import os
import app.pages.metabolites as metabolite_pages
import app.pages.search as search_pages
import app.pages.static as static_pages
import app.pages.help as help_pages
import app.pages.strains as strain_pages
import app.pages.studies as study_pages
import app.pages.experiments as experiment_pages
import app.pages.upload as upload_pages
import app.pages.submissions as submission_pages
import app.pages.users as user_pages
import app.pages.projects as project_pages
import app.pages.comparison as comparison_pages
import app.pages.excel_files as excel_file_pages
[docs]
APP_ENV = os.getenv('APP_ENV', 'development')
[docs]
def init_routes(app):
app.add_url_rule("/", view_func=static_pages.static_home_page)
app.add_url_rule("/about/", view_func=static_pages.static_about_page)
app.add_url_rule("/help/", view_func=help_pages.help_index_page)
app.add_url_rule("/help/<string:name>/", view_func=help_pages.help_show_page)
app.add_url_rule("/upload/", view_func=upload_pages.upload_status_page)
app.add_url_rule("/upload/1", view_func=upload_pages.upload_step1_page, methods=["GET", "POST"])
app.add_url_rule("/upload/2", view_func=upload_pages.upload_step2_page, methods=["GET", "POST"])
app.add_url_rule("/upload/3", view_func=upload_pages.upload_step3_page, methods=["GET", "POST"])
app.add_url_rule("/upload/4", view_func=upload_pages.upload_step4_page, methods=["GET", "POST"])
app.add_url_rule("/upload/5", view_func=upload_pages.upload_step5_page, methods=["GET", "POST"])
app.add_url_rule("/upload/6", view_func=upload_pages.upload_step6_page, methods=["GET", "POST"])
app.add_url_rule("/upload/7", view_func=upload_pages.upload_step7_page, methods=["GET", "POST"])
app.add_url_rule(
"/upload/new_submission/",
view_func=submission_pages.new_submission_action,
methods=["POST"],
)
app.add_url_rule(
"/upload/edit_submission/<id>",
view_func=submission_pages.edit_submission_action,
methods=["POST"],
)
app.add_url_rule(
"/upload/delete_submission/<id>",
view_func=submission_pages.delete_submission_action,
methods=["POST"],
)
app.add_url_rule("/upload/data_template.xlsx", view_func=upload_pages.download_data_template_xlsx, methods=["POST"])
app.add_url_rule(
"/upload/spreadsheet_preview/",
view_func=upload_pages.upload_spreadsheet_preview_fragment,
methods=["POST"],
)
app.add_url_rule("/study/<string:studyId>/", view_func=study_pages.study_show_page)
app.add_url_rule("/study/<string:studyId>.zip", view_func=study_pages.study_download_data_zip)
app.add_url_rule("/study/<string:studyId>/export/", view_func=study_pages.study_export_page)
app.add_url_rule("/study/<string:studyId>/export/preview", view_func=study_pages.study_export_preview_fragment)
app.add_url_rule("/study/<string:studyId>/manage/", view_func=study_pages.study_manage_page)
app.add_url_rule("/study/<string:studyId>/manage/models.csv", view_func=study_pages.study_download_models_csv, methods=["POST"])
app.add_url_rule("/study/<string:studyId>/visualize/", view_func=study_pages.study_visualize_page)
app.add_url_rule("/study/<string:studyId>/visualize/chart", view_func=study_pages.study_chart_fragment, methods=["POST"])
app.add_url_rule(
"/study/<string:studyId>/modeling/submit",
view_func=study_pages.study_modeling_submit_action,
methods=["POST"],
)
app.add_url_rule(
"/study/<string:studyId>/modeling/check.json",
view_func=study_pages.study_modeling_check_json,
)
app.add_url_rule(
"/study/<string:studyId>/modeling/<int:measurementContextId>/chart",
view_func=study_pages.study_modeling_chart_fragment,
)
app.add_url_rule("/experiment/<string:publicId>/", view_func=experiment_pages.experiment_show_page)
app.add_url_rule("/project/<string:projectId>", view_func=project_pages.project_show_page)
app.add_url_rule("/strains/completion/", view_func=strain_pages.taxa_completion_json)
app.add_url_rule("/metabolites/completion/", view_func=metabolite_pages.metabolites_completion_json)
app.add_url_rule("/comparison/", view_func=comparison_pages.comparison_show_page)
app.add_url_rule("/comparison/chart", view_func=comparison_pages.comparison_chart_fragment, methods=["POST"])
app.add_url_rule("/comparison/clear", view_func=comparison_pages.comparison_clear_action, methods=["POST"])
app.add_url_rule(
"/comparison/update/<action>.json",
view_func=comparison_pages.comparison_update_json,
methods=["POST"],
)
app.add_url_rule("/search/", view_func=search_pages.search_index_page)
app.add_url_rule("/profile/", view_func=user_pages.user_show_page)
app.add_url_rule("/login/", view_func=user_pages.user_login_page)
app.add_url_rule("/logout/", view_func=user_pages.user_logout_action, methods=["POST"])
if APP_ENV in ('development', 'test'):
app.add_url_rule("/backdoor/", view_func=user_pages.user_backdoor_page, methods=["GET", "POST"])
app.add_url_rule("/claim-project/", view_func=user_pages.user_claim_project_action, methods=["POST"])
app.add_url_rule("/claim-study/", view_func=user_pages.user_claim_study_action, methods=["POST"])
app.add_url_rule("/excel_files/<id>.xlsx", view_func=excel_file_pages.download_excel_file)
return app
[docs]
def dump_routes(rules, filename):
import json
mapping = {}
for rule in rules:
# Taken from werkzeug:
# https://github.com/pallets/werkzeug/blob/7868bef5d978093a8baa0784464ebe5d775ae92a/src/werkzeug/routing/rules.py#L920-L926
#
parts = []
for is_dynamic, data in rule._trace:
if is_dynamic:
parts.append(f"<{data}>")
else:
parts.append(data)
parts_str = "".join(parts).lstrip("|")
mapping[parts_str] = rule.endpoint
with open(filename, 'w') as f:
json.dump(mapping, f, indent=4)