class Project(Annotation):
"""The project associtated with this experiment"""
__tablename__ = "projects"
user_id = reference_col("users", nullable=False)
user = relationship("User", backref=__tablename__)
group_id = reference_col("groups", nullable=False)
group = relationship("Group", backref=__tablename__)
organism_id = reference_col("organisms", nullable=True)
organism = relationship("Organism", backref=__tablename__)
__icon__ = "fa-search"
__label__ = "Project"
class Tag(PkModel):
"""A single word tag"""
__tablename__ = "tags"
label = Column(db.String(128), nullable=False)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
class GeneMod(Annotation):
"""A protein / target pair
Examples
--------
- alpha-tubulin GFP
- P53-Alexa488
"""
__tablename__ = "gene_mods"
user_id = reference_col("users", nullable=True)
user = relationship("User", backref=__tablename__)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
gene_id = reference_col("genes", nullable=True)
gene = relationship("Gene", backref=__tablename__)
marker_id = reference_col("markers", nullable=True)
marker = relationship("Marker", backref=__tablename__)
class Gene(Annotation):
"""A target protein, primary antibody or other biochemical element
Examples
--------
- alpha-tubulin
- Myosin II
- CDC52
"""
__tablename__ = "genes"
__icon__ = "fa-bullseye"
__label__ = "Target"
user_id = reference_col("users", nullable=True)
user = relationship("User", backref=__tablename__)
ontology_id = reference_col("ontologies", nullable=True)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
ontology = relationship("Ontology", backref=__tablename__)
organism_id = reference_col("organisms", nullable=True)
organism = relationship("Organism", backref=__tablename__)
class Marker(Annotation):
"""A fluorescent marker, other contrast agent, or gene modification
Examples
--------
- eGFP
- Alexa 488
- RNAi
"""
__tablename__ = "markers"
__icon__ = "fa-map-marker"
__label__ = "Marker"
user_id = reference_col("users", nullable=True)
user = relationship("User", backref=__tablename__)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
ontology_id = reference_col("ontologies", nullable=True)
ontology = relationship("Ontology", backref=__tablename__)
organism_id = reference_col("organisms", nullable=True)
organism = relationship("Organism", backref=__tablename__)
class Method(Annotation):
"""An experimental method
Examples
--------
- optical tweezers
- laser ablation
- FISH
"""
__tablename__ = "methods"
__icon__ = "fa-tools"
__label__ = "Method"
user_id = reference_col("users", nullable=True)
user = relationship("User", backref=__tablename__)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
ontology_id = reference_col("ontologies", nullable=True)
ontology = relationship("Ontology", backref=__tablename__)
organism_id = reference_col("organisms", nullable=True)
organism = relationship("Organism", backref=__tablename__)
class Organism(Annotation):
"""An organism in the taxonomy sense
Examples
--------
- fruit fly (Drosophila melanogaster)
- mouse (Mus musculus)
- Xaenopus Laevis egg extract
"""
__tablename__ = "organisms"
user_id = reference_col("users", nullable=True)
user = relationship("User", backref=__tablename__)
ontology_id = reference_col("ontologies", nullable=True)
ontology = relationship("Ontology", backref=__tablename__)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
__icon__ = "fa-bug"
__label__ = "Organism"
class Sample(Annotation):
"""The biological sample studied
Examples
--------
- a cell population within the model (e.g. the mesoderm)
- an organ (e.g. cerebelum)
- a part of the epithelium (e.g apical)
- an organelle
"""
__tablename__ = "samples"
__icon__ = "fa-flask"
__label__ = "Sample"
user_id = reference_col("users", nullable=True)
user = relationship("User", backref=__tablename__)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
ontology_id = reference_col("ontologies", nullable=True)
ontology = relationship("Ontology", backref=__tablename__)
organism_id = reference_col("organisms", nullable=True)
organism = relationship("Organism", backref=__tablename__)
class Process(Annotation):
"""The biological process being studied
Examples
--------
- mesoderm invagination
- epithelio-mesenchymal transition
- colon cancer
- senescence
"""
__tablename__ = "processes"
__icon__ = "fa-cogs"
__label__ = "Observed Process"
user_id = reference_col("users", nullable=True)
user = relationship("User", backref=__tablename__)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
ontology_id = reference_col("ontologies", nullable=True)
ontology = relationship("Ontology", backref=__tablename__)
organism_id = reference_col("organisms", nullable=True)
organism = relationship("Organism", backref=__tablename__)
class Role(PkModel):
"""A role for a user."""
__tablename__ = "roles"
name = Column(db.String(80), unique=True, nullable=False)
user_id = reference_col("users", nullable=True)
user = relationship("User", backref="roles")
def __init__(self, name, **kwargs):
"""Create instance."""
super().__init__(name=name, **kwargs)
def __repr__(self):
"""Represent instance as a unique string."""
return f"<Role({self.name})>"
class User(UserMixin, PkModel):
"""A user of the app."""
__tablename__ = "users"
username = Column(db.String(80), unique=True, nullable=False)
email = Column(db.String(80), unique=True, nullable=True)
#: The hashed password
password = Column(db.LargeBinary(128), nullable=True)
created_at = Column(db.DateTime,
nullable=False,
default=dt.datetime.utcnow)
first_name = Column(db.String(30), nullable=True)
last_name = Column(db.String(30), nullable=True)
active = Column(db.Boolean(), default=False)
is_admin = Column(db.Boolean(), default=False)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
def __init__(self, username, password=None, **kwargs):
"""Create instance."""
super().__init__(username=username, **kwargs)
if password:
self.set_password(password)
else:
self.password = None
def set_password(self, password):
"""Set password."""
self.password = bcrypt.generate_password_hash(password)
def check_password(self, value):
"""Check password."""
return bcrypt.check_password_hash(self.password, value)
@property
def full_name(self):
"""Full user name."""
return f"{self.first_name} {self.last_name}"
def __repr__(self):
"""Represent instance as a unique string."""
return f"<User({self.username!r})>"
class Card(PkModel):
"""A card is a collection of annotations
This card can latter be used as key / value annotation tool
"""
__tablename__ = "cards"
title = Column(db.String(128), nullable=False)
user_id = reference_col("users", nullable=False)
user = relationship("User", backref=__tablename__)
group_id = reference_col("groups", nullable=True)
group = relationship("Group", backref=__tablename__)
project_id = reference_col("projects", nullable=True)
project = relationship("Project", backref=__tablename__)
organism_id = reference_col("organisms", nullable=True)
organism = relationship("Organism", backref=__tablename__)
sample_id = reference_col("samples", nullable=True)
sample = relationship("Sample", backref=__tablename__)
process_id = reference_col("processes", nullable=True)
process = relationship("Process", backref=__tablename__)
method_id = reference_col("methods", nullable=True)
method = relationship("Method", backref=__tablename__)
created_at = Column(db.DateTime, nullable=True, default=dt.datetime.utcnow)
gene_mods = relationship("GeneMod", secondary=gene_mod_card)
comment = Column(db.String, nullable=True)
def as_csv(self):
"""Writes the key - value pairs of the cards as CSV"""
username = self.user.full_name if self.user.first_name else self.user.username
lines = [
f"# {self.title}",
f"# {self.created_at}",
f"# by {username}",
f"# for project {self.project.label}",
"# ",
f"# {self.comment}",
f"organism,{self.organism.label}",
f"sample,{self.sample.label}",
f"method,{self.method.label}",
]
lines += [
f"channel_{i},{gm.label}" for i, gm in enumerate(self.gene_mods)
]
return "\n".join(lines)
@property
def tags(self):
_tags = [
w.lstrip("#") for w in self.comment.split() if w.startswith("#")
]
return set(_tags)
def as_dict(self):
kv_pairs = {}
if self.organism:
kv_pairs["organism"] = self.organism.label
if self.sample:
kv_pairs["sample"] = self.sample.label
if self.method:
kv_pairs["method"] = self.method.label
if self.process:
kv_pairs["process"] = self.method.label
kv_pairs.update(
{f"channel_{i}": gm.label
for i, gm in enumerate(self.gene_mods)})
card_dict = {
"title": self.title,
"created": self.created_at,
"project": self.project.label,
"user": self.user.username,
"group": self.group.groupname,
"comment": self.comment,
"kv_pairs": kv_pairs,
"tags": self.tags,
"accessed": str(dt.datetime.utcnow()),
}
return card_dict
def as_toml(self):
"""Output the card contents as toml"""
return toml.dumps(self.as_dict())
def as_markdown(self):
"""Writes the card contents as markdown"""
as_dict = self.as_dict()
lines = [
f"# {self.title}\n\n",
f"Created by {self.user.username}\n",
self.comment.replace("#", ""),
"## Key-value pairs:",
"|-----|------|",
]
for k, v in as_dict["kv_pairs"].items():
lines.append(f"| {k} | {v} |")
lines.append("|-----|------|\n")
lines.append("## Tags:")
lines.append(" ".join([f"**{tag}**" for tag in as_dict["tags"]]))
return "\n".join(lines)
@property
def html_comment(self):
lines = []
for line in self.comment.split("\n"):
if (line.startswith("Observed Process")
or line.startswith("Experimental Conditions")
or line.startswith("Additional Information")):
lines.append(
f"""<h5 style="margin-top: 1rem;"> {line} </h5>""")
else:
line = " ".join([
f"<b>{w}</b>" if w.startswith("#") else w
for w in line.split(" ")
])
lines.append(line)
html = "\n".join(lines)
return html
