Initial commit

.gitignore

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+# env file
+.env
+
+# media files
+media/annotations/*
+media/dbxrefs/*
+media/genes/*
+media/taxonomy/*
+
+# build files
+__pycache__
+.idea

Dockerfile

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+FROM python:3.6
+
+ENV PYTHONUNBUFFERED 1
+ENV DJANGO_ENV local
+
+COPY ./requirements.txt /app/requirements.txt
+RUN pip install -r /app/requirements.txt
+
+COPY . /app/
+WORKDIR /app/
+
+EXPOSE 8000

accounts/admin.py

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+from django.contrib import admin
+
+# Register your models here.

accounts/apps.py

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+from django.apps import AppConfig
+
+
+class AccountsConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'accounts'

accounts/forms.py

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+from django import forms
+from django.contrib.auth.forms import UserCreationForm, AuthenticationForm
+
+# models import
+from .models import User
+
+
+# orcID validator function
+def orcIDValidator(url):
+    # get the actual orcid part
+    orcid = url.split('/')[-1]
+    # remove and store the last digit as it is the checksum
+    digit = orcid[-1]
+    orcid = orcid[:-1]
+    # remove dashes
+    orcid = orcid.replace('-', '')
+    # calculate checksum
+    total = 0
+    for i in str(orcid):
+        total = (total + int(i)) * 2
+    remainder = total % 11
+    chksum = (12 - remainder) % 11
+    if chksum == 10:
+        chksum = "X"
+    if digit == str(chksum):
+        return orcid
+    else:
+        raise forms.ValidationError("This field is not a valid ORCID")
+
+class UserRegistrationForm(UserCreationForm):
+    ROLE_CHOICES = (
+        ("Requestor", "Requestor"),
+        ("Contributor", "Contributor"),
+        ("Curator", "Curator"),
+        ("Moderator", "Moderator"),
+        ("Superuser", "Superuser")
+    )
+    email = forms.EmailField(label='Email address:')
+    first_name = forms.CharField(label='First Name:')
+    last_name = forms.CharField(label='Last Name:')
+    affiliation = forms.CharField(label='Affiliation:')
+    orcid = forms.CharField(label='<a href="https://orcid.org">ORCID</a>', validators=[orcIDValidator],
+                            help_text="Example: https://orcid.org/0000-0012-3456-7890")
+    role = forms.ChoiceField(choices=ROLE_CHOICES, label='Role')
+
+    autofocus = 'email'
+
+    def signup(self, request, user):
+        pass
+
+    # Make sure no usernames with just digits, will mess up the account info lookups
+    def clean_username(self):
+        username = self.cleaned_data['username']
+        if username.isdigit():
+            raise forms.ValidationError("Usernames must contain at least one letter")
+        return username
+
+    class Meta(UserCreationForm.Meta):
+        model = User
+        fields = ['username', 'password1', 'password2', 'email', 'first_name', 'last_name', 'affiliation', 'orcid', 'role']
+
+    def save(self, commit=True):
+        user = super().save(commit=False)
+        user.email = self.cleaned_data['email']
+        user.first_name = self.cleaned_data['first_name']
+        user.last_name = self.cleaned_data['last_name']
+        user.affiliation = self.cleaned_data['affiliation']
+        user.orcid = self.cleaned_data['orcid']
+        user.role = self.cleaned_data['role']
+        user.is_active = False
+        user.needs_approval = True
+        self.approve(user)
+        if commit:
+            user.save()
+        return user
+
+    def approve(self, user):
+        # TODO: send email notification
+
+        return True
+
+
+class UserLoginForm(AuthenticationForm):
+    def __init__(self, *args, **kwargs):
+        super(UserLoginForm, self).__init__(*args, **kwargs)
+
+    username = forms.TextInput(attrs={'class': 'form-control', 'placeholder': ''})
+    password = forms.CharField(widget=forms.PasswordInput(attrs={'class': 'form-control', 'placeholder': ''}))
+
+
+class UserApprovalForm(forms.ModelForm):
+    needs_approval = forms.CheckboxInput(attrs={'class': 'form-control', 'name': 'approvalChkbox'})
+
+    class Meta:
+        model = User
+        fields = ('username', 'first_name', 'last_name', 'affiliation', 'orcid', 'role', 'needs_approval')
+

accounts/migrations/0001_initial.py

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+# Generated by Django 3.2.5 on 2021-07-22 22:05
+
+import django.contrib.auth.models
+import django.contrib.auth.validators
+from django.db import migrations, models
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('auth', '0012_alter_user_first_name_max_length'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='User',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('password', models.CharField(max_length=128, verbose_name='password')),
+                ('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
+                ('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
+                ('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
+                ('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
+                ('email', models.EmailField(blank=True, max_length=254, verbose_name='email address')),
+                ('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
+                ('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
+                ('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
+                ('affiliation', models.CharField(max_length=255)),
+                ('contact_email', models.EmailField(blank=True, max_length=254, verbose_name='Contact E-Mail')),
+                ('has_temp_password', models.BooleanField(default=False)),
+                ('is_requestor', models.BooleanField(default=False)),
+                ('is_contributor', models.BooleanField(default=False)),
+                ('is_curator', models.BooleanField(default=False)),
+                ('is_moderator', models.BooleanField(default=False)),
+                ('is_superuser', models.BooleanField(default=False)),
+                ('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.Group', verbose_name='groups')),
+                ('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.Permission', verbose_name='user permissions')),
+            ],
+            options={
+                'verbose_name': 'user',
+                'verbose_name_plural': 'users',
+                'abstract': False,
+            },
+            managers=[
+                ('objects', django.contrib.auth.models.UserManager()),
+            ],
+        ),
+    ]

accounts/migrations/0002_auto_20210726_2205.py

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+# Generated by Django 3.2.5 on 2021-07-26 22:05
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('accounts', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='user',
+            name='is_contributor',
+        ),
+        migrations.RemoveField(
+            model_name='user',
+            name='is_curator',
+        ),
+        migrations.RemoveField(
+            model_name='user',
+            name='is_moderator',
+        ),
+        migrations.RemoveField(
+            model_name='user',
+            name='is_requestor',
+        ),
+        migrations.AddField(
+            model_name='user',
+            name='role',
+            field=models.CharField(choices=[(1, 'Requestor'), (2, 'Contributor'), (3, 'Curator'), (4, 'Moderator'), (5, 'Superuser')], default=1, max_length=12),
+        ),
+        migrations.AlterField(
+            model_name='user',
+            name='is_superuser',
+            field=models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status'),
+        ),
+    ]

accounts/migrations/0003_auto_20210727_2011.py

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+# Generated by Django 3.2.5 on 2021-07-27 20:11
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('accounts', '0002_auto_20210726_2205'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='user',
+            name='needs_approval',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AlterField(
+            model_name='user',
+            name='role',
+            field=models.CharField(choices=[('Requestor', 'Requestor'), ('Contributor', 'Contributor'), ('Curator', 'Curator'), ('Moderator', 'Moderator'), ('Superuser', 'Superuser')], default='Requestor', max_length=12),
+        ),
+    ]

accounts/migrations/0004_remove_user_contact_email.py

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+# Generated by Django 3.2.5 on 2021-07-30 21:27
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('accounts', '0003_auto_20210727_2011'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='user',
+            name='contact_email',
+        ),
+    ]

accounts/migrations/0005_user_orcid.py

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+# Generated by Django 3.2.5 on 2021-08-25 21:35
+
+import accounts.models
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('accounts', '0004_remove_user_contact_email'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='user',
+            name='orcid',
+            field=models.URLField(default='https://orcid.org/0000-0002-1825-0097', help_text='Example: 0000-0001-2345-6789', max_length=40, validators=[django.core.validators.URLValidator, accounts.models.orcIDValidator]),
+            preserve_default=False,
+        ),
+    ]

accounts/migrations/0006_alter_user_orcid.py

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+# Generated by Django 3.2.5 on 2021-08-25 21:52
+
+import accounts.models
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('accounts', '0005_user_orcid'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='user',
+            name='orcid',
+            field=models.URLField(help_text='Example: https://orcid.org/0000-0001-2345-6789', max_length=40, validators=[django.core.validators.URLValidator, accounts.models.orcIDValidator]),
+        ),
+    ]

accounts/models.py

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+from django.db import models
+from django.contrib.auth.models import AbstractUser
+from django.core.exceptions import ValidationError
+
+# import validators
+from django.core.validators import URLValidator
+
+# orcID validator function
+def orcIDValidator(url):
+    # get the actual orcid part
+    orcid = url.split('/')[-1]
+    # remove and store the last digit as it is the checksum
+    digit = orcid[-1]
+    orcid = orcid[:-1]
+    # remove dashes
+    orcid = orcid.replace('-', '')
+    # calculate checksum
+    total = 0
+    for i in str(orcid):
+        total = (total + int(i)) * 2
+    remainder = total % 11
+    chksum = (12 - remainder) % 11
+    if chksum == 10:
+        chksum = "X"
+    if digit == str(chksum):
+        return orcid
+    else:
+        raise ValidationError("This field is not a valid ORCID")
+
+# Create your models here.
+class User(AbstractUser):
+    #user = models.OneToOneField(User, on_delete=models.PROTECT, related_name='userprofile')
+    affiliation = models.CharField(max_length=255)
+    orcid = models.URLField(max_length=40, validators=[URLValidator, orcIDValidator],
+                            help_text="Example: https://orcid.org/0000-0001-2345-6789")
+    has_temp_password = models.BooleanField(default=False)
+
+    # Roles
+    ROLE_CHOICES = (
+        ("Requestor", "Requestor"),
+        ("Contributor", "Contributor"),
+        ("Curator", "Curator"),
+        ("Moderator", "Moderator"),
+        ("Superuser", "Superuser")
+    )
+    role = models.CharField(
+        max_length=12,
+        choices=ROLE_CHOICES,
+        default="Requestor",
+    )
+
+    needs_approval = models.BooleanField(default=False)
+
+