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Updates and cleanup #155

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Merged
asherpasha merged 2 commits into from
Dec 31, 2022
Merged

Updates and cleanup #155

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2ab012a
Removed BAR Summarizations.
asherpasha Dec 26, 2022
cabcfce
Fixed a bug.
asherpasha Dec 26, 2022
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56 changes: 2 additions & 54 deletions api/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,62 +19,17 @@ def create_app():
# Travis
print("We are now loading configuration.")
bar_app.config.from_pyfile(os.getcwd() + "/config/BAR_API.cfg", silent=True)
if bar_app.config.get("ADMIN_ENCRYPT_KEY"):
os.environ["ADMIN_ENCRYPT_KEY"] = bar_app.config.get(
"TEST_ADMIN_ENCRYPT_KEY"
)
if bar_app.config.get("ADMIN_PASSWORD_FILE"):
os.environ["ADMIN_PASSWORD_FILE"] = bar_app.config.get(
"TEST_ADMIN_PASSWORD_FILE"
)
if bar_app.config.get("ADMIN_EMAIL"):
os.environ["ADMIN_EMAIL"] = bar_app.config.get("ADMIN_EMAIL")
if bar_app.config.get("EMAIL_PASS_KEY"):
os.environ["EMAIL_PASS_KEY"] = bar_app.config.get("EMAIL_PASS_KEY")
if bar_app.config.get("EMAIL_PASS_FILE"):
os.environ["EMAIL_PASS_FILE"] = bar_app.config.get("EMAIL_PASS_FILE")

elif os.environ.get("BAR"):
# The BAR
bar_app.config.from_pyfile(os.environ.get("BAR_API_PATH"), silent=True)
if bar_app.config.get("ADMIN_EMAIL"):
os.environ["ADMIN_EMAIL"] = bar_app.config.get("ADMIN_EMAIL")
if bar_app.config.get("EMAIL_PASS_KEY"):
os.environ["EMAIL_PASS_KEY"] = bar_app.config.get("EMAIL_PASS_KEY")
if bar_app.config.get("EMAIL_PASS_FILE"):
os.environ["EMAIL_PASS_FILE"] = bar_app.config.get("EMAIL_PASS_FILE")
if bar_app.config.get("ADMIN_ENCRYPT_KEY"):
os.environ["ADMIN_ENCRYPT_KEY"] = bar_app.config.get("ADMIN_ENCRYPT_KEY")
if bar_app.config.get("ADMIN_PASSWORD_FILE"):
os.environ["ADMIN_PASSWORD_FILE"] = bar_app.config.get(
"ADMIN_PASSWORD_FILE"
)
if bar_app.config.get("DRIVE_LIST_KEY"):
os.environ["DRIVE_LIST_KEY"] = bar_app.config.get("DRIVE_LIST_KEY")
if bar_app.config.get("DRIVE_LIST_FILE"):
os.environ["DRIVE_LIST_FILE"] = bar_app.config.get("DRIVE_LIST_FILE")
else:
# The localhost
bar_app.config.from_pyfile(
os.path.expanduser("~") + "/.config/BAR_API.cfg", silent=True
)

# Load environment variables
if bar_app.config.get("ADMIN_ENCRYPT_KEY"):
os.environ["ADMIN_ENCRYPT_KEY"] = bar_app.config.get("ADMIN_ENCRYPT_KEY")
if bar_app.config.get("ADMIN_PASSWORD_FILE"):
os.environ["ADMIN_PASSWORD_FILE"] = bar_app.config.get(
"ADMIN_PASSWORD_FILE"
)
if bar_app.config.get("ADMIN_EMAIL"):
os.environ["ADMIN_EMAIL"] = bar_app.config.get("ADMIN_EMAIL")
if bar_app.config.get("EMAIL_PASS_KEY"):
os.environ["EMAIL_PASS_KEY"] = bar_app.config.get("EMAIL_PASS_KEY")
if bar_app.config.get("EMAIL_PASS_FILE"):
os.environ["EMAIL_PASS_FILE"] = bar_app.config.get("EMAIL_PASS_FILE")
if bar_app.config.get("DRIVE_LIST_KEY"):
os.environ["DRIVE_LIST_KEY"] = bar_app.config.get("DRIVE_LIST_KEY")
if bar_app.config.get("DRIVE_LIST_FILE"):
os.environ["DRIVE_LIST_FILE"] = bar_app.config.get("DRIVE_LIST_FILE")
if bar_app.config.get("PHENIX"):
os.environ["PHENIX"] = bar_app.config.get("PHENIX")
if bar_app.config.get("PHENIX_VERSION"):
Expand All @@ -96,7 +51,6 @@ def create_app():
tomato_nssnp_db.init_app(bar_app)
tomato_seq_db.init_app(bar_app)
single_cell_db.init_app(bar_app)
summarization_db.init_app(bar_app)
rice_interactions_db.init_app(bar_app)

# Initialize the cache
Expand All @@ -115,10 +69,7 @@ def create_app():
# Now add routes
from api.resources.gene_information import gene_information
from api.resources.rnaseq_gene_expression import rnaseq_gene_expression
from api.resources.summarization_gene_expression import (
summarization_gene_expression,
)
from api.resources.api_manager import api_manager

from api.resources.proxy import bar_proxy
from api.resources.thalemine import thalemine
from api.resources.snps import snps
Expand All @@ -130,8 +81,6 @@ def create_app():

bar_api.add_namespace(gene_information)
bar_api.add_namespace(rnaseq_gene_expression)
bar_api.add_namespace(summarization_gene_expression)
bar_api.add_namespace(api_manager)
bar_api.add_namespace(bar_proxy)
bar_api.add_namespace(thalemine)
bar_api.add_namespace(snps)
Expand All @@ -158,7 +107,6 @@ def create_app():
soybean_nssnp_db = SQLAlchemy(metadata=MetaData())
tomato_seq_db = SQLAlchemy(metadata=MetaData())
single_cell_db = SQLAlchemy(metadata=MetaData())
summarization_db = SQLAlchemy(metadata=MetaData())
rice_interactions_db = SQLAlchemy(metadata=MetaData())

# Initialize Redis
Expand Down
32 changes: 0 additions & 32 deletions api/models/summarization.py
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201 changes: 0 additions & 201 deletions api/resources/api_manager.py
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