Package index • nfportalutils

Table Utils

Main PORTAL table data update and management

Augment and update one of the main portal tables (e.g. Portal - Studies)

add_publication_from_pubmed(): Add a publication to the publication table

add_publication_from_unpaywall(): Add a publication or preprint to the publication table via the Unpaywall API.

add_publications_from_file(): Add a batch of publications from spreadsheet

assign_study_data_types(): Summarize data types for the study

calculate_related_studies(): Calculate and add related studies to study table

register_study(): Register a NEW project for the NF Data Portal in Portal - Project View

add_people_from_table(): Update the People table from a source Table or View column

register_study_files(): Register a project's files in Portal - Files

summarize_attribute(): Helper summarization util

Lower-level table maintenance

adjust_view(): Adjust view

swap_col(): Swap out old column for a new column in a schema

byte_budget(): Calculate byte budget for a schema

Project Configuration and Management

Create or retrofit an NF project to expected default structure and assets

new_project(): Create a new project

add_default_fileview(): Create default project fileview

add_default_folders(): Create default folders

make_admin(): Make a user or group full admin of a Synapse entity

Metadata Utils

General annotations

Add and manage annotations on Synapse entities

update_study_annotations(): Updates a set of files with project-level annotations.

annotate_with_manifest(): Set annotations from a manifest

copy_annotations(): Copy annotations

.modify_annotation(): Modify a single annotation on a single file

meta_qc_dataset(): QC dataset metadata with pass/fail result

meta_qc_project(): QC metadata at the project level with pass/fail result

manifest_generate(): Generate manifest via schematic service

manifest_validate(): Validate manifest via schematic service

manifest_passed(): Provide a pass/fail summary result

precheck_manifest(): Precheck a manifest

remanifest(): Reconstitute a manifest

infer_data_type(): Infer data type of a dataset folder

Special annotation of nextflow processed data

map_reports_sarek(): Map out Sarek report files

map_sample_input_ss(): Parse nextflow samplesheet for sample inputs

map_sample_io(): Map sample input-output

map_sample_output_rnaseq(): Map sample to output from nf-rnaseq

map_sample_output_sarek(): Map sample to output from nf-sarek

annotate_aligned_reads(): Annotate processed aligned reads

annotate_called_variants(): Annotate somatic or germline variants output

annotate_expression(): Annotate processed expression output

annotate_cnv(): Annotate CNV outputs from CNVKit

annotate_reports_sarek(): Annotate Sarek reports

annotate_with_tool_stats(): Make annotations from workflow tool stats

nf_workflow_version(): Return workflow version according to workflow meta

Dataset Creation and Management

General dataset creation and citation

Create datasets in general

new_dataset(): Create new dataset with given items

Specialized dataset creation

Create specialized datasets for nextflow processed data, i.e. with some custom construction queries and title templating.

nf_sarek_datasets(): Create datasets for Sarek-called somatic or germline variants results

nf_star_salmon_datasets(): Create dataset for STAR-Salmon expression quantification results

nf_cnv_dataset(): Create dataset for CNVKit results

Working with dataset collections to manage datasets after creation

add_to_collection(): Add to collection

use_latest_in_collection(): Update item versions to "latest" in a collection

update_items(): Apply updates to current collection of items

Data Model Utils

Talk to a JSON-LD data model important to the portal data (i.e. NF-metadata-dictionary)

get_by_prop_from_json_schema(): Look up connected nodes by specified property in JSON-LD schema

get_dependency_from_json_schema(): Get dependencies for node in JSON-LD schema

get_valid_values_from_json_schema(): Retrieve valid subclasses of a value in a JSON-LD schema

key_label_to_id(): Query for schema key id given label

schema_max_str_len(): Consult schema about max string length

Governance Utils

Analyze and manage data access/restrictions

make_public_viewable(): Set public access to VIEW (READ) only for an entity

make_public(): Make public

check_access(): Check access

summarize_file_access(): Summarize file access for files within some view

grant_specific_file_access(): Provide access to a specific set of files using a query result.

Search Utils

Help locate Synapse accessions, etc.

find_child(): Find id of a child entity in a container

find_child_type(): Find children of type

find_data_root(): Find data folder

find_in(): Find in path

find_nf_asset(): Find a standard nextflow workflow output asset

Provenance Utils

Manage provenance metadata

add_activity(): Add activity to entity

add_activity_batch(): Add activity to multiple entities

delete_provenance(): Remove provenance info

Content Utils

Create and manage content for projects and pages

add_default_wiki(): Add default wiki

wiki_mod(): Add markup to a project wiki

remove_wiki_subpage(): Remove a subpage from a project wiki

data_curator_app_subpage(): Create NF Data Curator App subpage

get_project_wiki(): Get wiki content of synapse project(s)

check_wiki_links(): Check wiki links

remove_button(): Remove button from a project wiki

Figures and diagrams

Supplemental figures and diagrams that go into Wikis or other places

processing_flowchart(): Wrapper to create data-driven flowchart with pretty processing provenance mermaid template

dsp_dataset_mapping(): Wrapper to create Data Sharing Plan to project dataset comparison chart

bipartite_mmd_template(): Simple bipartite representation in mermaid charts

Export Data to Other Platforms

Helpers to export/release NF data to other platforms/databases.

cBioPortal

Export data as a cBioPortal study

cbp_new_study(): Initialize a new cBioPortal study dataset

cbp_new_cancer_type(): Create reference file for new cancer type

cbp_add_maf(): Export and add mutations data to cBioPortal dataset

cbp_add_clinical(): Export and add clinical data to cBioPortal dataset

cbp_add_expression(): Export and add expression data to cBioPortal dataset

cbp_add_cna(): Export and add CNA (seg) data to cBioPortal dataset

Quality Control and Testing Utils

QC data

check_readpair_validity(): Check fastq read pair matches samplesheet read pair assignment.

identify_read_pair(): Identify read pair from string

test_failed(): Format a test fail message.

test_passed(): Format a test passed message.

Basic Utils

Low-level functions

syn_login(): Logs into Synapse.

table_query(): Generic table query

as_table_schema(): Transform table data to target schema for Synapse storage

make_folder(): Create project folders

add_to_scope(): Add to scope

new_view(): Create a view

list_project_datasets(): List datasets in project

latest_version(): Get the latest version

walk(): Walk through a directory

copy(): Create copy of entity

convert_to_stringlist(): Convert a delimited string to a stringlist annotation

bare_syn_id(): Extract synapse id from URI or other string

bad_url(): Helper function to check urls

.update_table_data(): Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data.

.update_view_data(): Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update.

from_pubmed(): Get publication metadata from PubMed

Internal/experimental

Mostly meant to be internal or experimental stuff

.delim_string_to_vector(): Convert a delimited string to vector, utility function.

.replace_string_column_with_stringlist_column(): Replace string column with stringlist column

.store_rows(): Adds a row to a table.

missing_annotation_email(): Convert a delimited string to a stringlist annotation

get_doi_meta(): Get DOI metadata if it exists

cite_dataset(): Generate example dataset citation