def get_project_contributors(project_id, session=None):
if not session:
session = DBSessionMaker().session()
contributor_query = (session.query(
Contributor, ContributorJoinProject).filter(
Contributor.id == ContributorJoinProject.contributor_id,
ContributorJoinProject.project_id == project_id).all())
contributors = [{
"name":
f"{result.Contributor.first_name} {result.Contributor.last_name}",
"institution": f"{result.Contributor.institution}",
} for result in contributor_query]
return contributors
def get_project_organs(project_id, session=None):
"""
Query the DB to return all organs that are represented in a given project.
:param project_id: Project to return organs for
:param session: SQLAlchemy DBSession
:return: list of organ names
"""
if not session:
session = DBSessionMaker().session()
organs = []
for result in (session.query(OrganJoinProject, Organ).filter(
OrganJoinProject.organ_id == Organ.id,
OrganJoinProject.project_id == project_id).all()):
organs.append(result.Organ.name)
return organs
def get_project_species(project_id, session=None):
"""
Query the DB to return all species that are represented in a given project.
:param project_id: Project to return species for
:param session: SQLAlchemy DBSession
:return: list of species labels
"""
if not session:
session = DBSessionMaker().session()
species = []
for result in (session.query(SpeciesJoinProject, Species).filter(
SpeciesJoinProject.species_id == Species.id,
SpeciesJoinProject.project_id == project_id,
).all()):
species.append(result.Species.name)
return species
def get_project_assays(project_id, session=None):
"""
Query the DB to return all assays that are represented in a given project.
:param project_id: Project to return assays for
:param session: SQLAlchemy DBSession
:return: list of assay names
"""
if not session:
session = DBSessionMaker().session()
assays = []
for result in (session.query(
LibraryConstructionMethodJoinProject, LibraryConstructionMethod
).filter(
(LibraryConstructionMethodJoinProject.library_construction_method_id
== LibraryConstructionMethod.id),
LibraryConstructionMethodJoinProject.project_id == project_id,
).all()):
assays.append(result.LibraryConstructionMethod.name)
return assays
def get_downloadable_project_files(project_id, session=None):
"""
Query the DB to return all downloadable files for a project.
:param project_id: Project to return files for
:param session: SQLAlchemy DBSession
:return: list of file metadata objects
"""
if not session:
session = DBSessionMaker().session()
files = []
for file in session.query(File).filter(
File.project_id == project_id).filter(File.file_format == "LOOM"):
files.append({
"id": file.id,
"filename": file.filename,
"file_format": file.file_format,
"file_type": file.file_type,
"file_size": file.file_size,
})
return files
DBSessionMaker,
Project,
File,
LibraryConstructionMethod,
Organ,
Species,
Contributor,
DataRepository,
ExternalAccession,
LibraryConstructionMethodJoinProject,
OrganJoinProject,
SpeciesJoinProject,
ContributorJoinProject,
)
session = DBSessionMaker().session()
s3 = boto3.client("s3")
s3.download_file("dcp-test-artifacts", "Artifact.Mar18.json", "artifact.json")
with open("artifact.json", "r") as f:
data = json.load(f)
organs = {}
species = {}
libraries = {}
contributors = {}
# populate data repository
data_repo_names = [
"Array Express", "INSDC Project", "GEO Series", "Biostudies"
os.path.join(os.path.dirname(__file__), "chalicelib")) # noqa
sys.path.insert(0, pkg_root) # noqa
from browser.code.common.browser_orm import DBSessionMaker, Project, File
from browser.code.common.db_utils import (
get_project_assays,
get_project_organs,
get_project_species,
get_project_contributors,
get_downloadable_project_files,
)
from browser.code.common.s3_utils import generate_file_url
app = Chalice(
app_name=f"{os.environ['APP_NAME']}-{os.environ['DEPLOYMENT_STAGE']}")
session = DBSessionMaker().session()
@app.route("/")
def index():
return "render documentation here"
@app.route("/projects")
def get_projects():
projects = []
for project in session.query(Project).all():
projects.append({
"id": project.id,
"title": project.title,
"assays": get_project_assays(project.id),