication_year'] + # TO DO: should probably check that data is 4 digits... + venue_name_tokens = [w for w in venue_name.split(' ') if not w in english_stopwords] + venue_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in venue_name_tokens) + '+.*' + query = "MATCH (v:Venue) WHERE v.publication_date =~ '" + venue_publication_year[0:4] + \ + ".*' AND v.name =~ { venue_query } RETURN v" + results, meta = db.cypher_query(query, dict(venue_publication_year=venue_publication_year[0:4], + venue_query=venue_query)) + if len(results) > 0: + venues = [Venue.inflate(row[0]) for row in results] + print("Found {} venues that match".format(len(venues))) + return render(request, 'venues.html', {'venues': venues}) + else: + # render new Venue form with the searched name as + message = 'No matching venues found' + + if request.method == 'GET': + form = SearchVenuesForm() + message = None + + return render(request, 'venue_find.html', {'form': form, 'message': message}) + + +@login_required +def venue_create(request): + user = request.user + + if request.method == 'POST': + venue = Venue() + venue.created_by = user.id + form = VenueForm(instance=venue, data=request.POST) + if form.is_valid(): + form.save() + return HttpResponseRedirect(reverse('venues_index')) + else: # GET + form = VenueForm() + + return render(request, 'venue_form.html', {'form': form}) + + +@login_required +def venue_update(request, id): + # retrieve paper by ID + # https://github.com/neo4j-contrib/neomodel/issues/199 + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + venues = [Venue.inflate(row[0]) for row in results] + venue = venues[0] + else: + venue = Venue() + + # if this is POST request then process the Form data + if request.method == 'POST': + form = VenueForm(request.POST) + if form.is_valid(): + venue.name = form.cleaned_data['name'] + venue.publication_date = form.cleaned_data['publication_date'] + venue.type = form.cleaned_data['type'] + venue.publisher = form.cleaned_data['publisher'] + venue.keywords = form.cleaned_data['keywords'] + venue.peer_reviewed = form.cleaned_data['peer_reviewed'] + venue.website = form.cleaned_data['website'] + venue.save() + + return HttpResponseRedirect(reverse('venues_index')) + # GET request + else: + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + venues = [Venue.inflate(row[0]) for row in results] + venue = venues[0] + else: + venue = Venue() + form = VenueForm(initial={'name': venue.name, + 'type': venue.type, + 'publication_date': venue.publication_date, + 'publisher': venue.publisher, + 'keywords': venue.keywords, + 'peer_reviewed': venue.peer_reviewed, + 'website': venue.website, + } + ) + + return render(request, 'venue_update.html', {'form': form, 'venue': venue}) + + +# +# Comment Views +# +@login_required +def comments(request): + """ + We should only show the list of comments if the user is admin. Otherwise, the user should + be redirected to the home page. + :param request: + :return: + """ + # Only superusers can view all the comments + if request.user.is_superuser: + return render(request, 'comments.html', + {'comments': Comment.nodes.all(), 'num_comments': len(Comment.nodes.all())}) + else: + # other users are sent back to the paper index + return HttpResponseRedirect(reverse('papers_index')) + + +@login_required +def comment_detail(request, id): + # Only superusers can view comment details. + if request.user.is_superuser: + return render(request, 'comment_detail.html', {'comment': Comment.nodes.all()}) + else: + # other users are sent back to the papers index + return HttpResponseRedirect(reverse('papers_index')) + + +@login_required +def comment_create(request): + user = request.user + + # Retrieve paper using paper id + paper_id = request.session['last-viewed-paper'] + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=paper_id)) + if len(results) > 0: + all_papers = [Paper.inflate(row[0]) for row in results] + paper = all_papers[0] + else: # just send him to the list of papers + HttpResponseRedirect(reverse('papers_index')) + + if request.method == 'POST': + comment = Comment() + comment.created_by = user.id + comment.author = user.username + form = CommentForm(instance=comment, data=request.POST) + if form.is_valid(): + # add link from new comment to paper + form.save() + comment.discusses.connect(paper) + del request.session['last-viewed-paper'] + return redirect('paper_detail', id=paper_id) + else: # GET + form = CommentForm() + + return render(request, 'comment_form.html', {'form': form}) + + +@login_required +def comment_update(request, id): + # retrieve paper by ID + # https://github.com/neo4j-contrib/neomodel/issues/199 + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + comments = [Comment.inflate(row[0]) for row in results] + comment = comments[0] + else: + comment = Comment() + + # Retrieve paper using paper id + paper_id = request.session['last-viewed-paper'] + + # if this is POST request then process the Form data + if request.method == 'POST': + form = CommentForm(request.POST) + if form.is_valid(): + comment.text = form.cleaned_data['text'] + # comment.author = form.cleaned_data['author'] + comment.save() + # return HttpResponseRedirect(reverse('comments_index')) + del request.session['last-viewed-paper'] + return redirect('paper_detail', id=paper_id) + + # GET request + else: + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + comments = [Comment.inflate(row[0]) for row in results] + comment = comments[0] + else: + comment = Comment() + # form = CommentForm(initial={'author': comment.author, + # 'text': comment.text, + # 'publication_date': comment.publication_date, + # } + # ) + form = CommentForm(initial={'text': comment.text, + 'publication_date': comment.publication_date, + } + ) + + return render(request, 'comment_update.html', {'form': form, 'comment': comment}) + + +# +# Utility Views (admin required) +# +@login_required +def build(request): + try: + d1 = Dataset() + d1.name = 'Yelp' + d1.source_type = 'N' + d1.save() + + v1 = Venue() + v1.name = 'Neural Information Processing Systems' + v1.publication_date = date(2017, 12, 15) + v1.type = 'C' + v1.publisher = 'NIPS Foundation' + v1.keywords = 'machine learning, machine learning, computational neuroscience' + v1.website = 'https://nips.cc' + v1.peer_reviewed = 'Y' + v1.save() + + v2 = Venue() + v2.name = 'International Conference on Machine Learning' + v2.publication_date = date(2016, 5, 24) + v2.type = 'C' + v2.publisher = 'International Machine Learning Society (IMLS)' + v2.keywords = 'machine learning, computer science' + v2.peer_reviewed = 'Y' + v2.website = 'https://icml.cc/2016/' + v2.save() + + p1 = Paper() + p1.title = 'The best paper in the world.' + p1.abstract = 'Abstract goes here' + p1.keywords = 'computer science, machine learning, graphs' + p1.save() + + p1.evaluates_on.connect(d1) + p1.was_published_at.connect(v1) + + p2 = Paper() + p2.title = 'The second best paper in the world.' + p2.abstract = 'Abstract goes here' + p2.keywords = 'statistics, robust methods' + p2.save() + + p2.cites.connect(p1) + p2.was_published_at.connect(v2) + + p3 = Paper() + p3.title = 'I wish I could write a paper with a great title.' + p3.abstract = 'Abstract goes here' + p3.keywords = 'machine learning, neural networks, convolutional neural networks' + p3.save() + + p3.cites.connect(p1) + p3.was_published_at.connect(v1) + + a1 = Person() + a1.first_name = 'Pantelis' + a1.last_name = 'Elinas' + a1.save() + + a1.authors.connect(p1) + + a2 = Person() + a2.first_name = "Ke" + a2.last_name = "Sun" + a2.save() + + a2.authors.connect(p1) + a2.authors.connect(p2) + + a3 = Person() + a3.first_name = "Bill" + a3.last_name = "Gates" + a3.save() + + a3.authors.connect(p3) + a3.advisor_of.connect(a1) + + a4 = Person() + a4.first_name = "Steve" + a4.last_name = "Jobs" + a4.save() + + a4.authors.connect(p2) + a4.authors.connect(p3) + + a4.co_authors_with.connect(a3) + + c1 = Comment() + c1.author = "Pantelis Elinas" + c1.text = "This paper is flawless" + c1.save() + + c1.discusses.connect(p1) + + except Exception: + pass + + num_papers = len(Paper.nodes.all()) + num_people = len(Person.nodes.all()) + + return render(request, 'build.html', {'num_papers': num_papers, 'num_people': num_people}) diff --git a/gnosis/catalog/views/views_codes.py b/gnosis/catalog/views/views_codes.py new file mode 100644 index 0000000..bf94c2c --- /dev/null +++ b/gnosis/catalog/views/views_codes.py @@ -0,0 +1,147 @@ +from django.contrib.auth.decorators import login_required +from django.shortcuts import render +from catalog.models import Code +from catalog.forms import CodeForm +from catalog.forms import SearchCodesForm +from django.urls import reverse +from django.http import HttpResponseRedirect +from neomodel import db + + +# +# Code Views +# +def codes(request): + all_codes = Code.nodes.all() + return render(request, 'codes.html', {'codes': all_codes}) + + +def code_detail(request, id): + # Retrieve the paper from the database + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + # There should be only one result because ID should be unique. Here we check that at + # least one result has been returned and take the first result as the correct match. + # Now, it should not happen that len(results) > 1 since IDs are meant to be unique. + # For the MVP we are going to ignore the latter case and just continue but ultimately, + # we should be checking for > 1 and failing gracefully. + all_codes = [Code.inflate(row[0]) for row in results] + code = all_codes[0] + else: # go back to the paper index page + return render(request, 'codes.html', + {'codes': Code.nodes.all(), 'num_codes': len(Code.nodes.all())}) + + # + # TO DO: Retrieve and list all papers that evaluate on this dataset. + # + + request.session['last-viewed-code'] = id + + return render(request, + 'code_detail.html', + {'code': code}) + + +def _code_find(keywords): + """ + Helper method for searching Neo4J DB for code repo. + + :param keywords: Dataset keywords search query + :return: + """ + code_keywords = [w for w in keywords.split()] + codes = [] + if len(code_keywords) > 0: + # Search using the keywords + keyword_query = '(?i).*' + '+.*'.join('(' + w + ')' for w in code_keywords) + '+.*' + query = "MATCH (d:Code) WHERE d.keywords =~ { keyword_query} RETURN d LIMIT 25" + results, meta = db.cypher_query(query, dict(keyword_query=keyword_query)) + if len(results) > 0: + codes = [Code.inflate(row[0]) for row in results] + + return codes + + +def code_find(request): + """ + Searching for a Code repo in the DB view. + + :param request: + """ + message = None + if request.method == 'POST': + form = SearchCodesForm(request.POST) + print("Received POST request") + if form.is_valid(): + keywords = form.cleaned_data['keywords'].lower() # comma separated list + + codes = _code_find(keywords) + + if len(codes) > 0: + return render(request, 'codes.html', {'codes': codes}) + else: + message = "No results found. Please try again!" + elif request.method == 'GET': + print("Received GET request") + form = SearchCodesForm() + + return render(request, 'dataset_find.html', {'form': form, 'message': message}) + + +@login_required +def code_create(request): + user = request.user + + if request.method == 'POST': + code = Code() + code.created_by = user.id + form = CodeForm(instance=code, data=request.POST) + if form.is_valid(): + form.save() + return HttpResponseRedirect(reverse('codes_index')) + else: # GET + form = CodeForm() + + return render(request, 'code_form.html', {'form': form}) + + +@login_required +def code_update(request, id): + # retrieve code node by ID + # https://github.com/neo4j-contrib/neomodel/issues/199 + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + codes = [Code.inflate(row[0]) for row in results] + code = codes[0] + else: + code = Code() + + # if this is POST request then process the Form data + if request.method == 'POST': + form = CodeForm(request.POST) + if form.is_valid(): + code.keywords = form.cleaned_data['keywords'] + code.description = form.cleaned_data['description'] + code.website = form.cleaned_data['website'] + code.save() + + return HttpResponseRedirect(reverse('codes_index')) + # GET request + else: + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + codes = [Code.inflate(row[0]) for row in results] + code = codes[0] + else: + code = Code() + + form = CodeForm(initial={'keywords': code.keywords, + 'description': code.description, + 'website': code.website, + } + ) + + return render(request, 'code_update.html', {'form': form, 'code': code}) diff --git a/gnosis/catalog/views/views_people.py b/gnosis/catalog/views/views_people.py new file mode 100644 index 0000000..274b0b9 --- /dev/null +++ b/gnosis/catalog/views/views_people.py @@ -0,0 +1,154 @@ +from django.contrib.auth.decorators import login_required +from django.shortcuts import render +from catalog.models import Person +from catalog.forms import PersonForm +from catalog.forms import SearchPeopleForm +from django.urls import reverse +from django.http import HttpResponseRedirect +from neomodel import db + + +def _person_find(person_name, exact_match=False): + """ + Searches the DB for a person whose name matches the given name + :param person_name: + :return: + """ + person_name = person_name.lower() + person_name_tokens = [w for w in person_name.split()] + if exact_match: + if len(person_name_tokens) > 2: + query = ("MATCH (p:Person) WHERE LOWER(p.last_name) IN { person_tokens } AND LOWER(p.first_name) IN { person_tokens } AND LOWER(p.middle_name) IN { person_tokens } RETURN p LIMIT 20") + else: + query = ("MATCH (p:Person) WHERE LOWER(p.last_name) IN { person_tokens } AND LOWER(p.first_name) IN { person_tokens } RETURN p LIMIT 20") + else: + query = "MATCH (p:Person) WHERE LOWER(p.last_name) IN { person_tokens } OR LOWER(p.first_name) IN { person_tokens } OR LOWER(p.middle_name) IN { person_tokens } RETURN p LIMIT 20" + + results, meta = db.cypher_query(query, dict(person_tokens=person_name_tokens)) + + if len(results) > 0: + print("Found {} matching people".format(len(results))) + people = [Person.inflate(row[0]) for row in results] + return people + else: + return None + + +def person_find(request): + """ + Searching for a person in the DB. + + :param request: + :return: + """ + message = None + if request.method == 'POST': + form = SearchPeopleForm(request.POST) + print("Received POST request") + if form.is_valid(): + + people = _person_find(form.cleaned_data['person_name']) + if people is not None: + return render(request, 'people.html', {'people': people}) + else: + message = "No results found. Please try again!" + + elif request.method == 'GET': + print("Received GET request") + form = SearchPeopleForm() + + return render(request, 'person_find.html', {'form': form, 'message': message}) + + +# +# Person Views +# +def persons(request): + return render(request, 'people.html', {'people': Person.nodes.all(), 'num_people': len(Person.nodes.all())}) + + +def person_detail(request, id): + # Retrieve the paper from the database + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + # There should be only one results because ID should be unique. Here we check that at + # least one result has been returned and take the first result as the correct match. + # Now, it should not happen that len(results) > 1 since IDs are meant to be unique. + # For the MVP we are going to ignore the latter case and just continue but ultimately, + # we should be checking for > 1 and failing gracefully. + all_people = [Person.inflate(row[0]) for row in results] + person = all_people[0] + else: # go back to the paper index page + return render(request, 'people.html', {'people': Person.nodes.all(), 'num_people': len(Person.nodes.all())}) + + # + # TO DO: Retrieve all papers co-authored by this person and list them; same for + # co-authors and advisees. + # + request.session['last-viewed-person'] = id + return render(request, + 'person_detail.html', + {'person': person}) + + +@login_required +def person_create(request): + user = request.user + + if request.method == 'POST': + person = Person() + person.created_by = user.id + form = PersonForm(instance=person, data=request.POST) + if form.is_valid(): + form.save() + return HttpResponseRedirect(reverse('persons_index')) + else: # GET + form = PersonForm() + + return render(request, 'person_form.html', {'form': form}) + + +@login_required +def person_update(request, id): + # retrieve paper by ID + # https://github.com/neo4j-contrib/neomodel/issues/199 + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + all_people = [Person.inflate(row[0]) for row in results] + person_inst = all_people[0] + else: + person_inst = Person() + + # if this is POST request then process the Form data + if request.method == 'POST': + form = PersonForm(request.POST) + if form.is_valid(): + person_inst.first_name = form.cleaned_data['first_name'] + person_inst.middle_name = form.cleaned_data['middle_name'] + person_inst.last_name = form.cleaned_data['last_name'] + person_inst.affiliation = form.cleaned_data['affiliation'] + person_inst.website = form.cleaned_data['website'] + person_inst.save() + + return HttpResponseRedirect(reverse('persons_index')) + # GET request + else: + query = "MATCH (a) WHERE ID(a)={id} RETURN a" + results, meta = db.cypher_query(query, dict(id=id)) + if len(results) > 0: + all_people = [Person.inflate(row[0]) for row in results] + person_inst = all_people[0] + else: + person_inst = Person() + form = PersonForm(initial={'first_name': person_inst.first_name, + 'middle_name': person_inst.middle_name, + 'last_name': person_inst.last_name, + 'affiliation': person_inst.affiliation, + 'website': person_inst.website, + } + ) + + return render(request, 'person_update.html', {'form': form, 'person': person_inst}) + diff --git a/gnosis/gnosis/__init__.py b/gnosis/gnosis/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/gnosis/gnosis/settings.py b/gnosis/gnosis/settings.py new file mode 100644 index 0000000..df2060c --- /dev/null +++ b/gnosis/gnosis/settings.py @@ -0,0 +1,137 @@ +""" +Django settings for gnosis project. + +Generated by 'django-admin startproject' using Django 2.0.4. + +For more information on this file, see +https://docs.djangoproject.com/en/2.0/topics/settings/ + +For the full list of settings and their values, see +https://docs.djangoproject.com/en/2.0/ref/settings/ +""" + +import os + +# Build paths inside the project like this: os.path.join(BASE_DIR, ...) +BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) + +NEOMODEL_NEO4J_BOLT_URL = os.environ.get('NEO4J_BOLT_URL', 'bolt://neo4j:GnosisTest00@localhost:7687') + +# Quick-start development settings - unsuitable for production +# See https://docs.djangoproject.com/en/2.0/howto/deployment/checklist/ + +# SECURITY WARNING: keep the secret key used in production secret! +SECRET_KEY = '6pph^ipk8sow@%nw)s!l@klg4q8lnar2k6k$&e=26pqrm(zg^a' + +# SECURITY WARNING: don't run with debug turned on in production! +DEBUG = True + +ALLOWED_HOSTS = [] + + +SESSION_SAVE_EVERY_REQUEST = True + +# Application definition + +INSTALLED_APPS = [ + 'django.contrib.admin', + 'django.contrib.auth', + 'django.contrib.contenttypes', + 'django.contrib.sessions', + 'django.contrib.messages', + 'django.contrib.staticfiles', + 'django_neomodel', + 'django_registration', + 'el_pagination', + 'catalog.apps.CatalogConfig', + 'home.apps.HomeConfig', +] + +MIDDLEWARE = [ + 'django.middleware.security.SecurityMiddleware', + 'django.contrib.sessions.middleware.SessionMiddleware', + 'django.middleware.common.CommonMiddleware', + 'django.middleware.csrf.CsrfViewMiddleware', + 'django.contrib.auth.middleware.AuthenticationMiddleware', + 'django.contrib.messages.middleware.MessageMiddleware', + 'django.middleware.clickjacking.XFrameOptionsMiddleware', +] + +ROOT_URLCONF = 'gnosis.urls' + +TEMPLATES = [ + { + 'BACKEND': 'django.template.backends.django.DjangoTemplates', + 'DIRS': ['./templates', ], + 'APP_DIRS': True, + 'OPTIONS': { + 'context_processors': [ + 'django.template.context_processors.debug', + 'django.template.context_processors.request', + 'django.contrib.auth.context_processors.auth', + 'django.contrib.messages.context_processors.messages', + 'django.template.context_processors.request', ## For EL-pagination + ], + }, + }, +] + +WSGI_APPLICATION = 'gnosis.wsgi.application' + +# Increase this number when in production. +EL_PAGINATION_PER_PAGE = 3 + +# Database +# https://docs.djangoproject.com/en/2.0/ref/settings/#databases + +DATABASES = { + 'default': { + 'ENGINE': 'django.db.backends.sqlite3', + 'NAME': os.path.join(BASE_DIR, 'db.sqlite3'), + } +} + + +# Password validation +# https://docs.djangoproject.com/en/2.0/ref/settings/#auth-password-validators + +AUTH_PASSWORD_VALIDATORS = [ + { + 'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator', + }, +] + + +# Internationalization +# https://docs.djangoproject.com/en/2.0/topics/i18n/ + +LANGUAGE_CODE = 'en-us' + +TIME_ZONE = 'Australia/Sydney' + +USE_I18N = True + +USE_L10N = True + +USE_TZ = True + + +# Static files (CSS, JavaScript, Images) +# https://docs.djangoproject.com/en/2.0/howto/static-files/ + +STATIC_URL = '/static/' + +# After user login, she will be re-directed to home page instead of accounts/profile +LOGIN_REDIRECT_URL = '/' + +# This is for checking the password reset email when the email server is not configured +EMAIL_BACKEND = 'django.core.mail.backends.console.EmailBackend' \ No newline at end of file diff --git a/gnosis/gnosis/urls.py b/gnosis/gnosis/urls.py new file mode 100644 index 0000000..479cf91 --- /dev/null +++ b/gnosis/gnosis/urls.py @@ -0,0 +1,39 @@ +"""gnosis URL Configuration + +The `urlpatterns` list routes URLs to views. For more information please see: + https://docs.djangoproject.com/en/2.0/topics/http/urls/ +Examples: +Function views + 1. Add an import: from my_app import views + 2. Add a URL to urlpatterns: path('', views.home, name='home') +Class-based views + 1. Add an import: from other_app.views import Home + 2. Add a URL to urlpatterns: path('', Home.as_view(), name='home') +Including another URLconf + 1. Import the include() function: from django.urls import include, path + 2. Add a URL to urlpatterns: path('blog/', include('blog.urls')) +""" +from django.views.generic import RedirectView +from django.conf.urls.static import static +from django.conf.urls import include, url +from django.contrib import admin +from django.conf import settings +from django.urls import path + +urlpatterns = [ + path('admin/', admin.site.urls), + path('catalog/', include('catalog.urls')), + path('home/', include('home.urls')), + # the next one redirects the root URL to host/catalog/ + # change this as necessary later, maybe make it redirect to a welcome page + path('', RedirectView.as_view(url='/home/')), +] + +# for user authentication +urlpatterns += [ + url(r'^accounts/', include('django_registration.backends.one_step.urls')), + path('accounts/', include('django.contrib.auth.urls')), +] + +# Use static() to add url mapping to serve static files during development (only) +urlpatterns += static(settings.STATIC_URL, document_root=settings.STATIC_ROOT) diff --git a/gnosis/gnosis/wsgi.py b/gnosis/gnosis/wsgi.py new file mode 100644 index 0000000..1d0ac3d --- /dev/null +++ b/gnosis/gnosis/wsgi.py @@ -0,0 +1,16 @@ +""" +WSGI config for gnosis project. + +It exposes the WSGI callable as a module-level variable named ``application``. + +For more information on this file, see +https://docs.djangoproject.com/en/2.0/howto/deployment/wsgi/ +""" + +import os + +from django.core.wsgi import get_wsgi_application + +os.environ.setdefault("DJANGO_SETTINGS_MODULE", "gnosis.settings") + +application = get_wsgi_application() diff --git a/gnosis/home/__init__.py b/gnosis/home/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/gnosis/home/admin.py b/gnosis/home/admin.py new file mode 100644 index 0000000..8c38f3f --- /dev/null +++ b/gnosis/home/admin.py @@ -0,0 +1,3 @@ +from django.contrib import admin + +# Register your models here. diff --git a/gnosis/home/apps.py b/gnosis/home/apps.py new file mode 100644 index 0000000..90dc713 --- /dev/null +++ b/gnosis/home/apps.py @@ -0,0 +1,5 @@ +from django.apps import AppConfig + + +class HomeConfig(AppConfig): + name = 'home' diff --git a/gnosis/home/migrations/__init__.py b/gnosis/home/migrations/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/gnosis/home/models.py b/gnosis/home/models.py new file mode 100644 index 0000000..71a8362 --- /dev/null +++ b/gnosis/home/models.py @@ -0,0 +1,3 @@ +from django.db import models + +# Create your models here. diff --git a/gnosis/home/templates/home.html b/gnosis/home/templates/home.html new file mode 100644 index 0000000..2dd4d70 --- /dev/null +++ b/gnosis/home/templates/home.html @@ -0,0 +1,34 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

γνώσις

+ +

A knowledge management system for technical documents.

+ +{% if user.is_authenticated %} +

Hi {{ user.get_username }} (Logout)

+{% else %} +

Hi, login to make full use of γνώσις.

+

If you are new here then why not register a new account!

+{% endif %} + +

Statistics: We have {{ num_papers }} papers and {{ num_people }} people in our DB

+ +

Recently added papers

+
+{% for paper, authors in papers %} + +{% endfor %} + +{% if user.is_superuser %} +

Populate test DB

+{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/home/tests.py b/gnosis/home/tests.py new file mode 100644 index 0000000..7ce503c --- /dev/null +++ b/gnosis/home/tests.py @@ -0,0 +1,3 @@ +from django.test import TestCase + +# Create your tests here. diff --git a/gnosis/home/urls.py b/gnosis/home/urls.py new file mode 100644 index 0000000..9ec8361 --- /dev/null +++ b/gnosis/home/urls.py @@ -0,0 +1,6 @@ +from django.urls import path +from . import views + +urlpatterns = [ + path('', views.home, name='home'), +] diff --git a/gnosis/home/views.py b/gnosis/home/views.py new file mode 100644 index 0000000..fa98598 --- /dev/null +++ b/gnosis/home/views.py @@ -0,0 +1,31 @@ +from django.shortcuts import render +from catalog.models import Paper, Person +from neomodel import db + + +# Create your views here. +def home(request): + num_papers = len(Paper.nodes.all()) + num_people = len(Person.nodes.all()) + + recent_papers = Paper.nodes.order_by('-created')[:5] + authors = [', '.join(get_paper_authors(paper)) for paper in recent_papers] + + papers = list(zip(recent_papers, authors)) + + return render(request, 'home.html', {'papers': papers, + 'num_papers': num_papers, + 'num_people': num_people}) + + +def get_paper_authors(paper): + query = "MATCH (:Paper {title: {paper_title}})<--(a:Person) RETURN a" + results, meta = db.cypher_query(query, dict(paper_title=paper.title)) + if len(results) > 0: + authors = [Person.inflate(row[0]) for row in results] + else: + authors = [] + # pdb.set_trace() + authors = ['{}. {}'.format(author.first_name[0], author.last_name) for author in authors] + + return authors diff --git a/gnosis/manage.py b/gnosis/manage.py new file mode 100644 index 0000000..97faf2b --- /dev/null +++ b/gnosis/manage.py @@ -0,0 +1,15 @@ +#!/usr/bin/env python +import os +import sys + +if __name__ == "__main__": + os.environ.setdefault("DJANGO_SETTINGS_MODULE", "gnosis.settings") + try: + from django.core.management import execute_from_command_line + except ImportError as exc: + raise ImportError( + "Couldn't import Django. Are you sure it's installed and " + "available on your PYTHONPATH environment variable? Did you " + "forget to activate a virtual environment?" + ) from exc + execute_from_command_line(sys.argv) diff --git a/gnosis/templates/django_registration/registration_complete.html b/gnosis/templates/django_registration/registration_complete.html new file mode 100644 index 0000000..29dc94a --- /dev/null +++ b/gnosis/templates/django_registration/registration_complete.html @@ -0,0 +1,11 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

Account created successfully.

+ +

Enjoy your stay!

+ + + +{% endblock %} \ No newline at end of file diff --git a/gnosis/templates/django_registration/registration_form.html b/gnosis/templates/django_registration/registration_form.html new file mode 100644 index 0000000..ae9709a --- /dev/null +++ b/gnosis/templates/django_registration/registration_form.html @@ -0,0 +1,17 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +
+ {% csrf_token %} + {% for field in form %} +

+ {{ field.label_tag }}
+ {{ field }} + {% for error in field.errors %} +

{{ error }}

+ {% endfor %} +

+ {% endfor %} + +
+{% endblock %} \ No newline at end of file diff --git a/gnosis/templates/gnosis_theme.html b/gnosis/templates/gnosis_theme.html new file mode 100644 index 0000000..1eb346d --- /dev/null +++ b/gnosis/templates/gnosis_theme.html @@ -0,0 +1,190 @@ + + + + Gnosis Research Paper Management + + + + + + + + + + + + + +
+
+
+
+ {% if user.is_authenticated %} +

+
+
+ Papers   +
+ + + + +
+
+ +
+ People   +
+ + +
+
+ +
+ Venues   +
+ + +
+
+ +
+ Datasets +
+ + +
+
+ +
+ Codes +
+ + +
+
+ +
+ {% else %} +

+
+
+ Papers   +
+ +
+ People   +
+ +
+ Venues   +
+ +
+ Datasets +
+ +
+ Codes +
+ +
+ + {% endif %} +
+
+ {% block content %} + {% endblock %} +
+
+ + + + + +
+
+ +
+
+ {% block footer %} + {% load static %} + CSIRO and Data61 Logos + {% endblock %} +
+ + + diff --git a/gnosis/templates/registration/logged_out.html b/gnosis/templates/registration/logged_out.html new file mode 100644 index 0000000..c28f538 --- /dev/null +++ b/gnosis/templates/registration/logged_out.html @@ -0,0 +1,9 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

Logged out!

+ +Click here to login again. + +{% endblock %} \ No newline at end of file diff --git a/gnosis/templates/registration/login.html b/gnosis/templates/registration/login.html new file mode 100644 index 0000000..e2f98fb --- /dev/null +++ b/gnosis/templates/registration/login.html @@ -0,0 +1,48 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +
+ {% if next %} + {% if user.is_authenticated %} +

Your account doesn't have access to this page. To proceed, + please login with an account that has access.

+ {% else %} +

Log in to your account.

+ {% endif %} + {% endif %} +
+ +
+
+
+ {% csrf_token %} + + + + + + + + + +
+ {% if form.errors %} +

+ Your username and password didn't match. + Please try again. +

+ {% endif %} + + + +
+
+
+ +{# Assumes you setup the password_reset view in your URLconf #} +

Lost password?

+

New User? Register a new account!

+{% endblock %} \ No newline at end of file diff --git a/gnosis/templates/registration/password_reset_complete.html b/gnosis/templates/registration/password_reset_complete.html new file mode 100644 index 0000000..4046735 --- /dev/null +++ b/gnosis/templates/registration/password_reset_complete.html @@ -0,0 +1,9 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + + +

The password has been changed!

+

log in again?

+ +{% endblock %} \ No newline at end of file diff --git a/gnosis/templates/registration/password_reset_confirm.html b/gnosis/templates/registration/password_reset_confirm.html new file mode 100644 index 0000000..0562ff1 --- /dev/null +++ b/gnosis/templates/registration/password_reset_confirm.html @@ -0,0 +1,33 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +{% if validlink %} +

Please enter (and confirm) your new password.

+
+
+ +
+ + + + + + + + + + + + + +
{{ form.new_password1.errors }} + {{ form.new_password1 }}
{{ form.new_password2.errors }} + {{ form.new_password2 }}
+
+{% else %} +

Password reset failed

+

The password reset link was invalid, possibly because it has already been used. Please request a new password reset.

+{% endif %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/templates/registration/password_reset_done.html b/gnosis/templates/registration/password_reset_done.html new file mode 100644 index 0000000..7517ff5 --- /dev/null +++ b/gnosis/templates/registration/password_reset_done.html @@ -0,0 +1,8 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +

We've emailed you instructions for setting your password. If they haven't arrived in a few minutes, check your spam folder.

+ + +{% endblock %} \ No newline at end of file diff --git a/gnosis/templates/registration/password_reset_email.html b/gnosis/templates/registration/password_reset_email.html new file mode 100644 index 0000000..3142e75 --- /dev/null +++ b/gnosis/templates/registration/password_reset_email.html @@ -0,0 +1,8 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} + +Someone asked for password reset for email {{ email }}. Follow the link below: +{{ protocol}}://{{ domain }}{% url 'password_reset_confirm' uidb64=uid token=token %} + +{% endblock %} \ No newline at end of file diff --git a/gnosis/templates/registration/password_reset_form.html b/gnosis/templates/registration/password_reset_form.html new file mode 100644 index 0000000..b798bb8 --- /dev/null +++ b/gnosis/templates/registration/password_reset_form.html @@ -0,0 +1,11 @@ +{% extends "gnosis_theme.html" %} + +{% block content %} +

Reset your password.

+
{% csrf_token %} + {% if form.email.errors %} {{ form.email.errors }} {% endif %} +

Enter your email: {{ form.email }}

+ +
+ +{% endblock %} \ No newline at end of file diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..9d8daba --- /dev/null +++ b/requirements.txt @@ -0,0 +1,29 @@ +beautifulsoup4==4.6.3 +certifi==2018.1.18 +chardet==3.0.4 +confusable-homoglyphs==3.2.0 +cycler==0.10.0 +Django==2.0.4 +django-el-pagination==3.2.4 +django-neomodel==0.0.4 +django-registration==3.0 +docopt==0.6.2 +idna==2.6 +kiwisolver==1.0.1 +matplotlib==2.2.2 +neo4j-driver==1.5.2 +neomodel==3.2.6 +nltk==3.3 +numpy==1.14.2 +pandas==0.22.0 +pipreqs==0.4.9 +py2neo==3.1.2 +pyparsing==2.2.0 +python-dateutil==2.7.2 +pytz==2018.3 +requests==2.18.4 +scikit-learn==0.19.1 +scipy==1.0.1 +six==1.11.0 +urllib3==1.22 +yarg==0.1.9 diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..d8b9453 --- /dev/null +++ b/setup.py @@ -0,0 +1,26 @@ +# -*- coding: utf-8 -*- +# +# Copyright 2018 Data61, CSIRO +# +import setuptools + +DESCRIPTION = "Gnosis web application for paper management and collaboration." +URL = "https://github.com/stellargraph/stellar-gnosis" + +setuptools.setup( + name="gnosis", + version="0.1.0", + author="Pantelis Elinas, Data61, CSIRO", + author_email="pantelis.elinas@data61.csiro.au", + url=URL, + long_description=DESCRIPTION, + long_description_content_type="text/markdown", + python_requires='>3.5.0, <3.7.0', + classifiers=[ + "Programming Language :: Python :: 3", + "Operating System :: OS Independent", + "Development Status :: 3 - Alpha", + "Intended Audience :: Science/Research", + "Topic :: Scientific/Engineering :: Artificial Intelligence", + ], +) diff --git a/stellar-gnosis b/stellar-gnosis deleted file mode 160000 index 9ac34e9..0000000 --- a/stellar-gnosis +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 9ac34e9003bd6088251fdf6d02395a7fc7ad7413 From eff972bd30084dc017a656ce127294d3a52f9d7e Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Thu, 28 Mar 2019 17:01:17 +1100 Subject: [PATCH 004/154] add readme --- README.md | Bin 12 -> 146 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/README.md b/README.md index c4063c68ca30b2b2c2124649ea1e911724e8e94a..965140b7a854a2dcf38fbdd449ef257ef83de312 100644 GIT binary patch literal 146 zcmXwx*$IF^3`F0zU@2OPJ$Nj-c;bQDygD0JLdYcZGVfF1I7vwu@J#fkcWxFrn{AcU rF3PDUyDXIEuaR)%wCa%KxI_oCiSD8KXVuJ%`Yl=QmMPbZ@8b6dlQ9^h literal 12 TcmY#ZaL>yx&MekVNi72a7$yWG From a9dc2084bdcfef0dd280a105672ef4a31dcc76ec Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Sun, 31 Mar 2019 15:58:52 +1100 Subject: [PATCH 005/154] Update README.md --- README.md | 108 +++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 107 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index c4063c6..87b1c5a 100644 --- a/README.md +++ b/README.md @@ -1 +1,107 @@ -# Gnosis-dev \ No newline at end of file +# Gnosis + +**Gnosis** is an online paper management and collaboration tool. + + +## Installation Instructions + +These instructions are a brief overview of the steps required to run the **Gnosis** Django application on a development +server using Django's build in web server, the free version of Neo4j, and sqlite3. + +**Gnosis** is a Python Django web application. You should install a suitable version of Python in +order to proceed. We have tested **Gnosis** with Python version 3.6.5 but any 3.6.* version should +work. + +These installation instructions are for Mac OS. The instructions for any popular Linux distributions should be very +similar. We have not tested **Gnosis** on Windows 10. + +### Install Neo4j + +Download and install the free desktop version of the Neo3j Graph database from [here](https://neo4j.com/download/). + +We have installed and tested Gnosis with the Neo4j community version 3.3.4 although newer version should +work just as well. + +Let's assume that you have successfully installed Neo4j in the directory `/Neo4j/`. You can now start the neo4j server +by executing the command + +`/Neo4j/bin/neo4j start` + +If the database server starts without errors you should see the following message printed in the terminal, + + Started neo4j (pid 23687). It is available at http://localhost:7474/ + There may be a short delay until the server is ready. + +With your web browser, you can now access the Neo4j console by visiting http://localhost:7474/. + +**Important** When you first install Neo4j, you can create a user account and set a password. Remember these as you +will need them later in the instructions. + +### Install Gnosis + +First, you need to either clone or download the code from GitHub. + +To clone the **Gnosis** repo in the directory `/Projects`, change to the latter and then issue +the following command, + + git clone https://github.com/stellargraph/stellar-gnosis.git + +This command will clone the **Gnosis** repo into the directory `/Projects/stellar-gnosis`. + +Create a new Python virtual environment either using `virtualevn` or `conda` for a suitable version +of Python. Let's assume that the new environment is called `gnosis-env`. + +Activate `gnosis-env` and install the library requirements using the following command, + + pip install -r requirements.txt + +**Important:** As the next step you must apply a patch to the django-neomodel library. Locate +the file `/site-packages/django_neomodel/__init__.py` and the method `get_choices(self, include_blank=True)`. + +Then replace the line, + + choices=list(self.choices)if self.choices else [] + +with the following, + + choices=[(k, v)for k, v in self.choices.items()] if self.choices else [] + +Locate the `settings.py` file in the directory `/Projects/stellar-gnosis/gnosis/gnosis/`. You need to set your +Neo4j database password so that Django can access it. Find the line, + + NEOMODEL_NEO4J_BOLT_URL = os.environ.get('NEO4J_BOLT_URL', 'bolt://neo4j:GnosisTest00@localhost:7687') + +The string `bolt://neo4j:GnosisTest00@localhost:7687'` indicates that the default (for development) Neo4j user +name is *neo4j* and the password is `GnosisTest00`. Replace these with the username and password you created earlier +during the Neo4j installation. You do not need a strong password as this is only used for development. You can use the +values in `settings.py` if you want; in this case, you don't have to modify the above line. + +#### Prepare the databases + +Change to the directory `/Projects/stellar-gnosis/gnosis/` where you can find the file `manage.py`. + +Prepare the Neo4j and sqlite3 databases by using the following commands, + + python manage.py install_labels + python manage.py makemigrations + python manage.py migrate + +Create a **Gnosis** administrator account using the below command and following the prompts: + + python manage.py createsuperuser + +You can now start the development server by issuing the command, + + python manage.py runserver + +You can access **Gnosis** running on your local machine by pointing your web browser to `http://127.0.0.1:8000/` + +## License + +Copyright 2010-2019 Commonwealth Scientific and Industrial Research Organisation (CSIRO). + +All Rights Reserved. + +NOTICE: All information contained herein remains the property of the CSIRO. The intellectual and technical concepts +contained herein are proprietary to the CSIRO and are protected by copyright law. Dissemination of this information +or reproduction of this material is strictly forbidden unless prior written permission is obtained from the CSIRO. From 6f99aa319d81fdb1a868c78cfd13d8685ab87ce8 Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Tue, 2 Apr 2019 12:42:13 +1100 Subject: [PATCH 006/154] bug fixes --- dist/gnosis-0.1.0-py3.6.egg | Bin 0 -> 1115 bytes gnosis.egg-info/PKG-INFO | 17 +++++++++++++++++ gnosis.egg-info/SOURCES.txt | 6 ++++++ gnosis.egg-info/dependency_links.txt | 1 + gnosis.egg-info/top_level.txt | 1 + gnosis/catalog/models.py | 2 +- 6 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 dist/gnosis-0.1.0-py3.6.egg create mode 100644 gnosis.egg-info/PKG-INFO create mode 100644 gnosis.egg-info/SOURCES.txt create mode 100644 gnosis.egg-info/dependency_links.txt create mode 100644 gnosis.egg-info/top_level.txt diff --git a/dist/gnosis-0.1.0-py3.6.egg b/dist/gnosis-0.1.0-py3.6.egg new file mode 100644 index 0000000000000000000000000000000000000000..5d6ea31e941d8d028e82623557e948144065e3a6 GIT binary patch literal 1115 zcmWIWW@Zs#U|`^2*t4d_FMFPG%oIijhIvd341z#WS9f<^Pd_(*{Qz$WBXrW;yxRsm zt?zk%$o^p1I7jCOo5bM@3YyyzVuOy{tvY*Rjjm7qgr)x+uXjovlu0pKM=$`=%eSctYi> z<)nf>ZCv>}ZfT+o_e&pH;mqEJ{4d&H`wmu!Eybu})V$F{ZhXjwESN8Zu&G`l3-Z{202G2g;-YpG3M@YjNmJu1Iu zXZd|uU3|Wb&Fq8f?Ur;a=Bo8mkF4bL*W1AE&&U&XE;oYrLYac>a_ij_3x- z);n?SF^Q{_7ipFj>=8?z^7bKLuKgx4lbHPlQPy*>eQs2~fAUt(cJa8SGbbc-SKpqf z{_lp#^YSn4TRz{6pKZ`<*zLqB{g!>s;oq6svZWg&tzE;?wAY?F{>x>e!HGn>PY?D? zS|9Of)tda=^*VtwVv5p*iy{}E6VF)t%X5Q{-#|MjzHyiZ@}|4?@Q>zCrs$0u-n3.5.0, <3.7.0 +Description-Content-Type: text/markdown diff --git a/gnosis.egg-info/SOURCES.txt b/gnosis.egg-info/SOURCES.txt new file mode 100644 index 0000000..a9d010c --- /dev/null +++ b/gnosis.egg-info/SOURCES.txt @@ -0,0 +1,6 @@ +README.md +setup.py +gnosis.egg-info/PKG-INFO +gnosis.egg-info/SOURCES.txt +gnosis.egg-info/dependency_links.txt +gnosis.egg-info/top_level.txt \ No newline at end of file diff --git a/gnosis.egg-info/dependency_links.txt b/gnosis.egg-info/dependency_links.txt new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/gnosis.egg-info/dependency_links.txt @@ -0,0 +1 @@ + diff --git a/gnosis.egg-info/top_level.txt b/gnosis.egg-info/top_level.txt new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/gnosis.egg-info/top_level.txt @@ -0,0 +1 @@ + diff --git a/gnosis/catalog/models.py b/gnosis/catalog/models.py index fafd42b..1a5f15c 100644 --- a/gnosis/catalog/models.py +++ b/gnosis/catalog/models.py @@ -64,7 +64,7 @@ class Meta: ordering = ['last_name', 'first_name', 'affiliation'] def __str__(self): - if self.middle_name is not None or len(self.middle_name) > 0: + if self.middle_name is not None and len(self.middle_name) > 0: return '{} {} {}'.format(self.first_name, self.middle_name, self.last_name) return '{} {}'.format(self.first_name, self.last_name) From a9eb8630ebfdd4ffb8b213e65e66d652f29b98cc Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Tue, 2 Apr 2019 12:51:59 +1100 Subject: [PATCH 007/154] Update README.md --- README.md | 107 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 107 insertions(+) diff --git a/README.md b/README.md index e69de29..16c6c81 100644 --- a/README.md +++ b/README.md @@ -0,0 +1,107 @@ +# Gnosis + +**Gnosis** is an online paper management and collaboration tool. + + +## Installation Instructions + +These instructions are a brief overview of the steps required to run the **Gnosis** Django application on a development +server using Django's build in web server, the free version of Neo4j, and sqlite3. + +**Gnosis** is a Python Django web application. You should install a suitable version of Python in +order to proceed. We have tested **Gnosis** with Python version 3.6.5 but any 3.6.* version should +work. + +These installation instructions are for Mac OS. The instructions for any popular Linux distributions should be very +similar. We have not tested **Gnosis** on Windows 10. + +### Install Neo4j + +Download and install the free desktop version of the Neo3j Graph database from [here](https://neo4j.com/download/). + +We have installed and tested Gnosis with the Neo4j community version 3.3.4 although newer version should +work just as well. + +Let's assume that you have successfully installed Neo4j in the directory `/Neo4j/`. You can now start the neo4j server +by executing the command + +`/Neo4j/bin/neo4j start` + +If the database server starts without errors you should see the following message printed in the terminal, + + Started neo4j (pid 23687). It is available at http://localhost:7474/ + There may be a short delay until the server is ready. + +With your web browser, you can now access the Neo4j console by visiting http://localhost:7474/. + +**Important** When you first install Neo4j, you can create a user account and set a password. Remember these as you +will need them later in the instructions. + +### Install Gnosis + +First, you need to either clone or download the code from GitHub. + +To clone the **Gnosis** repo in the directory `/Projects`, change to the latter and then issue +the following command, + + git clone https://github.com/stellargraph/stellar-gnosis.git + +This command will clone the **Gnosis** repo into the directory `/Projects/stellar-gnosis`. + +Create a new Python virtual environment either using `virtualevn` or `conda` for a suitable version +of Python. Let's assume that the new environment is called `gnosis-env`. + +Activate `gnosis-env` and install the library requirements using the following command, + + pip install -r requirements.txt + +**Important:** As the next step you must apply a patch to the django-neomodel library. Locate +the file `/site-packages/django_neomodel/__init__.py` and the method `get_choices(self, include_blank=True)`. + +Then replace the line, + + choices=list(self.choices)if self.choices else [] + +with the following, + + choices=[(k, v)for k, v in self.choices.items()] if self.choices else [] + +Locate the `settings.py` file in the directory `/Projects/stellar-gnosis/gnosis/gnosis/`. You need to set your +Neo4j database password so that Django can access it. Find the line, + + NEOMODEL_NEO4J_BOLT_URL = os.environ.get('NEO4J_BOLT_URL', 'bolt://neo4j:GnosisTest00@localhost:7687') + +The string `bolt://neo4j:GnosisTest00@localhost:7687'` indicates that the default (for development) Neo4j user +name is *neo4j* and the password is `GnosisTest00`. Replace these with the username and password you created earlier +during the Neo4j installation. You do not need a strong password as this is only used for development. You can use the +values in `settings.py` if you want; in this case, you don't have to modify the above line. + +#### Prepare the databases + +Change to the directory `/Projects/stellar-gnosis/gnosis/` where you can find the file `manage.py`. + +Prepare the Neo4j and sqlite3 databases by using the following commands, + + python manage.py install_labels + python manage.py makemigrations + python manage.py migrate + +Create a **Gnosis** administrator account using the below command and following the prompts: + + python manage.py createsuperuser + +You can now start the development server by issuing the command, + + python manage.py runserver + +You can access **Gnosis** running on your local machine by pointing your web browser to `http://127.0.0.1:8000/` + +## License + +Copyright 2010-2019 Commonwealth Scientific and Industrial Research Organisation (CSIRO). + +All Rights Reserved. + +NOTICE: All information contained herein remains the property of the CSIRO. The intellectual and technical concepts +contained herein are proprietary to the CSIRO and are protected by copyright law. Dissemination of this information +or reproduction of this material is strictly forbidden unless prior written permission is obtained from the CSIRO. From 15d981469ca87afed106aa70975c32b7bb8217ca Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Tue, 2 Apr 2019 13:12:02 +1100 Subject: [PATCH 008/154] update gitignore, remove ignored folders --- .gitignore | 125 ++++++++++++++++++++++++++- dist/gnosis-0.1.0-py3.6.egg | Bin 1115 -> 0 bytes gnosis.egg-info/PKG-INFO | 17 ---- gnosis.egg-info/SOURCES.txt | 6 -- gnosis.egg-info/dependency_links.txt | 1 - gnosis.egg-info/top_level.txt | 1 - 6 files changed, 122 insertions(+), 28 deletions(-) delete mode 100644 dist/gnosis-0.1.0-py3.6.egg delete mode 100644 gnosis.egg-info/PKG-INFO delete mode 100644 gnosis.egg-info/SOURCES.txt delete mode 100644 gnosis.egg-info/dependency_links.txt delete mode 100644 gnosis.egg-info/top_level.txt diff --git a/.gitignore b/.gitignore index 01294de..aee0e03 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,123 @@ -.idea/ -.DS_Store -*.sqlite3 +# Byte-compiled / optimized / DLL files __pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don’t work, or not +# install all needed dependencies. +#Pipfile.lock + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ \ No newline at end of file diff --git a/dist/gnosis-0.1.0-py3.6.egg b/dist/gnosis-0.1.0-py3.6.egg deleted file mode 100644 index 5d6ea31e941d8d028e82623557e948144065e3a6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1115 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100644 index 8b13789..0000000 --- a/gnosis.egg-info/dependency_links.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/gnosis.egg-info/top_level.txt b/gnosis.egg-info/top_level.txt deleted file mode 100644 index 8b13789..0000000 --- a/gnosis.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ - From 1190c69acc9db000372945f014e34cf715971eb0 Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Tue, 2 Apr 2019 13:22:04 +1100 Subject: [PATCH 009/154] Update .gitignore --- .gitignore | 122 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 122 insertions(+) diff --git a/.gitignore b/.gitignore index 01294de..8e487cd 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,126 @@ .idea/ .DS_Store *.sqlite3 +# Byte-compiled / optimized / DLL files __pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don’t work, or not +# install all needed dependencies. +#Pipfile.lock + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ From 6940408a1085a5db4abbfa157f896b176a99a85f Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Tue, 9 Apr 2019 00:28:22 +1000 Subject: [PATCH 010/154] rename branch --- .gitignore | 122 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 122 insertions(+) diff --git a/.gitignore b/.gitignore index 01294de..4d3dd4b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,126 @@ .idea/ .DS_Store *.sqlite3 +# Byte-compiled / optimized / DLL files __pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don’t work, or not +# install all needed dependencies. +#Pipfile.lock + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ \ No newline at end of file From bf35ff5edfb0425e0965ae37f99f21345b1b1817 Mon Sep 17 00:00:00 2001 From: PantelisElinas Date: Tue, 9 Apr 2019 10:06:36 +1000 Subject: [PATCH 011/154] Bumped version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index c22855b..d642214 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ setuptools.setup( name="gnosis", - version="0.2.1", + version="0.3.0b", author="Pantelis Elinas, Data61, CSIRO", author_email="pantelis.elinas@data61.csiro.au", url=URL, From 832288c55ed5e10e91fb9c0eb15e9be092e98df5 Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Tue, 9 Apr 2019 20:35:52 +1000 Subject: [PATCH 012/154] updates --- .idea/Gnosis-dev.iml | 21 ++ .idea/encodings.xml | 6 + .idea/inspectionProfiles/Project_Default.xml | 14 ++ .idea/misc.xml | 7 + .idea/modules.xml | 8 + .idea/vcs.xml | 6 + .idea/workspace.xml | 232 +++++++++++++++++++ 7 files changed, 294 insertions(+) create mode 100644 .idea/Gnosis-dev.iml create mode 100644 .idea/encodings.xml create mode 100644 .idea/inspectionProfiles/Project_Default.xml create mode 100644 .idea/misc.xml create mode 100644 .idea/modules.xml create mode 100644 .idea/vcs.xml create mode 100644 .idea/workspace.xml diff --git a/.idea/Gnosis-dev.iml b/.idea/Gnosis-dev.iml new file mode 100644 index 0000000..53328dd --- /dev/null +++ b/.idea/Gnosis-dev.iml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/encodings.xml b/.idea/encodings.xml new file mode 100644 index 0000000..004e846 --- /dev/null +++ b/.idea/encodings.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml new file mode 100644 index 0000000..1bbf15d --- /dev/null +++ b/.idea/inspectionProfiles/Project_Default.xml @@ -0,0 +1,14 @@ + + + + \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml new file mode 100644 index 0000000..b9951f5 --- /dev/null +++ b/.idea/misc.xml @@ -0,0 +1,7 @@ + + + + + + \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml new file mode 100644 index 0000000..8bf3d5b --- /dev/null +++ b/.idea/modules.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 0000000..94a25f7 --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/.idea/workspace.xml b/.idea/workspace.xml new file mode 100644 index 0000000..9c9e972 --- /dev/null +++ b/.idea/workspace.xml @@ -0,0 +1,232 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - 1554269292495 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file From d5647ad4b67cc06a4241c59b0291c9a708db15d1 Mon Sep 17 00:00:00 2001 From: Zhenghao-Zhao Date: Tue, 9 Apr 2019 21:43:55 +1000 Subject: [PATCH 015/154] Update .gitignore --- .gitignore | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 7085b7b..8e487cd 100644 --- a/.gitignore +++ b/.gitignore @@ -88,7 +88,7 @@ ipython_config.py # pipenv # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. # However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don’t work, or not +# having no cross-platform support, pipenv may install dependencies that don’t work, or not # install all needed dependencies. #Pipfile.lock @@ -124,4 +124,3 @@ dmypy.json # Pyre type checker .pyre/ -__pycache__/ From c0b78dff94d6201b44142c595dcdcf37ae361c0b Mon Sep 17 00:00:00 2001 From: PantelisElinas Date: Wed, 10 Apr 2019 10:43:05 +1000 Subject: [PATCH 016/154] Invalid arXiv URL is now correctly detected and a message informing the user is shown. Also, the import view now uses card format like the rest of the site. --- gnosis/catalog/templates/paper_form.html | 35 ++++++++++++------------ gnosis/catalog/views/views.py | 15 +++++++--- 2 files changed, 28 insertions(+), 22 deletions(-) diff --git a/gnosis/catalog/templates/paper_form.html b/gnosis/catalog/templates/paper_form.html index 3d1914a..759094a 100644 --- a/gnosis/catalog/templates/paper_form.html +++ b/gnosis/catalog/templates/paper_form.html @@ -1,26 +1,25 @@ {% extends "gnosis_theme.html" %} {% block content %} -
-

New Paper

+
+
+

New Paper

+
+
-
- {% csrf_token %} - - {{ form }} -
-
- -
+ {% if message %} +

{{ message }}

+ {% endif %} -
-

{{ message }}

+
+ {% csrf_token %} + + {{ form }} +
+
+ +
+

*required
- - {% if message %} -

{{ message }}

- {% endif %} -

*required
-
{% endblock %} \ No newline at end of file diff --git a/gnosis/catalog/views/views.py b/gnosis/catalog/views/views.py index 6199bb3..cbf651e 100644 --- a/gnosis/catalog/views/views.py +++ b/gnosis/catalog/views/views.py @@ -986,11 +986,18 @@ def paper_create_from_arxiv(request): # get the data from arxiv url = request.POST["url"] # check if url includes https, and if not add it - if not url.startswith("https://"): + if not url.startswith("https://") and not url.startswith("http://"): url = "https://" + url - # retrieve paper info. If the information cannot be retrieved from remote - # server, then we will return an error message and redirect to paper_form.html. - title, authors, abstract = get_paper_info(url) + + print("Given url: {}".format(url)) + # check if valid url before trying to get the data. + if not url.startswith("https://arxiv.org/abs/") and not url.startswith("http://arxiv.org/abs/"): + title, authors, abstract = None, None, None + else: + # retrieve paper info. If the information cannot be retrieved from remote + # server, then we will return an error message and redirect to paper_form.html. + title, authors, abstract = get_paper_info(url) + if title is None or authors is None or abstract is None: form = PaperImportForm() return render( From 9f900bb463cdff3b170a01c75bbf8123229e652f Mon Sep 17 00:00:00 2001 From: PantelisElinas Date: Wed, 10 Apr 2019 12:53:10 +1000 Subject: [PATCH 017/154] Maximum width set to 1024px so that if the browser window is made larger, the amount of content displayed does not overwhelm the user. --- gnosis/templates/gnosis_theme.html | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnosis/templates/gnosis_theme.html b/gnosis/templates/gnosis_theme.html index 4caa6ef..e8bd57b 100644 --- a/gnosis/templates/gnosis_theme.html +++ b/gnosis/templates/gnosis_theme.html @@ -11,6 +11,10 @@ -