From ba003dc88dab344541a47af2a09a42232ef72754 Mon Sep 17 00:00:00 2001 From: TeresasaZ Date: Tue, 22 Apr 2025 19:29:59 -0400 Subject: [PATCH 1/6] all agent changes, including model, database, cfg, interactions, test code, and testing json files. --- api/models/interactions_vincent_v2.py | 70 + api/resources/interactions.py | 522 + config/BAR_API.cfg | 1 + config/databases/interactions_vincent_v2.sql | 12146 +++++++++++++++++ config/init.sh | 1 + tests/data/all_tags.json | 6 + tests/data/get_all_grns.json | 148 + tests/data/get_all_papers.json | 135 + tests/data/get_paper_by_agi.json | 32 + tests/data/get_paper_by_agi_pair.json | 32 + tests/data/interactions_by_ref.json | 11625 ++++++++++++++++ tests/data/search_by_tag.json | 27 + tests/resources/test_interactions.py | 202 + 13 files changed, 24947 insertions(+) create mode 100644 api/models/interactions_vincent_v2.py create mode 100644 config/databases/interactions_vincent_v2.sql create mode 100644 tests/data/all_tags.json create mode 100644 tests/data/get_all_grns.json create mode 100644 tests/data/get_all_papers.json create mode 100644 tests/data/get_paper_by_agi.json create mode 100644 tests/data/get_paper_by_agi_pair.json create mode 100644 tests/data/interactions_by_ref.json create mode 100644 tests/data/search_by_tag.json diff --git a/api/models/interactions_vincent_v2.py b/api/models/interactions_vincent_v2.py new file mode 100644 index 0000000..696c56a --- /dev/null +++ b/api/models/interactions_vincent_v2.py @@ -0,0 +1,70 @@ +from api import db +from sqlalchemy import Enum +from sqlalchemy.orm import relationship +from sqlalchemy.dialects.mysql import TEXT +from sqlalchemy import ForeignKey +from typing import List +from datetime import datetime + + +class Interactions(db.Model): + __bind_key__ = "interactions_vincent_v2" + __tablename__ = "interactions" + + interaction_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True) + pearson_correlation_coeff: db.Mapped[float] = db.mapped_column(db.Float, nullable=True, primary_key=False) + entity_1: db.Mapped[str] = db.mapped_column(db.String(50), nullable=False, primary_key=False) + entity_2: db.Mapped[str] = db.mapped_column(db.String(50), nullable=False, primary_key=False) + interaction_type_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=False) + children: db.Mapped[List["InteractionsSourceMiJoin"]] = relationship() + + +class InteractionsSourceMiJoin(db.Model): + __bind_key__ = "interactions_vincent_v2" + __tablename__ = "interactions_source_mi_join_table" + + interaction_id: db.Mapped[int] = db.mapped_column(ForeignKey("interactions.interaction_id"), primary_key=True) + source_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=False) + external_db_id: db.Mapped[str] = db.mapped_column(db.String(30), nullable=False, primary_key=False) + mode_of_action: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=False) + mi_detection_method: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False, primary_key=False) + mi_detection_type: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False, primary_key=False) + + +class TagLookupTable(db.Model): + __bind_key__ = "interactions_vincent_v2" + __tablename__ = "tag_lookup_table" + + tag_name: db.Mapped[str] = db.mapped_column(db.String(20), nullable=False, primary_key=True) + tag_group: db.Mapped[str] = db.mapped_column(Enum("Gene", "Experiment", "Condition", "Misc"), nullable=False, primary_key=False) + + +class ExternalSource(db.Model): + __bind_key__ = "interactions_vincent_v2" + __tablename__ = "external_source" + + source_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, comment="surrogate key", primary_key=True) + source_name: db.Mapped[str] = db.mapped_column(db.String(500), nullable=False, comment="name of the source, can be a pubmed identifier like “PMIDXXXXXXX” or “Asher’s sql dump”", primary_key=False) + comments: db.Mapped[str] = db.mapped_column(TEXT(), nullable=False, comment="Comments regarding the source", primary_key=False) + date_uploaded: db.Mapped[datetime] = db.mapped_column(db.Date(), nullable=False, comment="When it was uploaded to database", primary_key=False) + url: db.Mapped[str] = db.mapped_column(db.String(350), nullable=True, comment="URL if available to paper/source (does not have to be a DOI, can be a link to a databases’ source)", primary_key=False) + image_url: db.Mapped[str] = db.mapped_column(db.String(300), nullable=True, primary_key=False) + grn_title: db.Mapped[str] = db.mapped_column(db.String(200), nullable=True, primary_key=False) + cyjs_layout: db.Mapped[str] = db.mapped_column(db.String(1000), nullable=True, primary_key=False) + children: db.Mapped[List["SourceTagJoinTable"]] = relationship() + + +class SourceTagJoinTable(db.Model): + __bind_key__ = "interactions_vincent_v2" + __tablename__ = "source_tag_join_table" + + source_id: db.Mapped[int] = db.mapped_column( + db.Integer(), + db.ForeignKey("external_source.source_id"), + primary_key=True + ) + tag_name: db.Mapped[str] = db.mapped_column( + db.String(20), + db.ForeignKey("tag_lookup_table.tag_name"), + primary_key=True + ) diff --git a/api/resources/interactions.py b/api/resources/interactions.py index 7fa2c9e..e567e58 100644 --- a/api/resources/interactions.py +++ b/api/resources/interactions.py @@ -13,6 +13,11 @@ from api import db from api.models.rice_interactions import Interactions as RiceInteractions from sqlalchemy import or_ +from api.models.interactions_vincent_v2 import Interactions as PostInteractions +from api.models.interactions_vincent_v2 import InteractionsSourceMiJoin as PostInteractionsSourceMiJoin +from api.models.interactions_vincent_v2 import TagLookupTable as TagLookupTable +from api.models.interactions_vincent_v2 import ExternalSource as ExternalSource +from api.models.interactions_vincent_v2 import SourceTagJoinTable as SourceTagJoinTable itrns = Namespace( "Interactions", @@ -43,6 +48,54 @@ }, ) +single_itrns = itrns.model( + "SingleItrn", + { + "interaction_id": fields.Integer(required=True, example=70), + }, +) + + +itrns_by_ref = itrns.model( + "ItrnsByRef", + { + "paper_id": fields.Integer(required=True, example=15), + }, +) + + +search_by_tag = itrns.model( + "searchByTag", + { + "tag": fields.String(required=True, example="APETALA2"), + }, +) + + +get_paper = itrns.model( + "getPaper", + { + "number": fields.Integer(required=True, example=14), + }, +) + + +get_paper_by_agi = itrns.model( + "getPaperByAGI", + { + "stringAGI": fields.String(required=True, example="AT2G30530"), + }, +) + + +get_paper_by_agi_pair = itrns.model( + "getPaperByAGIPair", + { + "AGI_1": fields.String(required=True, example="AT2G30530"), + "AGI_2": fields.String(required=True, example="AT4G33430"), + }, +) + class GeneIntrnsSchema(Schema): species = marshmallow_fields.String(required=True) @@ -53,6 +106,31 @@ class MFinderDataSchema(Schema): data = marshmallow_fields.List(marshmallow_fields.List(marshmallow_fields.String())) +class GetSingleItrnSchema(Schema): + interaction_id = marshmallow_fields.Integer(required=True) + + +class GetIntrnsByRefSchema(Schema): + paper_id = marshmallow_fields.Integer(required=True) + + +class SearchByTagSchema(Schema): + tag = marshmallow_fields.String(required=True) + + +class GetPaperSchema(Schema): + number = marshmallow_fields.Integer(required=True) + + +class GetPaperByAGISchema(Schema): + stringAGI = marshmallow_fields.String(required=True) + + +class GetPaperByAGIPairSchema(Schema): + AGI_1 = marshmallow_fields.String(required=True) + AGI_2 = marshmallow_fields.String(required=True) + + @itrns.route("//") class Interactions(Resource): @itrns.param("species", _in="path", default="rice") @@ -180,3 +258,447 @@ def post(self): settings = MfinderUtils.settings_validation(data.get("options", {})) ret_json = MfinderUtils.create_files_and_mfinder(filtered_valid_arr, settings) return jsonify(MfinderUtils.beautify_results(ret_json)) + + +@itrns.route("/single_interaction/") +class SingleInteraction(Resource): + @itrns.param("interaction_id", _in="path", default=70) + def get(self, interaction_id=""): + """ + Returns a single interaction record by its interaction ID. + """ + result = [] + + try: + number = int(interaction_id) + except ValueError: + return BARUtils.error_exit("ID given was not a number!"), 400 + + try: + interactions_database = PostInteractions + query = db.select(interactions_database).where(interactions_database.interaction_id == number) + rows = db.session.execute(query).scalars().all() + for row in rows: + result.append( + { + "interaction_id": row.interaction_id, + "pearson_correlation_coeff": row.pearson_correlation_coeff, + "entity_1": row.entity_1, + "entity_2": row.entity_2, + "interaction_type_id": row.interaction_type_id, + } + ) + + if len(result) == 0: + return BARUtils.error_exit("Invalid interaction ID"), 400 + return BARUtils.success_exit(result) + except ValidationError as e: + return BARUtils.error_exit(e.messages), 400 + + +@itrns.route("/interactions_by_ref/") +class InteractionsByRef(Resource): + @itrns.param("paper_id", _in="path", default=15) + def get(self, paper_id=""): + """ + Returns all interactions associated with a given source ID. + """ + result = [] + + # Ensure paper_id is an integer + try: + paper_id = int(paper_id) + except ValueError: + return BARUtils.error_exit("ID given was not a number!"), 400 + + try: + interactions_database = PostInteractions + itnsjoin_database = PostInteractionsSourceMiJoin + query = db.select( + interactions_database, + itnsjoin_database + ).select_from(interactions_database).join( + itnsjoin_database, + interactions_database.interaction_id == itnsjoin_database.interaction_id + ).where(itnsjoin_database.source_id == paper_id) + rows = db.session.execute(query).all() + for i, m in rows: + result.append( + { + "interaction_id": i.interaction_id, + "pearson_correlation_coeff": i.pearson_correlation_coeff, + "entity_1": i.entity_1, + "entity_2": i.entity_2, + "interaction_type_id": i.interaction_type_id, + "mode_of_action": m.mode_of_action, + "mi_detection_method": m.mi_detection_method, + "mi_detection_type": m.mi_detection_type, + } + ) + + if len(result) == 0: + return BARUtils.error_exit("Invalid paper ID"), 400 + return BARUtils.success_exit(result) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + +@itrns.route("/all_tags") +class AllTags(Resource): + def get(self): + """ + Returns all tags in the format 'tag_name:tag_group' as a single pipe-separated string. + """ + grouped_result = [] + + try: + tag_database = TagLookupTable + query = db.select(tag_database.tag_name, tag_database.tag_group) + rows = db.session.execute(query).all() + + for tag_name, tag_group in rows: + grouped_result.append(f"{tag_name}:{tag_group}") + grouped_result = "|".join(grouped_result) + result = {"tag": grouped_result} + return BARUtils.success_exit(result) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + +@itrns.route("/search_by_tag/") +class SearchByTag(Resource): + @itrns.param("tag", _in="path", default="CBF") + def get(self, tag=""): + """ + Returns a list of sources that are associated with the given tag. + """ + result = [] + + try: + ext_src_database = ExternalSource + src_tag_join_database = SourceTagJoinTable + tag_lkup_database = TagLookupTable + + # Step 1: Get source_ids that contain the searched tag + + matching_source_ids = [] + query_source = db.select(src_tag_join_database.source_id).where( + src_tag_join_database.tag_name == tag + ) + rows_source = db.session.execute(query_source).all() + matching_source_ids = [row[0] for row in rows_source] + + if not matching_source_ids: + return BARUtils.error_exit("Invalid tag name"), 400 + + # Step 2: Get all tags for those sources + query = ( + db.select( + ext_src_database, + src_tag_join_database.tag_name, + tag_lkup_database.tag_group + ) + .join(src_tag_join_database, ext_src_database.source_id == src_tag_join_database.source_id) + .join(tag_lkup_database, src_tag_join_database.tag_name == tag_lkup_database.tag_name) + .where(ext_src_database.source_id.in_(matching_source_ids)) # Keep all tags for matched sources + ) + rows = db.session.execute(query).all() + + src_tag_match = {} + for ex, name, group in rows: + if ex.source_id not in src_tag_match: + src_tag_match[ex.source_id] = [f"{name}:{group}"] + else: + src_tag_match[ex.source_id].append(f"{name}:{group}") + + one_source = {} + + for ex, name, group in rows: + source_id = ex.source_id + if source_id not in one_source: + one_source[source_id] = { + "source_id": source_id, + "source_name": ex.source_name, + "comments": ex.comments, + "date_uploaded": ex.date_uploaded.isoformat() if ex.date_uploaded else None, + "url": ex.url, + "image_url": ex.image_url, + "grn_title": ex.grn_title, + "cyjs_layout": ex.cyjs_layout, + "tag": "|".join(src_tag_match[ex.source_id]) + } + result.append(one_source[source_id]) + + return BARUtils.success_exit(result) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + +@itrns.route("/get_all_papers") +class GetAllPapers(Resource): + def get(self): + """ + Returns a list of all papers stored in the database. + """ + result = [] + + try: + ext_src_database = ExternalSource + query = db.select(ext_src_database) + rows = db.session.execute(query).scalars().all() + + for row in rows: + result.append( + { + "source_id": row.source_id, + "source_name": row.source_name, + "comments": row.comments, + "date_uploaded": row.date_uploaded.strftime("%Y/%m/%d") if row.date_uploaded else None, + "url": row.url, + "image_url": row.image_url, + "grn_title": row.grn_title, + "cyjs_layout": row.cyjs_layout, + } + ) + return BARUtils.success_exit(result) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + +@itrns.route("/get_paper/") +class GetPaper(Resource): + @itrns.param("number", _in="path", default=14) + def get(self, number=""): + """ + Returns information for a single external source by its source ID. + """ + result = [] + + try: + number = int(number) + except ValueError: + return BARUtils.error_exit("Input number is not an integer!"), 400 + + try: + ext_src_database = ExternalSource + query = db.select(ext_src_database).where(ext_src_database.source_id == number) + rows = db.session.execute(query).scalars().all() + + for row in rows: + result.append( + { + "source_id": row.source_id, + "source_name": row.source_name, + "comments": row.comments, + "date_uploaded": row.date_uploaded.strftime("%Y/%m/%d") if row.date_uploaded else None, + "url": row.url, + "image_url": row.image_url, + "grn_title": row.grn_title, + "cyjs_layout": row.cyjs_layout + } + ) + + if len(result) == 0: + return BARUtils.error_exit("Invalid source ID"), 400 + return BARUtils.success_exit(result) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + +@itrns.route("/get_paper_by_agi/") +class GetPaperByAGI(Resource): + @itrns.param("stringAGI", _in="path", default="AT2G30530") + def get(self, stringAGI=""): + """ + Returns papers where the AGI appears in either `entity_1` or `entity_2` + """ + + try: + es = ExternalSource + i_s_mi_join_table = PostInteractionsSourceMiJoin + i = PostInteractions + stjt = SourceTagJoinTable + tlt = TagLookupTable + + # Step 1: Query Data (Including Tags) + query = ( + db.select( + es.source_id, + es.grn_title, + es.image_url, + es.source_name, + es.comments, + es.cyjs_layout, + stjt.tag_name, + tlt.tag_group + ) + .join(i_s_mi_join_table, i_s_mi_join_table.source_id == es.source_id) + .join(i, i.interaction_id == i_s_mi_join_table.interaction_id) + .join(stjt, es.source_id == stjt.source_id) + .join(tlt, stjt.tag_name == tlt.tag_name) + .filter( + (i.entity_1 == stringAGI) | (i.entity_2 == stringAGI) # Either entity 1 or entity 2 is stringAGI + ) + .filter(es.grn_title.isnot(None)) + ) + rows = db.session.execute(query).all() + + # Step 2: Group Results Manually + result_dict = {} + + for row in rows: + source_id = row.source_id + + if source_id not in result_dict: + result_dict[source_id] = { + "source_id": row.source_id, + "grn_title": row.grn_title, + "image_url": row.image_url, + "source_name": row.source_name, + "comments": row.comments, + "cyjs_layout": row.cyjs_layout, + "tags": [] + } + + tag_entry = f"{row.tag_name}:{row.tag_group}" + if tag_entry not in result_dict[source_id]["tags"]: # DISTINCT + result_dict[source_id]["tags"].append(tag_entry) + + result = [ + { + **data, + "tags": "|".join(data["tags"]) # overwrites tags + } + for data in result_dict.values() + ] + + if len(result) == 0: + return BARUtils.error_exit("Invalid AGI"), 400 + return BARUtils.success_exit(result) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + +@itrns.route("/get_paper_by_agi_pair//") +class GetPaperByAGIPair(Resource): + @itrns.param("AGI_1", _in="path", default="AT2G30530") + @itrns.param("AGI_2", _in="path", default="AT4G33430") + def get(self, AGI_1="", AGI_2=""): + """ + Returns papers where either AGI appears in `entity_1` or `entity_2` + """ + try: + es = ExternalSource + i_s_mi_join_table = PostInteractionsSourceMiJoin + i = PostInteractions + stjt = SourceTagJoinTable + tlt = TagLookupTable + + query = ( + db.select( + es.source_id, + es.grn_title, + es.image_url, + es.source_name, + es.comments, + es.cyjs_layout, + stjt.tag_name, + tlt.tag_group + ) + .join(i_s_mi_join_table, i_s_mi_join_table.source_id == es.source_id) + .join(i, i.interaction_id == i_s_mi_join_table.interaction_id) + .join(stjt, es.source_id == stjt.source_id) + .join(tlt, stjt.tag_name == tlt.tag_name) + .filter( + ((i.entity_1 == AGI_1) | (i.entity_2 == AGI_1)) # Matches first AGI + | ((i.entity_1 == AGI_2) | (i.entity_2 == AGI_2)) # Matches second AGI + ) + .filter(es.grn_title.isnot(None)) + ) + rows = db.session.execute(query).all() + + result_dict = {} + + for row in rows: + source_id = row.source_id + + if source_id not in result_dict: + result_dict[source_id] = { + "source_id": row.source_id, + "grn_title": row.grn_title, + "image_url": row.image_url, + "source_name": row.source_name, + "comments": row.comments, + "cyjs_layout": row.cyjs_layout, + "tags": set() + } + + result_dict[source_id]["tags"].add(f"{row.tag_name}:{row.tag_group}") # ensures uniqueness automatically with `set` + + result = [ + { + **data, + "tags": "|".join(sorted(data["tags"])) + } + for data in result_dict.values() + ] + + if len(result) == 0: + return BARUtils.error_exit("Both AGI invalid"), 400 + return BARUtils.success_exit(result) + + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + +@itrns.route("/get_all_grns") +class GetAllGRNs(Resource): + def get(self): + """ + Returns + """ + result = [] + + try: + es = ExternalSource + stjt = SourceTagJoinTable + tlt = TagLookupTable + query = ( + db.select( + es, + stjt.tag_name, + tlt.tag_group + ) + .join(stjt, es.source_id == stjt.source_id) + .join(tlt, stjt.tag_name == tlt.tag_name) + ) + rows = db.session.execute(query).all() + + src_tag_match = {} + for ex, name, group in rows: + if ex.source_id not in src_tag_match: + src_tag_match[ex.source_id] = [f"{name}:{group}"] + else: + src_tag_match[ex.source_id].append(f"{name}:{group}") + + one_source = {} + + for ex, name, group in rows: + source_id = ex.source_id + if source_id not in one_source: + one_source[source_id] = { + "source_id": source_id, + "source_name": ex.source_name, + "comments": ex.comments, + "date_uploaded": ex.date_uploaded.isoformat() if ex.date_uploaded else None, + "url": ex.url, + "image_url": ex.image_url, + "grn_title": ex.grn_title, + "cyjs_layout": ex.cyjs_layout, + "tag": "|".join(src_tag_match[ex.source_id]) + } + result.append(one_source[source_id]) + + return BARUtils.success_exit(result) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg index f6e0ab2..f23ab7b 100644 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -24,6 +24,7 @@ SQLALCHEMY_BINDS = { 'eplant_tomato' : 'mysql://root:root@localhost/eplant_tomato', 'fastpheno' : 'mysql://root:root@localhost/fastpheno', 'germination': 'mysql://root:root@localhost/germination', + 'interactions_vincent_v2': 'mysql://root:root@localhost/interactions_vincent_v2', 'kalanchoe': 'mysql://root:root@localhost/kalanchoe', 'klepikova': 'mysql://root:root@localhost/klepikova', 'llama3': 'mysql://root:root@localhost/llama3', diff --git a/config/databases/interactions_vincent_v2.sql b/config/databases/interactions_vincent_v2.sql new file mode 100644 index 0000000..6b2bd60 --- /dev/null +++ b/config/databases/interactions_vincent_v2.sql @@ -0,0 +1,12146 @@ +-- phpMyAdmin SQL Dump +-- version 5.2.1deb1 +-- https://www.phpmyadmin.net/ +-- +-- Host: localhost:3306 +-- Generation Time: Oct 24, 2024 at 07:54 PM +-- Server version: 8.4.3 +-- PHP Version: 8.2.24 + +SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO"; +START TRANSACTION; +SET time_zone = "+00:00"; + + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!40101 SET NAMES utf8mb4 */; + +-- +-- Database: `interactions_vincent_v2` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `interactions_vincent_v2` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `interactions_vincent_v2`; + +-- -------------------------------------------------------- + +-- +-- Table structure for table `algorithms_lookup_table` +-- + +CREATE TABLE `algorithms_lookup_table` ( + `algo_name` varchar(100) NOT NULL COMMENT 'Algorithm name to be used in place of a surrogate key, assume they’re going to be unique. Like “FIMO”.', + `algo_desc` varchar(500) NOT NULL COMMENT 'Describe the named algorithm in algo_name.', + `algo_ranges` varchar(200) NOT NULL COMMENT 'Briefly describe the range of values' +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- -------------------------------------------------------- + +-- +-- Table structure for table `external_source` +-- + +CREATE TABLE `external_source` ( + `source_id` int NOT NULL COMMENT 'surrogate key', + `source_name` varchar(500) NOT NULL COMMENT 'name of the source, can be a pubmed identifier like “PMIDXXXXXXX” or “Asher’s sql dump”', + `comments` text NOT NULL COMMENT 'Comments regarding the source', + `date_uploaded` date NOT NULL COMMENT 'When it was uploaded to database', + `url` varchar(350) DEFAULT NULL COMMENT 'URL if available to paper/source (does not have to be a DOI, can be a link to a databases’ source)', + `image_url` varchar(300) DEFAULT NULL, + `grn_title` varchar(200) DEFAULT NULL, + `cyjs_layout` varchar(1000) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- +-- Dumping data for table `external_source` +-- + +INSERT INTO `external_source` (`source_id`, `source_name`, `comments`, `date_uploaded`, `url`, `image_url`, `grn_title`, `cyjs_layout`) VALUES +(14, '17237218', 'Flowering Time analysis with genome-wide expression variation analysis (combining eQTL mapping and regulator candidate gene selection) in an RIL population of Arabidopsis thaliana. Data From: manual annotation of Figure 2.', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/17237218', 'https://bar.utoronto.ca/GRN_Images/17237218.jpg', 'Keurentjes et al. (Proc Nat Acad Sci, 2007) Flowering Time Network', '{\"name\": \"cose\", \"animate\" : \"true\"}'), +(15, '25736223#1', 'Topic:Investigating cold regulation of the CBF regulon. Methods include transgenic lines that constitutively overexpressed a truncated version of CBF2, quantitative real time PCR analysis, affymetrix GeneChip hybridization. Data From: Table S5. This GRN specifically represents COR genes regulated by first wave transcription factors', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/25736223', 'https://bar.utoronto.ca/GRN_Images/25736223%231.jpg', 'Park et al.(The Plant Journal, 2015) CBF Regulon Low Temperature Network', '{\"name\": \"breadthfirst\", \"animate\" : \"true\"}'), +(16, '25736223#2', 'Topic:Investigating cold regulation of the CBF regulon. Methods include transgenic lines that constitutively overexpressed a truncated version of CBF2, quantitative real time PCR analysis, affymetrix GeneChip hybridization. Data From: Table S6. This GRN is specifically for HSFC1 regulon genes up-regulated by first wave transcription factors.', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/25736223', 'https://bar.utoronto.ca/GRN_Images/25736223%232.jpg', 'Park et al.(The Plant Journal, 2015) CBF Regulon Low Temperature Network', '{\"name\": \"breadthfirst\", \"animate\" : \"true\"}'), +(17, '27923776', 'Y1H Assays Define a Network of Ground Tissue Transcription Factor Interactions. Data From: Figure 2. and supplement', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/27923776', 'https://bar.utoronto.ca/GRN_Images/27923776.jpg', 'Sparks et al.(Developmental Cell, 2016) SHORTROOT-SCARECROW Transcriptional Cascade Network', '{\"name\": \"breadthfirst\", \"animate\" : \"true\"}'), +(18, '30616516', 'Existing time-course gene expression data for flower development was used to find dynamical network biomarker to create a gene regulatory network.', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/30616516', 'https://bar.utoronto.ca/GRN_Images/30616516.jpg', 'Zhang et al. (BMC Plant Biology, 2019) Flowering Development Network', '{\"name\": \"cose\", \"animate\" : \"true\"}'), +(19, '26247122', 'Transcription factors involved in nitrate signaling and the control of prototypical nitrate-responsive genes. Data From: Figure 1.', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/26247122', 'https://bar.utoronto.ca/GRN_Images/26247122-ss.png', 'Vidal et al.(Curr Opin Plant Biol., 2015) Aggregated Nitrate Response Network', '{\"name\": \"cose\", \"animate\" : \"true\"}'), +(20, '29462363', 'Used enhanced yeast one-hybrid (Y1H) and induced wounds to identify regulatory relationships between TFs and promoters. PLETHORA 3 (PLT3), ENHANCER OF SHOOT REGENERATION 1 (ESR1) and HEAT SHOCK FACTOR B 1 (HSFB1) act as critical nodes, cytokinin and auxin are important horomones. Data From: Supplement', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/29462363', 'https://bar.utoronto.ca/GRN_Images/29462363.jpg', 'Ikeuchi et al. (Plant Cell Physiol., 2018) Wound Response Network', '{\"name\": \"breadthfirst\", \"animate\" : \"true\"}'), +(21, '31595065', 'Cambium cell-specific transcript profiling followed by a combination of transcription factor network and genetic analyses was used to identify 62 new transcription factor genotypes in the Vascular cambium (meristem). Key TFs in cambial cell proliferation and xylem differentiation are, WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Data manually annotated from: Figure 2c.', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/31595065', 'https://bar.utoronto.ca/GRN_Images/31595065-ss.png', 'Zhang et al. (Nature Plants, 2019) Vascular Cambium Development Network', '{\"name\": \"cose\", \"animate\" : \"true\"}'), +(22, '21245844', 'Root stele gene network initially mapped with Y1H and Y2H on highly-enriched TFs (based on root spatiotemporal map) and miRNA-of-interest promoters. In planta confirmation and regulation determined via ChIP and qPCR. GRN derived from figure 2. - Vincent', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/21245844', 'https://bar.utoronto.ca/GRN_Images/21245844.jpg', 'Brady et al.(Mol Syst Biol, 2011) Root Stele Network', '{\"name\": \"breadthfirst\", \"animate\" : \"true\"}'), +(23, '25533953', 'Authors used Y1H to generate network for how secondary cell wall metabolites (cellulose, lignin, hemicellulose) is synthesized. Used reporter assay to determine key interactions involving E2Fc. Data from Table S2.', '2019-11-12', 'www.ncbi.nlm.nih.gov/pubmed/25533953', 'https://bar.utoronto.ca/GRN_Images/25533953.jpg', 'Taylor-Teeples et al. (Nature, 2015) Secondary Cell Wall Network', '{\"name\": \"breadthfirst\", \"animate\" : \"true\"}'), +(32, '31806676', 'Y1H Assays Define a Network of TF-promoter interactions Data From: Supplemental Data Set 2.', '2020-01-11', 'www.ncbi.nlm.nih.gov/pubmed/31806676', 'https://bar.utoronto.ca/GRN_Images/31806676.jpg', 'Smit et al.(THE PLANT CELL, 2019) Vascular Development Network', '{\"name\": \"breadthfirst\", \"animate\" : \"true\"}'), +(35, '25750178', 'The authors collected data from literature and with text mining tools and manual curation. Data from: http://atrm.cbi.pku.edu.cn/', '2020-01-14', 'www.ncbi.nlm.nih.gov/pubmed/25750178', 'https://bar.utoronto.ca/GRN_Images/25750178.jpg', 'Jin et al.(MOLECULAR BIOLOGY AND EVOLUTION, 2015) Curated Combined Network', '{\"name\": \"breadthfirst\", \"animate\" : \"true\"}'), +(36, '15486106', 'This is a manually curated network from 2004, more research is required to determine MI term and type as well as validate old experimental evidence and mechanism of action.', '2020-01-14', 'www.ncbi.nlm.nih.gov/pubmed/15486106', 'https://bar.utoronto.ca/GRN_Images/15486106.jpg', 'Espinosa-Soto et al.(THE PLANT CELL, 2004) Flower Development Network', '{\"name\": \"cose\", \"animate\" : \"true\"}'); + +-- -------------------------------------------------------- + +-- +-- Table structure for table `interactions` +-- + +CREATE TABLE `interactions` ( + `interaction_id` int NOT NULL COMMENT 'surrogate key', + `pearson_correlation_coeff` decimal(6,5) DEFAULT NULL COMMENT 'PCC score imported from interactions table', + `entity_1` varchar(50) NOT NULL COMMENT 'Following the interaction_type_id (referencing the lookup table), define the first entity. For example if it is a PPI relationship than the entity 1 shall be a protein with an AGI (ex AT5G01010).', + `entity_2` varchar(50) NOT NULL COMMENT 'Following the interaction_type_id (referencing the lookup table), define the first entity. For example if it is a PPI relationship than the entity 2 shall be a protein with an AGI (ex AT5G01010).', + `interaction_type_id` int NOT NULL COMMENT 'Reference to the lookup of a interactions_lookup_table. Define what type of interaction these two genes are. For example if the value were ‘3’ and it looksup to a PPI, then both members are proteins.' +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- +-- Dumping data for table `interactions` +-- + +INSERT INTO `interactions` (`interaction_id`, `pearson_correlation_coeff`, `entity_1`, `entity_2`, `interaction_type_id`) VALUES +(14, NULL, 'AT2G30530', 'AT4G33430', 2), +(15, NULL, 'AT1G15260', 'AT3G47500', 2), +(16, NULL, 'AT2G26500', 'AT1G14920', 2), +(17, NULL, 'AT2G15810', 'AT1G09570', 2), +(18, NULL, 'AT5G50730', 'AT1G78050', 2), +(19, NULL, 'AT1G12350', 'AT5G62430', 2), +(20, NULL, 'AT1G12350', 'AT2G46340', 2), +(21, NULL, 'AT1G12350', 'AT1G61040', 2), +(22, NULL, 'AT1G12350', 'AT2G19520', 2), +(23, NULL, 'AT1G12350', 'AT2G38050', 2), +(24, NULL, 'AT2G17390', 'AT2G19520', 2), +(25, NULL, 'AT2G23590', 'AT2G28550', 2), +(26, NULL, 'AT5G23460', 'AT1G77080', 2), +(27, NULL, 'AT5G23460', 'AT5G65080', 2), +(28, NULL, 'AT5G23460', 'AT5G65070', 2), +(29, NULL, 'AT5G23460', 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Reference it here to the lookup.', + `mi_detection_method` varchar(10) NOT NULL, + `mi_detection_type` varchar(10) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- +-- Dumping data for table `interactions_source_mi_join_table` +-- + +INSERT INTO `interactions_source_mi_join_table` (`interaction_id`, `source_id`, `external_db_id`, `mode_of_action`, `mi_detection_method`, `mi_detection_type`) VALUES +(8640, 35, '', 1, '000', '000'), +(8645, 35, '', 1, '000', '000'), +(8985, 35, '', 1, '000', '000'), +(1568, 17, '', 1, '1195', '2286'), +(1583, 17, '', 1, '1195', '2286'), +(1584, 17, '', 1, '1195', '2286'), +(1585, 17, '', 1, '1195', '2286'), +(1586, 17, '', 1, '1195', '2286'), +(1829, 19, '', 1, '1195', '2286'), +(1830, 19, '', 1, '1195', '2286'), +(1831, 19, '', 1, '1195', '2286'), +(1832, 19, '', 1, '1195', '2286'), +(1833, 19, '', 1, '1195', '2286'), +(1837, 19, '', 1, '1195', '2286'), +(1838, 19, '', 1, '1195', '2286'), +(1839, 19, '', 1, '1195', 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+(74, 14, '', 3, '225', '2286'), +(75, 14, '', 3, '225', '2286'), +(3069, 22, '', 3, '432', '915'), +(3071, 22, '', 3, '432', '915'), +(3072, 22, '', 3, '432', '915'), +(3073, 22, '', 3, '432', '915'), +(3075, 22, '', 3, '432', '915'), +(3078, 22, '', 3, '432', '915'), +(3081, 22, '', 3, '432', '915'), +(3084, 22, '', 3, '432', '915'), +(3086, 22, '', 3, '432', '915'), +(3087, 22, '', 3, '432', '915'), +(3089, 22, '', 3, '432', '915'), +(3094, 22, '', 3, '432', '915'); + +-- -------------------------------------------------------- + +-- +-- Table structure for table `interaction_lookup_table` +-- + +CREATE TABLE `interaction_lookup_table` ( + `interaction_type_id` int NOT NULL COMMENT 'Surrogate key', + `description` varchar(100) NOT NULL COMMENT 'Describe the binary interaction of the entities. For example ‘ppi - protein interaction where entity_1_alias and entity_2_alias represent proteins’', + `entity_1_alias` varchar(50) NOT NULL COMMENT 'Can be a protein, miRNA, etc.', + `entity_2_alias` varchar(50) NOT NULL COMMENT 'Can be a protein, miRNA, etc.' +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- +-- Dumping data for table `interaction_lookup_table` +-- + +INSERT INTO `interaction_lookup_table` (`interaction_type_id`, `description`, `entity_1_alias`, `entity_2_alias`) VALUES +(1, 'protein-protein interaction (ppi)', 'protein', 'protein'), +(2, 'protein-dna interaction (pdi)', 'protein', 'dna'), +(3, 'mirna-mrna interaction (mimi)', 'mirna', 'mrna'); + +-- -------------------------------------------------------- + +-- +-- Table structure for table `interolog_confidence_subset_table` +-- + +CREATE TABLE `interolog_confidence_subset_table` ( + `interaction_id` int NOT NULL COMMENT 'surrogate key', + `s_cerevisiae` tinyint NOT NULL COMMENT 'species score… repeat for all other species', + `s_pombe` tinyint NOT NULL, + `worm` tinyint NOT NULL, + `fly` tinyint NOT NULL, + `human` tinyint NOT NULL, + `mouse` tinyint NOT NULL, + `e_coli` tinyint NOT NULL, + `total_hits` smallint NOT NULL, + `num_species` tinyint NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- -------------------------------------------------------- + +-- +-- Table structure for table `modes_of_action_lookup_table` +-- + +CREATE TABLE `modes_of_action_lookup_table` ( + `m_of_a_pk` tinyint(1) NOT NULL COMMENT 'surrogate key', + `description` varchar(20) NOT NULL COMMENT 'Describe the mode of action of the interaction, is it repression or activation for example?' +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- +-- Dumping data for table `modes_of_action_lookup_table` +-- + +INSERT INTO `modes_of_action_lookup_table` (`m_of_a_pk`, `description`) VALUES +(2, 'activation'), +(3, 'repression'), +(1, 'unknown'); + +-- -------------------------------------------------------- + +-- +-- Table structure for table `source_tag_join_table` +-- + +CREATE TABLE `source_tag_join_table` ( + `source_id` int NOT NULL, + `tag_name` varchar(20) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- +-- Dumping data for table `source_tag_join_table` +-- + +INSERT INTO `source_tag_join_table` (`source_id`, `tag_name`) VALUES +(18, 'APETALA2'), +(20, 'auxin'), +(19, 'bZIP1'), +(18, 'CBC'), +(15, 'CBF'), +(16, 'CBF'), +(15, 'CBF1'), +(16, 'CBF1'), +(15, 'CBF2'), +(16, 'CBF2'), +(15, 'CBF3'), +(16, 'CBF3'), +(18, 'CBP20'), +(19, 'ChIP'), +(22, 'ChIP'), +(36, 'CLF'), +(15, 'Cold Stress'), +(16, 'Cold Stress'), +(35, 'curation'), +(20, 'cytokinin'), +(15, 'CZF1'), +(16, 'CZF1'), +(17, 'DDF1'), +(18, 'DNB'), +(15, 'DREB1b'), +(16, 'DREB1b'), +(15, 'DREB1c'), +(16, 'DREB1c'), +(15, 'DREB2a'), +(16, 'DREB2a'), +(23, 'E2Fc'), +(36, 'EMF1'), +(14, 'eQTL mapping'), +(14, 'ERECTA'), +(20, 'ESR1'), +(19, 'expression change'), +(32, 'eY1H'), +(14, 'Flower'), +(18, 'Flower'), +(36, 'flower'), +(36, 'FT'), +(14, 'GIGANTEA'), +(20, 'HSFB1'), +(15, 'HSFC1'), +(16, 'HSFC1'), +(21, 'KNAT1'), +(32, 'LBD4'), +(18, 'LEA'), +(36, 'LFY'), +(14, 'Linkage Mapping'), +(36, 'LUG'), +(21, 'meristem'), +(32, 'meristems'), +(19, 'NAC4'), +(18, 'NAP12'), +(35, 'network structure'), +(19, 'Nitrate'), +(19, 'NLP'), +(19, 'NLP7'), +(22, 'OBP2'), +(20, 'PLT3'), +(21, 'PTL'), +(32, 'PXY'), +(22, 'qPCR'), +(15, 'qRT-PCR'), +(16, 'qRT-PCR'), +(17, 'qRT-PCR'), +(15, 'RAV1'), +(16, 'RAV1'), +(22, 'REV'), +(18, 'RIE1'), +(14, 'RIL'), +(17, 'root'), +(19, 'root'), +(22, 'Root Stele'), +(17, 'SCARECROW'), +(23, 'Secondary Cell Wall'), +(17, 'SHORTROOT'), +(21, 'SVP'), +(36, 'TFL1'), +(19, 'TGA1'), +(19, 'TGA4'), +(20, 'tissue'), +(32, 'TMO6'), +(36, 'UFO'), +(32, 'vascular'), +(21, 'Vascular cambium'), +(23, 'VND6'), +(35, 'wiring preference'), +(20, 'wound'), +(32, 'WOX14'), +(21, 'WOX4'), +(21, 'xylem'), +(17, 'Y1H'), +(20, 'Y1H'), +(22, 'Y1H'), +(23, 'Y1H'), +(22, 'Y2H'), +(15, 'ZAT10'), +(16, 'ZAT10'), +(15, 'ZAT12'), +(16, 'ZAT12'), +(15, 'ZF'), +(16, 'ZF'), +(17, 'ZML1'); + +-- -------------------------------------------------------- + +-- +-- Table structure for table `tag_lookup_table` +-- + +CREATE TABLE `tag_lookup_table` ( + `tag_name` varchar(20) NOT NULL, + `tag_group` enum('Gene','Experiment','Condition','Misc') NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; + +-- +-- Dumping data for table `tag_lookup_table` +-- + +INSERT INTO `tag_lookup_table` (`tag_name`, `tag_group`) VALUES +('APETALA2', 'Misc'), +('auxin', 'Misc'), +('bZIP1', 'Gene'), +('CBC', 'Misc'), +('CBF', 'Gene'), +('CBF1', 'Gene'), +('CBF2', 'Gene'), +('CBF3', 'Gene'), +('CBP20', 'Gene'), +('ChIP', 'Experiment'), +('CLF', 'Gene'), +('Cold Stress', 'Condition'), +('curation', 'Misc'), +('cytokinin', 'Misc'), +('CZF1', 'Gene'), +('DDF1', 'Gene'), +('DNB', 'Experiment'), +('DREB1b', 'Gene'), +('DREB1c', 'Gene'), +('DREB2a', 'Gene'), +('E2Fc', 'Gene'), +('EMF1', 'Gene'), +('eQTL mapping', 'Experiment'), +('ERECTA', 'Gene'), +('ESR1', 'Gene'), +('expression change', 'Experiment'), +('eY1H', 'Experiment'), +('Flower', 'Condition'), +('FT', 'Gene'), +('GIGANTEA', 'Gene'), +('HSFB1', 'Gene'), +('HSFC1', 'Gene'), +('KNAT1', 'Gene'), +('LBD4', 'Gene'), +('LEA', 'Gene'), +('LFY', 'Gene'), +('Linkage Mapping', 'Experiment'), +('LUG', 'Gene'), +('meristem', 'Condition'), +('meristems', 'Condition'), +('NAC4', 'Gene'), +('NAP12', 'Gene'), +('network structure', 'Misc'), +('Nitrate', 'Condition'), +('NLP', 'Gene'), +('NLP7', 'Gene'), +('OBP2', 'Gene'), +('PLT3', 'Gene'), +('PTL', 'Gene'), +('PXY', 'Gene'), +('qPCR', 'Experiment'), +('qRT-PCR', 'Experiment'), +('RAV1', 'Gene'), +('REV', 'Gene'), +('RIE1', 'Gene'), +('RIL', 'Experiment'), +('root', 'Condition'), +('Root Stele', 'Condition'), +('SCARECROW', 'Gene'), +('Secondary Cell Wall', 'Condition'), +('SHORTROOT', 'Gene'), +('SVP', 'Gene'), +('TFL1', 'Gene'), +('TGA1', 'Gene'), +('TGA4', 'Gene'), +('tissue', 'Condition'), +('TMO6', 'Gene'), +('UFO', 'Gene'), +('vascular', 'Condition'), +('Vascular cambium', 'Condition'), +('VND6', 'Gene'), +('wiring preference', 'Misc'), +('wound', 'Condition'), +('WOX14', 'Gene'), +('WOX4', 'Gene'), +('xylem', 'Condition'), +('Y1H', 'Experiment'), +('Y2H', 'Experiment'), +('ZAT10', 'Gene'), +('ZAT12', 'Gene'), +('ZF', 'Gene'), +('ZML1', 'Gene'); + +-- +-- Indexes for dumped tables +-- + +-- +-- Indexes for table `algorithms_lookup_table` +-- +ALTER TABLE `algorithms_lookup_table` + ADD PRIMARY KEY (`algo_name`); + +-- +-- Indexes for table `external_source` +-- +ALTER TABLE `external_source` + ADD PRIMARY KEY (`source_id`), + ADD UNIQUE KEY `source_name_UNIQUE` (`source_name`); + +-- +-- Indexes for table `interactions` +-- +ALTER TABLE `interactions` + ADD PRIMARY KEY (`interaction_id`), + ADD UNIQUE KEY `unique_interaction_index` (`entity_1`,`entity_2`,`interaction_type_id`), + ADD KEY `interaction_type_id_idx` (`interaction_type_id`); + +-- +-- Indexes for table `interactions_algo_score_join_table` +-- +ALTER TABLE `interactions_algo_score_join_table` + ADD PRIMARY KEY (`algo_name`,`interaction_id`,`algo_score`), + ADD KEY `interaction_id_idx` (`interaction_id`); + +-- +-- Indexes for table `interactions_source_mi_join_table` +-- +ALTER TABLE `interactions_source_mi_join_table` + ADD PRIMARY KEY (`mi_detection_method`,`mi_detection_type`,`external_db_id`,`interaction_id`,`source_id`), + ADD KEY `source_id_idx` (`source_id`), + ADD KEY `m_o_a_db_FK_idx` (`mode_of_action`), + ADD KEY `int_id_FK_on_mi_int_src` (`interaction_id`); + +-- +-- Indexes for table `interaction_lookup_table` +-- +ALTER TABLE `interaction_lookup_table` + ADD PRIMARY KEY (`interaction_type_id`), + ADD UNIQUE KEY `description_UNIQUE` (`description`); + +-- +-- Indexes for table `interolog_confidence_subset_table` +-- +ALTER TABLE `interolog_confidence_subset_table` + ADD PRIMARY KEY (`interaction_id`), + ADD KEY `pdi_interaction_id_idx` (`interaction_id`); + +-- +-- Indexes for table `modes_of_action_lookup_table` +-- +ALTER TABLE `modes_of_action_lookup_table` + ADD PRIMARY KEY (`m_of_a_pk`), + ADD UNIQUE KEY `description_UNIQUE` (`description`); + +-- +-- Indexes for table `source_tag_join_table` +-- +ALTER TABLE `source_tag_join_table` + ADD PRIMARY KEY (`source_id`,`tag_name`), + ADD KEY `tag_join_tag_names_FK_idx` (`tag_name`); + +-- +-- Indexes for table `tag_lookup_table` +-- +ALTER TABLE `tag_lookup_table` + ADD PRIMARY KEY (`tag_name`); + +-- +-- AUTO_INCREMENT for dumped tables +-- + +-- +-- AUTO_INCREMENT for table `external_source` +-- +ALTER TABLE `external_source` + MODIFY `source_id` int NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', AUTO_INCREMENT=37; + +-- +-- AUTO_INCREMENT for table `interactions` +-- +ALTER TABLE `interactions` + MODIFY `interaction_id` int NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', AUTO_INCREMENT=9069; + +-- +-- AUTO_INCREMENT for table `interaction_lookup_table` +-- +ALTER TABLE `interaction_lookup_table` + MODIFY `interaction_type_id` int NOT NULL AUTO_INCREMENT COMMENT 'Surrogate key', AUTO_INCREMENT=4; + +-- +-- AUTO_INCREMENT for table `modes_of_action_lookup_table` +-- +ALTER TABLE `modes_of_action_lookup_table` + MODIFY `m_of_a_pk` tinyint(1) NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', AUTO_INCREMENT=4; + +-- +-- Constraints for dumped tables +-- + +-- +-- Constraints for table `interactions` +-- +ALTER TABLE `interactions` + ADD CONSTRAINT `interaction_type_id` FOREIGN KEY (`interaction_type_id`) REFERENCES `interaction_lookup_table` (`interaction_type_id`); + +-- +-- Constraints for table `interactions_algo_score_join_table` +-- +ALTER TABLE `interactions_algo_score_join_table` + ADD CONSTRAINT `algo_name` FOREIGN KEY (`algo_name`) REFERENCES `algorithms_lookup_table` (`algo_name`), + ADD CONSTRAINT `interaction_id` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`); + +-- +-- Constraints for table `interactions_source_mi_join_table` +-- +ALTER TABLE `interactions_source_mi_join_table` + ADD CONSTRAINT `int_id_FK_on_mi_int_src` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`), + ADD CONSTRAINT `m_o_a_db_FK` FOREIGN KEY (`mode_of_action`) REFERENCES `modes_of_action_lookup_table` (`m_of_a_pk`), + ADD CONSTRAINT `source_id_FK` FOREIGN KEY (`source_id`) REFERENCES `external_source` (`source_id`); + +-- +-- Constraints for table `interolog_confidence_subset_table` +-- +ALTER TABLE `interolog_confidence_subset_table` + ADD CONSTRAINT `interolog_int_id_FK` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`); + +-- +-- Constraints for table `source_tag_join_table` +-- +ALTER TABLE `source_tag_join_table` + ADD CONSTRAINT `tag_join_source_id_FK` FOREIGN KEY (`source_id`) REFERENCES `external_source` (`source_id`), + ADD CONSTRAINT `tag_join_tag_names_FK` FOREIGN KEY (`tag_name`) REFERENCES `tag_lookup_table` (`tag_name`); +COMMIT; + +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; diff --git a/config/init.sh b/config/init.sh index 23bd482..c895f8e 100755 --- a/config/init.sh +++ b/config/init.sh @@ -23,6 +23,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_soybean.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_tomato.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/fastpheno.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/germination.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/interactions_vincent_v2.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/kalanchoe.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/klepikova.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/llama3.sql diff --git a/tests/data/all_tags.json b/tests/data/all_tags.json new file mode 100644 index 0000000..43579b1 --- /dev/null +++ b/tests/data/all_tags.json @@ -0,0 +1,6 @@ +{ + "wasSuccessful": true, + "data": { + "tag": "APETALA2:Misc|auxin:Misc|bZIP1:Gene|CBC:Misc|CBF:Gene|CBF1:Gene|CBF2:Gene|CBF3:Gene|CBP20:Gene|ChIP:Experiment|CLF:Gene|Cold Stress:Condition|curation:Misc|cytokinin:Misc|CZF1:Gene|DDF1:Gene|DNB:Experiment|DREB1b:Gene|DREB1c:Gene|DREB2a:Gene|E2Fc:Gene|EMF1:Gene|eQTL mapping:Experiment|ERECTA:Gene|ESR1:Gene|expression change:Experiment|eY1H:Experiment|Flower:Condition|FT:Gene|GIGANTEA:Gene|HSFB1:Gene|HSFC1:Gene|KNAT1:Gene|LBD4:Gene|LEA:Gene|LFY:Gene|Linkage Mapping:Experiment|LUG:Gene|meristem:Condition|meristems:Condition|NAC4:Gene|NAP12:Gene|network structure:Misc|Nitrate:Condition|NLP:Gene|NLP7:Gene|OBP2:Gene|PLT3:Gene|PTL:Gene|PXY:Gene|qPCR:Experiment|qRT-PCR:Experiment|RAV1:Gene|REV:Gene|RIE1:Gene|RIL:Experiment|root:Condition|Root Stele:Condition|SCARECROW:Gene|Secondary Cell Wall:Condition|SHORTROOT:Gene|SVP:Gene|TFL1:Gene|TGA1:Gene|TGA4:Gene|tissue:Condition|TMO6:Gene|UFO:Gene|vascular:Condition|Vascular cambium:Condition|VND6:Gene|wiring preference:Misc|wound:Condition|WOX14:Gene|WOX4:Gene|xylem:Condition|Y1H:Experiment|Y2H:Experiment|ZAT10:Gene|ZAT12:Gene|ZF:Gene|ZML1:Gene" + } +} \ No newline at end of file diff --git a/tests/data/get_all_grns.json b/tests/data/get_all_grns.json new file mode 100644 index 0000000..75157bc --- /dev/null +++ b/tests/data/get_all_grns.json @@ -0,0 +1,148 @@ +{ + "wasSuccessful": true, + "data": [ + { + "source_id": 14, + "source_name": "17237218", + "comments": "Flowering Time analysis with genome-wide expression variation analysis (combining eQTL mapping and regulator candidate gene selection) in an RIL population of Arabidopsis thaliana. Data From: manual annotation of Figure 2.", + "date_uploaded": "2019-11-12", + "url": "www.ncbi.nlm.nih.gov/pubmed/17237218", + "image_url": "https://bar.utoronto.ca/GRN_Images/17237218.jpg", + "grn_title": "Keurentjes et al. (Proc Nat Acad Sci, 2007) Flowering Time Network", + "cyjs_layout": "{\"name\": \"cose\", \"animate\" : \"true\"}", + "tag": "eQTL mapping:Experiment|ERECTA:Gene|Flower:Condition|GIGANTEA:Gene|Linkage Mapping:Experiment|RIL:Experiment" + }, + { + "source_id": 15, + "source_name": "25736223#1", + "comments": "Topic:Investigating cold regulation of the CBF regulon. Methods include transgenic lines that constitutively overexpressed a truncated version of CBF2, quantitative real time PCR analysis, affymetrix GeneChip hybridization. Data From: Table S5. This GRN specifically represents COR genes regulated by first wave transcription factors", + "date_uploaded": "2019-11-12", + "url": "www.ncbi.nlm.nih.gov/pubmed/25736223", + "image_url": "https://bar.utoronto.ca/GRN_Images/25736223%231.jpg", + "grn_title": "Park et al.(The Plant Journal, 2015) CBF Regulon Low Temperature Network", + "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}", + "tag": "CBF:Gene|CBF1:Gene|CBF2:Gene|CBF3:Gene|Cold Stress:Condition|CZF1:Gene|DREB1b:Gene|DREB1c:Gene|DREB2a:Gene|HSFC1:Gene|qRT-PCR:Experiment|RAV1:Gene|ZAT10:Gene|ZAT12:Gene|ZF:Gene" + }, + { + "source_id": 16, + "source_name": "25736223#2", + "comments": "Topic:Investigating cold regulation of the CBF regulon. Methods include transgenic lines that constitutively overexpressed a truncated version of CBF2, quantitative real time PCR analysis, affymetrix GeneChip hybridization. Data From: Table S6. This GRN is specifically for HSFC1 regulon genes up-regulated by first wave transcription factors.", + "date_uploaded": "2019-11-12", + "url": "www.ncbi.nlm.nih.gov/pubmed/25736223", + "image_url": "https://bar.utoronto.ca/GRN_Images/25736223%232.jpg", + "grn_title": "Park et al.(The Plant Journal, 2015) CBF Regulon Low Temperature Network", + "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}", + "tag": "CBF:Gene|CBF1:Gene|CBF2:Gene|CBF3:Gene|Cold Stress:Condition|CZF1:Gene|DREB1b:Gene|DREB1c:Gene|DREB2a:Gene|HSFC1:Gene|qRT-PCR:Experiment|RAV1:Gene|ZAT10:Gene|ZAT12:Gene|ZF:Gene" + }, + { + "source_id": 17, + "source_name": "27923776", + "comments": "Y1H Assays Define a Network of Ground Tissue Transcription Factor Interactions. Data From: Figure 2. and supplement", + "date_uploaded": "2019-11-12", + "url": "www.ncbi.nlm.nih.gov/pubmed/27923776", + "image_url": "https://bar.utoronto.ca/GRN_Images/27923776.jpg", + "grn_title": "Sparks et al.(Developmental Cell, 2016) SHORTROOT-SCARECROW Transcriptional Cascade Network", + "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}", + "tag": "DDF1:Gene|qRT-PCR:Experiment|root:Condition|SCARECROW:Gene|SHORTROOT:Gene|Y1H:Experiment|ZML1:Gene" + }, + { + "source_id": 18, + "source_name": "30616516", + "comments": "Existing time-course gene expression data for flower development was used to find dynamical network biomarker to create a gene regulatory network.", + "date_uploaded": "2019-11-12", + "url": "www.ncbi.nlm.nih.gov/pubmed/30616516", + "image_url": "https://bar.utoronto.ca/GRN_Images/30616516.jpg", + "grn_title": "Zhang et al. 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+ "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3005, + "pearson_correlation_coeff": null, + "entity_1": "AT4G00238", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3006, + "pearson_correlation_coeff": null, + "entity_1": "AT4G00270", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3007, + "pearson_correlation_coeff": null, + "entity_1": "AT4G00390", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3008, + "pearson_correlation_coeff": null, + "entity_1": "AT4G31615", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3009, + "pearson_correlation_coeff": null, + "entity_1": "AT5G05550", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3010, + "pearson_correlation_coeff": null, + "entity_1": "AT5G51790", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3011, + "pearson_correlation_coeff": null, + "entity_1": "AT4G34590", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3012, + "pearson_correlation_coeff": null, + "entity_1": "AT5G05410", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3013, + "pearson_correlation_coeff": null, + "entity_1": "AT1G03800", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3014, + "pearson_correlation_coeff": null, + "entity_1": "AT5G25190", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3015, + "pearson_correlation_coeff": null, + "entity_1": "AT1G12980", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3016, + "pearson_correlation_coeff": null, + "entity_1": "AT1G14687", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3017, + "pearson_correlation_coeff": null, + "entity_1": "AT4G36740", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3018, + "pearson_correlation_coeff": null, + "entity_1": "AT5G52170", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3019, + "pearson_correlation_coeff": null, + "entity_1": "AT2G24430", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3020, + "pearson_correlation_coeff": null, + "entity_1": "AT3G18400", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3021, + "pearson_correlation_coeff": null, + "entity_1": "AT5G39610", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + }, + { + "interaction_id": 3022, + "pearson_correlation_coeff": null, + "entity_1": "AT5G10510", + "entity_2": "AT2G17950", + "interaction_type_id": 2, + "mode_of_action": 1, + "mi_detection_method": "432", + "mi_detection_type": "915" + } + ] +} \ No newline at end of file diff --git a/tests/data/search_by_tag.json b/tests/data/search_by_tag.json new file mode 100644 index 0000000..a0a25b2 --- /dev/null +++ b/tests/data/search_by_tag.json @@ -0,0 +1,27 @@ +{ + "wasSuccessful": true, + "data": [ + { + "source_id": 15, + "source_name": "25736223#1", + "comments": "Topic:Investigating cold regulation of the CBF regulon. Methods include transgenic lines that constitutively overexpressed a truncated version of CBF2, quantitative real time PCR analysis, affymetrix GeneChip hybridization. Data From: Table S5. This GRN specifically represents COR genes regulated by first wave transcription factors", + "date_uploaded": "2019-11-12", + "url": "www.ncbi.nlm.nih.gov/pubmed/25736223", + "image_url": "https://bar.utoronto.ca/GRN_Images/25736223%231.jpg", + "grn_title": "Park et al.(The Plant Journal, 2015) CBF Regulon Low Temperature Network", + "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}", + "tag": "CBF:Gene|CBF1:Gene|CBF2:Gene|CBF3:Gene|Cold Stress:Condition|CZF1:Gene|DREB1b:Gene|DREB1c:Gene|DREB2a:Gene|HSFC1:Gene|qRT-PCR:Experiment|RAV1:Gene|ZAT10:Gene|ZAT12:Gene|ZF:Gene" + }, + { + "source_id": 16, + "source_name": "25736223#2", + "comments": "Topic:Investigating cold regulation of the CBF regulon. Methods include transgenic lines that constitutively overexpressed a truncated version of CBF2, quantitative real time PCR analysis, affymetrix GeneChip hybridization. Data From: Table S6. This GRN is specifically for HSFC1 regulon genes up-regulated by first wave transcription factors.", + "date_uploaded": "2019-11-12", + "url": "www.ncbi.nlm.nih.gov/pubmed/25736223", + "image_url": "https://bar.utoronto.ca/GRN_Images/25736223%232.jpg", + "grn_title": "Park et al.(The Plant Journal, 2015) CBF Regulon Low Temperature Network", + "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}", + "tag": "CBF:Gene|CBF1:Gene|CBF2:Gene|CBF3:Gene|Cold Stress:Condition|CZF1:Gene|DREB1b:Gene|DREB1c:Gene|DREB2a:Gene|HSFC1:Gene|qRT-PCR:Experiment|RAV1:Gene|ZAT10:Gene|ZAT12:Gene|ZF:Gene" + } + ] +} \ No newline at end of file diff --git a/tests/resources/test_interactions.py b/tests/resources/test_interactions.py index fdb3a2b..2f1cec4 100644 --- a/tests/resources/test_interactions.py +++ b/tests/resources/test_interactions.py @@ -186,3 +186,205 @@ def test_mfinder(self): data = json.loads(response.get_data(as_text=True)) expected = {"wasSuccessful": False, "error": "Invalid gene ID contained!"} self.assertEqual(data, expected) + + def test_single_itrn(self): + """ + This function tests retrieving a single interaction by ID. + """ + + # Valid request + response = self.app_client.get("/interactions/single_interaction/80") + expected = { + "wasSuccessful": True, + "data": [ + { + "interaction_id": 80, + "pearson_correlation_coeff": None, + "entity_1": "AT4G25470", + "entity_2": "AT5G50720", + "interaction_type_id": 1 + } + ] + } + self.assertEqual(response.json, expected) + + # Input not a number + response = self.app_client.get("/interactions/single_interaction/g") + expected = { + "wasSuccessful": False, + "error": "ID given was not a number!" + } + self.assertEqual(response.json, expected) + + # Not a valid interaction ID + response = self.app_client.get("/interactions/single_interaction/3") + expected = { + "wasSuccessful": False, + "error": "Invalid interaction ID" + } + self.assertEqual(response.json, expected) + + def test_itrn_by_ref(self): + """ + This function tests retrieving interactions linked to a specific paper ID + """ + + # Valid request + response = self.app_client.get("/interactions/interactions_by_ref/20") + with open("tests/data/interactions_by_ref.json") as json_file: + expected = load(json_file) + self.assertEqual(response.json, expected) + + # Input not a number + response = self.app_client.get("/interactions/interactions_by_ref/k") + expected = { + "wasSuccessful": False, + "error": "ID given was not a number!" + } + self.assertEqual(response.json, expected) + + # Not a valid paper ID + response = self.app_client.get("/interactions/interactions_by_ref/1") + expected = { + "wasSuccessful": False, + "error": "Invalid paper ID" + } + self.assertEqual(response.json, expected) + + def test_all_tags(self): + """ + This function tests retrieval of all available tag names and their groups. + """ + + # Valid request + response = self.app_client.get("/interactions/all_tags") + with open("tests/data/all_tags.json") as json_file: + expected = load(json_file) + self.assertEqual(response.json, expected) + + def test_search_by_tag(self): + """ + This function tests searching for sources associated with a given tag. + """ + + # Valid request + response = self.app_client.get("/interactions/search_by_tag/CZF1") + with open("tests/data/search_by_tag.json") as json_file: + expected = load(json_file) + self.assertEqual(response.json, expected) + + # Invalid tag name + response = self.app_client.get("/interactions/search_by_tag/p") + expected = { + "wasSuccessful": False, + "error": "Invalid tag name" + } + self.assertEqual(response.json, expected) + + def test_get_all_papers(self): + """ + This function tests retrieval of all papers with their metadata. + """ + + # Valid request + response = self.app_client.get("/interactions/get_all_papers") + with open("tests/data/get_all_papers.json") as json_file: + expected = load(json_file) + self.assertEqual(response.json, expected) + + def test_get_paper(self): + """ + This function tests retrieving a single paper by its ID. + """ + + # Valid request + response = self.app_client.get("/interactions/get_paper/16") + expected = { + "wasSuccessful": True, + "data": [ + { + "source_id": 16, + "source_name": "25736223#2", + "comments": "Topic:Investigating cold regulation of the CBF regulon. Methods include transgenic lines that constitutively overexpressed a truncated version of CBF2, quantitative real time PCR analysis, affymetrix GeneChip hybridization. Data From: Table S6. This GRN is specifically for HSFC1 regulon genes up-regulated by first wave transcription factors.", + "date_uploaded": "2019/11/12", + "url": "www.ncbi.nlm.nih.gov/pubmed/25736223", + "image_url": "https://bar.utoronto.ca/GRN_Images/25736223%232.jpg", + "grn_title": "Park et al.(The Plant Journal, 2015) CBF Regulon Low Temperature Network", + "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}" + } + ] + } + self.assertEqual(response.json, expected) + + # Input not an integer, a string + response = self.app_client.get("/interactions/get_paper/p") + expected = { + "wasSuccessful": False, + "error": "Input number is not an integer!" + } + self.assertEqual(response.json, expected) + + # Input not an integer, a float + response = self.app_client.get("/interactions/get_paper/2.2") + expected = { + "wasSuccessful": False, + "error": "Input number is not an integer!" + } + self.assertEqual(response.json, expected) + + # Invalid source ID + response = self.app_client.get("/interactions/get_paper/3") + expected = { + "wasSuccessful": False, + "error": "Invalid source ID" + } + self.assertEqual(response.json, expected) + + def test_get_paper_by_agi(self): + """ + This function tests retrieving papers that contain a specific AGI in interaction data. + """ + + # Valid request + response = self.app_client.get("/interactions/get_paper_by_agi/AT1G22770") + with open("tests/data/get_paper_by_agi.json") as json_file: + expected = load(json_file) + self.assertEqual(response.json, expected) + + # Invalid AGI + response = self.app_client.get("/interactions/get_paper_by_agi/AT1G00000") + expected = { + "wasSuccessful": False, + "error": "Invalid AGI" + } + self.assertEqual(response.json, expected) + + def test_get_paper_by_agi_pair(self): + """ + This function tests retrieving papers where either AGIs appear in interaction data. + """ + + # Valid request + response = self.app_client.get("/interactions/get_paper_by_agi_pair/AT5G50000/AT1G77120") + with open("tests/data/get_paper_by_agi_pair.json") as json_file: + expected = load(json_file) + self.assertEqual(response.json, expected) + + # Both AGI invalid + response = self.app_client.get("/interactions/get_paper_by_agi_pair/AT1G00000/AT2G00000") + expected = { + "wasSuccessful": False, + "error": "Both AGI invalid" + } + self.assertEqual(response.json, expected) + + def test_get_all_grns(self): + """ + This function tests retrieval of all GRNs with their associated tags. + """ + + # Valid request + response = self.app_client.get("/interactions/get_all_grns") + with open("tests/data/get_all_grns.json") as json_file: + expected = load(json_file) + self.assertEqual(response.json, expected) From 5cb744da22e356bdc6b0ed939f80303d8eaa9d91 Mon Sep 17 00:00:00 2001 From: TeresasaZ Date: Tue, 22 Apr 2025 22:17:21 -0400 Subject: [PATCH 2/6] modified mfinder, added github environment skip pytest --- api/resources/interactions.py | 26 +++- api/utils/mfinder_utils.py | 193 +++++++++++++++++++++++++++ tests/resources/test_interactions.py | 63 +++++++++ 3 files changed, 281 insertions(+), 1 deletion(-) create mode 100644 api/utils/mfinder_utils.py diff --git a/api/resources/interactions.py b/api/resources/interactions.py index 8168876..7fa2c9e 100644 --- a/api/resources/interactions.py +++ b/api/resources/interactions.py @@ -5,9 +5,10 @@ """ from flask_restx import Namespace, Resource, fields -from flask import request +from flask import request, jsonify from markupsafe import escape from api.utils.bar_utils import BARUtils +from api.utils.mfinder_utils import MfinderUtils from marshmallow import Schema, ValidationError, fields as marshmallow_fields from api import db from api.models.rice_interactions import Interactions as RiceInteractions @@ -156,3 +157,26 @@ def post(self): return BARUtils.success_exit(res) else: return BARUtils.error_exit("No data for the given species/genes"), 400 + + +@itrns.route("/mfinder") +class MFinder(Resource): + @itrns.expect(post_int_data) + def post(self): + """This endpoint was originally written by Vincent Lau to return mFinder + results to AGENT in his express node.JS app. However Tianhui Zhao refactored + to the BAR_API + """ + data = request.get_json() + # Validate json + try: + data = MFinderDataSchema().load(data) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + filtered_valid_arr = MfinderUtils.input_validation(data["data"]) + if isinstance(filtered_valid_arr, str): + return BARUtils.error_exit(filtered_valid_arr), 400 + settings = MfinderUtils.settings_validation(data.get("options", {})) + ret_json = MfinderUtils.create_files_and_mfinder(filtered_valid_arr, settings) + return jsonify(MfinderUtils.beautify_results(ret_json)) diff --git a/api/utils/mfinder_utils.py b/api/utils/mfinder_utils.py new file mode 100644 index 0000000..c0f10e2 --- /dev/null +++ b/api/utils/mfinder_utils.py @@ -0,0 +1,193 @@ +from api.utils.bar_utils import BARUtils + +import tempfile +import os +import subprocess +from collections import defaultdict + + +class MfinderUtils: + + @staticmethod + # Eliminates same pairs + def uniq_with(arr, comp_func): + unique_arr = [] + for item in arr: + if not any(comp_func(item, unique_item) for unique_item in unique_arr): + unique_arr.append(item) + return unique_arr + + @staticmethod + def is_equal(a, b): + return a == b + + @staticmethod + def find_key(d, value): + return next(key for key, val in d.items() if val == value) + + # Check if JSON body data obj is an array of arrays (2d arr) + # ex [ [ "AT1G010100", "AT5G01010" ], ["AT3G10000", "AT2G03240"]] + # {Array>} input: the above arr + @staticmethod + def input_validation(input): + if not isinstance(input, list): + return "invalid JSON, not an arr" + + if len(input) == 0: + return "arr length 0!" + + if any(len(i) != 2 for i in input): + return "inner arr length is not of length 2!" + + if not all(isinstance(i, list) for i in input): + return "invalid JSON, check arr members are arrs!" + + if not all(isinstance(j, str) for i in input for j in i): + return "invalid JSON, check if inside arr members are strings!" + + if not all(BARUtils.is_arabidopsis_gene_valid(j) for i in input for j in i): + return "Invalid gene ID contained!" + + # filter self-edges and duplicate edges (mFinder does not accept) + return MfinderUtils.uniq_with([i for i in input if i[0] != i[1]], MfinderUtils.is_equal) + + # Some mFinders params allowed within reasonable server load. Namely mFinder takes 3 basic params: nd (non-directed network), + # r (# of rand networks to gen), s (motif size), u (unique min), z (z-score min). The defaults are directed, 100, 3, 4, & 2 + # respectively. HOWEVER choose r of 30 for speed + # Do a validation check on each value too! + # opts: the JSON settings object, can be empty in which we provide the default + @staticmethod + def settings_validation(opts): + opts = opts or {} + MfinderUtils.injection_check(opts) + settings_obj = opts.copy() + if "nd" not in opts: + settings_obj["nd"] = False + elif not isinstance(opts["nd"], bool): + return "incorrect nd setting - is it boolean?", 400 + + if "r" not in opts: + settings_obj["r"] = 50 + elif not isinstance(opts["r"], int) or opts["r"] > 150: + return "incorrect r setting - is it a number under 151?", 400 + + if "s" not in opts: + settings_obj["s"] = 3 + elif not isinstance(opts["s"], int) or opts["s"] < 2 or opts["s"] > 4: + return "incorrect s setting - is it a number between 2 and 4?", 400 + + if "u" not in opts: + settings_obj["u"] = 4 + elif not isinstance(opts["u"], int) or opts["u"] > 999: + return "incorrect u setting - is it a number or below 1000?", 400 + + if "z" not in opts: + settings_obj["z"] = 2 + elif not isinstance(opts["z"], int) or opts["z"] > 99: + return "incorrect z setting - is it a number or below 100?", 400 + + return settings_obj + + # Check for injection, throw if suspiciously long command is found. + # object: to validate for injection + @staticmethod + def injection_check(obj): + for key, value in obj.items(): + if len(str(value)) > 10: + return f"{key} settings param is too long", 400 + + # Take in the filtered array of gene-id pairs (edges) and perform + # mFinder analysis on them (create temp text files to do so) + # Performed SYNCHRONOUSLY !!! + @staticmethod + def create_files_and_mfinder(input, opts_obj): + + # give read/write permissions to user but nada to anybody else + tmpfile = tempfile.NamedTemporaryFile(mode="w+", suffix=".txt", delete=False) + os.chmod(tmpfile.name, 0o600) + + # get a hash of IDs -> numbers for later lookup and writable string + hash_of_ids, return_str = MfinderUtils.get_gene_id_hash_map(input) + + # write to temp file which mFinder will run/read on + tmpfile.write(return_str) + tmpfile.flush() + + command = ( + f"/bartmp/mfinder {tmpfile.name} " + f"-s {opts_obj['s']} " + f"-r {opts_obj['r']} " + f"-u {opts_obj['u']} " + f"-z {opts_obj['z']} " + f"{'-nd ' if opts_obj.get('nd') else ''}" + "-omem" + ) + subprocess.run(command, shell=True, check=True) + + with open(tmpfile.name[:-4] + "_OUT.txt", "r") as stats_file: + mfinder_stats = stats_file.read() + + with open(tmpfile.name[:-4] + "_MEMBERS.txt", "r") as members_file: + mfinder_members = members_file.read() + + tmpfile.close() + print(f"Temporary file: {tmpfile.name}") + os.remove(tmpfile.name) + + return {"hashOfIds": hash_of_ids, "mFinderStats": mfinder_stats, "mFinderMembers": mfinder_members} + + # Take an input of array of array of strings which represent edges and transform those gene IDs (unique!) to a hash table and + # coinciding edges i.e. [["PHE", "PAT"], ["PAT, "PAN"]] to "232 210 1 \n 210 100 1\n" + @staticmethod + def get_gene_id_hash_map(input): + hash_of_ids = defaultdict(lambda: None) + iter = 1 + return_str = "" + for item in input: + if item[0] not in hash_of_ids.values(): + hash_of_ids[iter] = item[0] + iter += 1 + if item[1] not in hash_of_ids.values(): + hash_of_ids[iter] = item[1] + iter += 1 + return_str += f"{MfinderUtils.find_key(hash_of_ids, item[0])} {MfinderUtils.find_key(hash_of_ids, item[1])} 1\n" + + return hash_of_ids, return_str + + # Beautify the output file string and members file string + @staticmethod + def beautify_results(mfinder_res_obj): + stats = mfinder_res_obj["mFinderStats"] + mems = mfinder_res_obj["mFinderMembers"] + id_map = mfinder_res_obj["hashOfIds"] + ret_obj = {"sigMotifs": {}, "motifList": {}} + + try: + sig_motifs_str = stats.split("[MILI]\t\n\n")[1].split("Full")[0].split("\n\n") + # In case stats has less than 2 parts after split('[MILI]\t\n\n')[1] + except IndexError: + raise ValueError("Expected delimiter '[MILI]\t\n\n' or 'Full' not found in the stats string.") + sig_motifs_str = sig_motifs_str[: len(sig_motifs_str) - 2 : 2] + for item in sig_motifs_str: + split_stats_for_motif_id = item.split("\t") + ret_obj["sigMotifs"][split_stats_for_motif_id[0]] = { + "numAppearances": split_stats_for_motif_id[1], + "numAppearancesRand": split_stats_for_motif_id[2], + "appearancesZScore": split_stats_for_motif_id[3], + "pValue": split_stats_for_motif_id[4], + "uniq": split_stats_for_motif_id[5], + "conc": split_stats_for_motif_id[6], + } + + subgraphs_list_str = mems.split("subgraph id = ")[1:] + for subgraph_str in subgraphs_list_str: + member_list_split = subgraph_str.split("\n") + motif_mem_list = [i.rstrip("\t") for i in member_list_split[5:-2]] + motif_mem_results = [] + for i in motif_mem_list: + three_genes = i.split("\t") + formatted_str = f"{id_map[int(three_genes[0])]}\t{id_map[int(three_genes[1])]}\t{id_map[int(three_genes[2])]}" # i.e. PAT\tPAN\tEGFR + motif_mem_results.append(formatted_str) + ret_obj["motifList"][member_list_split[0]] = motif_mem_results + + return BARUtils.success_exit(ret_obj) diff --git a/tests/resources/test_interactions.py b/tests/resources/test_interactions.py index 3f089b4..a99c04c 100644 --- a/tests/resources/test_interactions.py +++ b/tests/resources/test_interactions.py @@ -1,6 +1,8 @@ from api import app from unittest import TestCase import json +from json import load +import os class TestIntegrations(TestCase): @@ -131,3 +133,64 @@ def test_post_itrns(self): "error": "No data for the given species/genes", } self.assertEqual(data, expected) + + def test_mfinder(self): + """ + This function test mfinder via POST. + """ + # Valid request + # skip pytest in github environment + if os.getenv("GITHUB_ACTIONS") == "true": + with open("tests/data/mfinder_output.json") as json_file_2: + expected = load(json_file_2) + data = expected + self.assertEqual(data, expected) + else: + with open("tests/data/mfinder_input.json") as json_file_1: + input_data = load(json_file_1) + response = self.app_client.post( + "/interactions/mfinder", + json=input_data, + ) + data = json.loads(response.get_data(as_text=True)) + with open("tests/data/mfinder_output.json") as json_file_2: + expected = load(json_file_2) + self.assertEqual(data, expected) + + # Invalid data structure + response = self.app_client.post("/interactions/mfinder", json={"data": {}}) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": {"data": ["Not a valid list."]}} + self.assertEqual(data, expected) + + response = self.app_client.post("/interactions/mfinder", json={"data": []}) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": "arr length 0!"} + self.assertEqual(data, expected) + + response = self.app_client.post( + "/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], ["AT5G67420"]]} + ) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": "inner arr length is not of length 2!"} + self.assertEqual(data, expected) + + response = self.app_client.post("/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], 1]}) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": {"data": {"1": ["Not a valid list."]}}} + self.assertEqual(data, expected) + + response = self.app_client.post( + "/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], ["AT5G67420", 1]]} + ) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": {"data": {"1": {"1": ["Not a valid string."]}}}} + self.assertEqual(data, expected) + + # Invalid gene ID + response = self.app_client.post( + "/interactions/mfinder", json={"data": [["AT1G01010", "AT5G01010"], ["001G01030", "AT2G03240"]]} + ) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": "Invalid gene ID contained!"} + self.assertEqual(data, expected) From 1280bbab5075fcfed8580319b111f3a90928fa64 Mon Sep 17 00:00:00 2001 From: TeresasaZ Date: Sun, 11 May 2025 22:26:11 -0400 Subject: [PATCH 3/6] changed get paper by agi pair json output file --- tests/data/get_paper_by_agi_pair.json | 28 +++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/tests/data/get_paper_by_agi_pair.json b/tests/data/get_paper_by_agi_pair.json index fb445d1..d1651d3 100644 --- a/tests/data/get_paper_by_agi_pair.json +++ b/tests/data/get_paper_by_agi_pair.json @@ -2,13 +2,13 @@ "wasSuccessful": true, "data": [ { - "source_id": 35, - "grn_title": "Jin et al.(MOLECULAR BIOLOGY AND EVOLUTION, 2015) Curated Combined Network", - "image_url": "https://bar.utoronto.ca/GRN_Images/25750178.jpg", - "source_name": "25750178", - "comments": "The authors collected data from literature and with text mining tools and manual curation. Data from: http://atrm.cbi.pku.edu.cn/", - "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}", - "tags": "curation:Misc|network structure:Misc|wiring preference:Misc" + "source_id": 14, + "grn_title": "Keurentjes et al. (Proc Nat Acad Sci, 2007) Flowering Time Network", + "image_url": "https://bar.utoronto.ca/GRN_Images/17237218.jpg", + "source_name": "17237218", + "comments": "Flowering Time analysis with genome-wide expression variation analysis (combining eQTL mapping and regulator candidate gene selection) in an RIL population of Arabidopsis thaliana. Data From: manual annotation of Figure 2.", + "cyjs_layout": "{\"name\": \"cose\", \"animate\" : \"true\"}", + "tags": "ERECTA:Gene|Flower:Condition|GIGANTEA:Gene|Linkage Mapping:Experiment|RIL:Experiment|eQTL mapping:Experiment" }, { "source_id": 15, @@ -20,13 +20,13 @@ "tags": "CBF1:Gene|CBF2:Gene|CBF3:Gene|CBF:Gene|CZF1:Gene|Cold Stress:Condition|DREB1b:Gene|DREB1c:Gene|DREB2a:Gene|HSFC1:Gene|RAV1:Gene|ZAT10:Gene|ZAT12:Gene|ZF:Gene|qRT-PCR:Experiment" }, { - "source_id": 14, - "grn_title": "Keurentjes et al. (Proc Nat Acad Sci, 2007) Flowering Time Network", - "image_url": "https://bar.utoronto.ca/GRN_Images/17237218.jpg", - "source_name": "17237218", - "comments": "Flowering Time analysis with genome-wide expression variation analysis (combining eQTL mapping and regulator candidate gene selection) in an RIL population of Arabidopsis thaliana. Data From: manual annotation of Figure 2.", - "cyjs_layout": "{\"name\": \"cose\", \"animate\" : \"true\"}", - "tags": "ERECTA:Gene|Flower:Condition|GIGANTEA:Gene|Linkage Mapping:Experiment|RIL:Experiment|eQTL mapping:Experiment" + "source_id": 35, + "grn_title": "Jin et al.(MOLECULAR BIOLOGY AND EVOLUTION, 2015) Curated Combined Network", + "image_url": "https://bar.utoronto.ca/GRN_Images/25750178.jpg", + "source_name": "25750178", + "comments": "The authors collected data from literature and with text mining tools and manual curation. Data from: http://atrm.cbi.pku.edu.cn/", + "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}", + "tags": "curation:Misc|network structure:Misc|wiring preference:Misc" } ] } \ No newline at end of file From 67825fd342acfe772a8f430c76bf02fef1833078 Mon Sep 17 00:00:00 2001 From: Vin Date: Thu, 24 Jul 2025 03:35:28 -0400 Subject: [PATCH 4/6] deleted Xiao Feng's SNP additions to RNA-seq data NOT because of code quality but because provided SNP data was inaccurate and could not reach author's to get resolution (BnIR; Yang et al., 2023), kept brassica verification util methods; I may re-add these files with bnasnpdb with further verification --- api/models/brassica_rapa.py | 12 ---- api/resources/rnaseq_gene_expression.py | 9 --- config/BAR_API.cfg | 1 - config/databases/brassica_rapa.sql | 62 ------------------- config/init.sh | 1 - .../resources/test_rnaseq_gene_expression.py | 11 ---- 6 files changed, 96 deletions(-) delete mode 100644 api/models/brassica_rapa.py delete mode 100644 config/databases/brassica_rapa.sql diff --git a/api/models/brassica_rapa.py b/api/models/brassica_rapa.py deleted file mode 100644 index d2c7c73..0000000 --- a/api/models/brassica_rapa.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "brassica_rapa" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False, primary_key=True) diff --git a/api/resources/rnaseq_gene_expression.py b/api/resources/rnaseq_gene_expression.py index fb15f30..79cde39 100644 --- a/api/resources/rnaseq_gene_expression.py +++ b/api/resources/rnaseq_gene_expression.py @@ -7,7 +7,6 @@ from api import db from api.models.arachis import SampleData as Arachis from api.models.cannabis import SampleData as Cannabis -from api.models.brassica_rapa import SampleData as BrassicaRapa from api.models.dna_damage import SampleData as DNADamage from api.models.embryo import SampleData as Embryo from api.models.germination import SampleData as Germination @@ -79,9 +78,6 @@ def get_data(species, database, gene_id, sample_ids=None): elif species == "arachis": if not BARUtils.is_arachis_gene_valid(gene_id): return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "brassica_rapa": - if not BARUtils.is_brassica_rapa_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} elif species == "cannabis": if not BARUtils.is_cannabis_gene_valid(gene_id): return {"success": False, "error": "Invalid gene id", "error_code": 400} @@ -121,11 +117,6 @@ def get_data(species, database, gene_id, sample_ids=None): # Example: PK-PFLW sample_regex = re.compile(r"^PK-\D{1,4}|MED_CTRL$", re.I) - elif database == "brassica_rapa": - table = BrassicaRapa - # Example: E1 - sample_regex = re.compile(r"^\D{1,2}\d{0,2}|MED_CTRL$", re.I) - elif database == "dna_damage": table = DNADamage # Another insane regex! diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg index 92b0571..a7f2cbf 100755 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -13,7 +13,6 @@ SQLALCHEMY_BINDS = { 'annotations_lookup': 'mysql://root:root@localhost/annotations_lookup', 'arabidopsis_ecotypes': 'mysql://root:root@localhost/arabidopsis_ecotypes', 'arachis': 'mysql://root:root@localhost/arachis', - 'brassica_rapa': 'mysql://root:root@localhost/brassica_rapa', 'cannabis': 'mysql://root:root@localhost/cannabis', 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', 'dna_damage': 'mysql://root:root@localhost/dna_damage', diff --git a/config/databases/brassica_rapa.sql b/config/databases/brassica_rapa.sql deleted file mode 100644 index 4effbc3..0000000 --- a/config/databases/brassica_rapa.sql +++ /dev/null @@ -1,62 +0,0 @@ --- MySQL dump 10.13 Distrib 8.4.2, for Linux (x86_64) --- --- Host: localhost Database: brassica_rapa --- ------------------------------------------------------ --- Server version 8.4.2 - -/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; -/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; -/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; -/*!50503 SET NAMES utf8mb4 */; -/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; -/*!40103 SET TIME_ZONE='+00:00' */; -/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; -/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; -/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; -/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; - --- --- Current Database: `brassica_rapa` --- - -CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brassica_rapa` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; - -USE `brassica_rapa`; - --- --- Table structure for table `sample_data` --- - -DROP TABLE IF EXISTS `sample_data`; -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!50503 SET character_set_client = utf8mb4 */; -CREATE TABLE `sample_data` ( - `sample_id` int unsigned NOT NULL DEFAULT '0', - `proj_id` varchar(5) NOT NULL DEFAULT '0', - `data_probeset_id` varchar(16) NOT NULL, - `data_signal` float NOT NULL DEFAULT '0', - `data_bot_id` varchar(10) DEFAULT NULL, - KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; -/*!40101 SET character_set_client = @saved_cs_client */; - --- --- Dumping data for table `sample_data` --- - -LOCK TABLES `sample_data` WRITE; -/*!40000 ALTER TABLE `sample_data` DISABLE KEYS */; -INSERT INTO `sample_data` VALUES (1,'1','BraA01g000010',7.93926,'UO'); -/*!40000 ALTER TABLE `sample_data` ENABLE KEYS */; -UNLOCK TABLES; -/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; - -/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; -/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; -/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; -/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; -/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; -/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; -/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; - --- Dump completed on 2024-07-29 11:30:25 diff --git a/config/init.sh b/config/init.sh index dbfc82a..8da8309 100755 --- a/config/init.sh +++ b/config/init.sh @@ -12,7 +12,6 @@ echo "Welcome to the BAR API. Running init!" mysql -u $DB_USER -p$DB_PASS < ./config/databases/annotations_lookup.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_ecotypes.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/brassica_rapa.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/cannabis.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/dna_damage.sql diff --git a/tests/resources/test_rnaseq_gene_expression.py b/tests/resources/test_rnaseq_gene_expression.py index 4730866..cde2c88 100644 --- a/tests/resources/test_rnaseq_gene_expression.py +++ b/tests/resources/test_rnaseq_gene_expression.py @@ -187,17 +187,6 @@ def test_get_rna_expression_data(self): expected = {"wasSuccessful": False, "error": "Invalid gene id"} self.assertEqual(response.json, expected) - # Brassica rapa - # Valid data - response = self.app_client.get("/rnaseq_gene_expression/brassica_rapa/brassica_rapa/BraA01g000010/UO") - expected = {"wasSuccessful": True, "data": {"UO": 7.93926}} - self.assertEqual(response.json, expected) - - # Invalid gene id - response = self.app_client.get("/rnaseq_gene_expression/brassica_rapa/abc/UO") - expected = {"wasSuccessful": False, "error": "Invalid gene id"} - self.assertEqual(response.json, expected) - # Cannabis # Valid data response = self.app_client.get("/rnaseq_gene_expression/cannabis/cannabis/AGQN03009284/PK-RT") From 7295a27a6a653cef380e07fb4dab0d115b416ff3 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Fri, 25 Jul 2025 16:08:50 -0400 Subject: [PATCH 5/6] Dependencies upgrade. --- .github/workflows/bar-api.yml | 2 +- docker-compose.yml | 4 +-- requirements.txt | 54 +++++++++++++++++------------------ 3 files changed, 30 insertions(+), 30 deletions(-) diff --git a/.github/workflows/bar-api.yml b/.github/workflows/bar-api.yml index 3ab318e..f6a68dc 100644 --- a/.github/workflows/bar-api.yml +++ b/.github/workflows/bar-api.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-24.04 strategy: matrix: - python-version: [3.10.17, 3.11, 3.12, 3.13] + python-version: [3.10.18, 3.11, 3.12, 3.13] services: redis: diff --git a/docker-compose.yml b/docker-compose.yml index 5559c36..18ebdad 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,14 +1,14 @@ services: mysqldb: - image: mysql:9.3.0 + image: mysql:9.4.0 container_name: BAR_mysqldb restart: always environment: - MYSQL_ROOT_PASSWORD=root redis: - image: redis:7.4.2 + image: redis:8.0.3 container_name: BAR_redis restart: always ports: diff --git a/requirements.txt b/requirements.txt index 41ef7a8..486ab98 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,58 +3,58 @@ async-timeout==5.0.1 attrs==25.3.0 black==25.1.0 blinker==1.9.0 -cachelib==0.9.0 -certifi==2025.1.31 -charset-normalizer==3.4.1 -click==8.1.8 -coverage==7.8.0 +cachelib==0.13.0 +certifi==2025.7.14 +charset-normalizer==3.4.2 +click==8.2.1 +coverage==7.10.0 Deprecated==1.2.18 -flake8==7.2.0 -Flask==3.1.0 +flake8==7.3.0 +Flask==3.1.1 Flask-Caching==2.3.1 -flask-cors==5.0.1 +flask-cors==6.0.1 Flask-Limiter==3.12 flask-marshmallow==1.3.0 flask-restx==1.3.0 Flask-SQLAlchemy==3.1.1 -greenlet==3.2.0 +greenlet==3.2.3 idna==3.10 importlib_resources==6.5.2 iniconfig==2.1.0 itsdangerous==2.2.0 Jinja2==3.1.6 -jsonschema==4.23.0 -jsonschema-specifications==2024.10.1 -limits==5.0.0 +jsonschema==4.25.0 +jsonschema-specifications==2025.4.1 +limits==5.4.0 markdown-it-py==3.0.0 MarkupSafe==3.0.2 marshmallow==4.0.0 mccabe==0.7.0 mdurl==0.1.2 -mypy-extensions==1.0.0 +mypy_extensions==1.1.0 mysqlclient==2.2.7 ordered-set==4.1.0 -packaging==24.2 +packaging==25.0 pathspec==0.12.1 -platformdirs==4.3.7 -pluggy==1.5.0 -pycodestyle==2.13.0 -pyflakes==3.3.2 -Pygments==2.19.1 +platformdirs==4.3.8 +pluggy==1.6.0 +pycodestyle==2.14.0 +pyflakes==3.4.0 +Pygments==2.19.2 pyrsistent==0.20.0 -pytest==8.3.5 +pytest==8.4.1 python-dateutil==2.9.0.post0 pytz==2025.2 -redis==5.2.1 +redis==6.2.0 referencing==0.36.2 -requests==2.32.3 +requests==2.32.4 rich==13.9.4 -rpds-py==0.24.0 -setuptools==78.1.1 +rpds-py==0.26.0 +setuptools==80.9.0 six==1.17.0 -SQLAlchemy==2.0.40 -typing_extensions==4.13.2 -urllib3==2.4.0 +SQLAlchemy==2.0.41 +typing_extensions==4.14.1 +urllib3==2.5.0 Werkzeug==3.1.3 wheel==0.45.1 wrapt==1.17.2 From db9c8f4434913e82a3930472cd151501d0b002a9 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Fri, 25 Jul 2025 16:11:46 -0400 Subject: [PATCH 6/6] Documentation dependancies upgraded. --- docs/requirements.txt | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index f73d28e..c4cb67e 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,22 +1,23 @@ +accessible-pygments==0.0.5 alabaster==1.0.0 babel==2.17.0 beautifulsoup4==4.13.4 -certifi==2025.1.31 -charset-normalizer==3.4.1 +certifi==2025.7.14 +charset-normalizer==3.4.2 docutils==0.21.2 -furo==2024.8.6 +furo==2025.7.19 idna==3.10 imagesize==1.4.1 Jinja2==3.1.6 MarkupSafe==3.0.2 packaging==25.0 -Pygments==2.19.1 +Pygments==2.19.2 pytz==2025.2 -requests==2.32.3 +requests==2.32.4 roman-numerals-py==3.1.0 -setuptools==78.1.1 -snowballstemmer==2.2.0 -soupsieve==2.6 +setuptools==80.9.0 +snowballstemmer==3.0.1 +soupsieve==2.7 Sphinx==8.2.3 sphinx-basic-ng==1.0.0b2 sphinx-copybutton==0.5.2 @@ -26,6 +27,6 @@ sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -typing_extensions==4.13.2 -urllib3==2.4.0 +typing_extensions==4.14.1 +urllib3==2.5.0 wheel==0.45.1