Report Manager (report_manager)

app.py

dataset.py

class Dataset(identifier, dataset_type, configuration=None, data={}, analysis_queries={}, report=None)[source]

Bases: object

property identifier
property dataset_type
property data
property configuration
property analysis_queries
property report
generate_dataset()[source]
update_report(report)[source]
update_analysis_queries(query)[source]
get_dataframe(dataset_name)[source]
get_dataframes(dataset_names)[source]
list_dataframes()[source]
update_data(new)[source]
set_configuration_from_file(configuration_file)[source]
update_configuration_from_file(configuration_file)[source]
get_dataset_data_directory(directory='../../../data/reports')[source]
query_data()[source]
send_query(query)[source]
extract_configuration(configuration)[source]
add_configuration_to_report(report_pipeline)[source]
generate_report()[source]
save_dataset_recursively(dset, group, dt)[source]
save_dataset(dataset_directory)[source]
save_dataset_recursively_to_file(dset, dataset_directory, base_name='')[source]
save_dataset_to_file(dataset_directory)[source]
save_report(dataset_directory)[source]
load_dataset_recursively(dset, loaded_dset={})[source]
load_dataset(dataset_directory)[source]
load_dataset_report(report_dir)[source]
generate_knowledge()[source]
class MultiOmicsDataset(identifier, data, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.Dataset

get_dataframes(datasets)[source]
generate_knowledge()[source]
class ProteomicsDataset(identifier, dataset_type='proteomics', data={}, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.Dataset

generate_dataset()[source]
process_dataset()[source]
processing()[source]
generate_knowledge()[source]
class PTMDataset(identifier, data={}, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.ProteomicsDataset

class PhosphoproteomicsDataset(identifier, data={}, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.PTMDataset

class InteractomicsDataset(identifier, data={}, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.ProteomicsDataset

class LongitudinalProteomicsDataset(identifier, data={}, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.ProteomicsDataset

class ClinicalDataset(identifier, data={}, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.Dataset

generate_dataset()[source]
process_dataset()[source]
widen_original_dataset()[source]
processing()[source]
generate_knowledge()[source]
class DNAseqDataset(identifier, dataset_type, data={}, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.Dataset

generate_dataset()[source]
class RNAseqDataset(identifier, data={}, configuration=None, analysis_queries={}, report=None)[source]

Bases: src.report_manager.dataset.Dataset

generate_dataset()[source]

index.py

display_page(pathname)[source]
get_project_params_from_url(pathname)[source]
return_docs(value)[source]
update_output(contents, value, fname)[source]
update_db_date(df)[source]
number_panel_update(df)[source]
update_project_url(value)[source]
route_login()[source]
route_logout()[source]
generate_report_url(n_clicks, pathname)[source]
route_report_url(value)[source]
regenerate_report(n_clicks, title, pathname)[source]
image_formatter(im)[source]
create_project(n_clicks, name, acronym, responsible, participant, datatype, timepoints, related_to, disease, tissue, intervention, number_subjects, description, start_date, end_date)[source]
change_style(style)[source]
serve_static(value)[source]
activate_upload_form(projectid)[source]
show_proteomics_options(datatype, prot_tool)[source]
show_proteomics_file_options(datatype, prot_tool, prot_file)[source]
save_files_in_tmp(content, dataset, prot_tool, prot_file, projectid, uploaded_file)[source]
run_processing(n_clicks, project_id)[source]
change_style_data_upload(upload_result)[source]
generate_upload_zip(n_clicks, project_id)[source]
route_upload_url(value)[source]

knowledge.py

class Knowledge(identifier, data, nodes={}, relationships={}, queries_file=None, colors={}, graph=None, report={})[source]

Bases: object

property identifier
property data
property entities
property nodes
update_nodes(nodes)[source]
property relationships
update_relationships(relationships)[source]
property queries_file
property colors
property default_color
property report
property graph
generate_knowledge_from_regulation(entity)[source]
genreate_knowledge_from_correlation(entity_node1, entity_node2, filter, cutoff=0.5)[source]
generate_knowledge_from_wgcna(data, entity1, entity2, cutoff=0.2)[source]
generate_knowledge_from_edgelist(edgelist, entity1, entity2, source, target, rtype, weight)[source]
generate_knowledge_from_annotations(entity1, entity2, filter=None)[source]
generate_knowledge_from_similarity(entity='Project')[source]
generate_knowledge_from_queries(entity, queries_results)[source]
send_query(query)[source]
query_data(replace)[source]
generate_cypher_nodes_list()[source]
generate_knowledge_graph()[source]
reduce_to_subgraph(nodes)[source]
get_knowledge_graph_plot()[source]
generate_report(visualization='sankey')[source]
save_report(directory)[source]
class ProjectKnowledge(identifier, data, nodes={}, relationships={}, colors={}, graph=None, report={})[source]

Bases: src.report_manager.knowledge.Knowledge

generate_knowledge()[source]
class ProteomicsKnowledge(identifier, data, nodes={}, relationships={}, colors={}, graph=None, report={})[source]

Bases: src.report_manager.knowledge.Knowledge

generate_knowledge()[source]
class ClinicalKnowledge(identifier, data, nodes={}, relationships={}, colors={}, graph=None, report={})[source]

Bases: src.report_manager.knowledge.Knowledge

generate_knowledge()[source]
class MultiOmicsKnowledge(identifier, data, nodes={}, relationships={}, colors={}, graph=None, report={})[source]

Bases: src.report_manager.knowledge.Knowledge

generate_knowledge()[source]

project.py

class Project(identifier, configuration_files={}, datasets={}, knowledge=None, report={})[source]

Bases: object

A project class that defines an experimental project. A project can be of different types, contain several datasets and reports.

Example:

p = Project(identifier="P0000001", datasets=None, report=None)
p.show_report(environment="notebook")
property identifier
property configuration_files
property queries_file
property name
property acronym
property data_types
append_data_type(data_type)[source]
property responsible
property description
property status
property num_subjects
property datasets
property knowledge
property report
property similar_projects
property overlap
get_dataset(dataset)[source]
update_dataset(dataset)[source]
update_report(new)[source]
remove_project(host='localhost', port=7687, user='neo4j', password='password')[source]
get_report_directory()[source]
get_downloads_directory()[source]
set_attributes(project_info)[source]
from_dict(attributes)[source]
to_dict()[source]
to_dataframe()[source]
list_datasets()[source]
to_json()[source]
from_json(json_str)[source]
query_data()[source]
check_report_exists()[source]
load_project_report()[source]
load_project(directory)[source]
load_project_data()[source]
build_project(force=False)[source]
get_projects_overlap(project_info)[source]
get_similar_projects(project_info)[source]
generate_project_attributes_plot()[source]
generate_project_similarity_plots()[source]
generate_overlap_plots()[source]
get_similarity_network_style()[source]
get_similarity_network()[source]
generate_knowledge()[source]
generate_project_info_report()[source]
generate_report()[source]
notify_project_ready(message_type='slack')[source]
empty_report()[source]
save_project_report()[source]
save_project_datasets_reports()[source]
save_project()[source]
save_project_datasets_data()[source]
show_report(environment)[source]
download_project()[source]
download_project_report()[source]
download_knowledge(directory)[source]
download_project_datasets()[source]

report.py

class Report(identifier, plots={})[source]

Bases: object

property identifier
property plots
get_plot(plot)[source]
update_plots(plot)[source]
list_plots()[source]
print_report(directory, plot_format='pdf')[source]
save_report(directory)[source]
read_report(directory)[source]
visualize_report(environment)[source]
visualize_plot(environment, plot_type)[source]
download_report(directory)[source]

user.py

class User(username)[source]

Bases: object

find()[source]
register(password)[source]
verify_password(password)[source]

utils.py

copy_file_to_destination(cfile, destination)[source]
send_message_to_slack_webhook(message, message_to, username='albsantosdel')[source]
send_email(message, subject, message_from, message_to)[source]
compress_directory(name, directory, compression_format='zip')[source]
get_markdown_date(extra_text)[source]
convert_html_to_dash(el, style=None)[source]
extract_style(el)[source]
get_image(figure, width, height)[source]
parse_html(html_snippet)[source]
hex2rgb(color)[source]
getNumberText(num)[source]
get_rgb_colors(n)[source]
get_hex_colors(n)[source]
convert_html_to_pdf(source_html, output_filename)[source]

worker.py