hfp_cronology_awsbatch: 0.2.0/bin/microreact

comparison 0.2.0/bin/microreact_post.py @ 0:9e8b1c747a6a draft default tip

planemo upload

author	galaxytrakr
date	Fri, 29 May 2026 13:32:17 +0000
parents
children

comparison

equal deleted inserted replaced

--1:000000000000
+:9e8b1c747a6a
+#!/usr/bin/env python3
+import argparse
+import base64
+import csv
+import inspect
+import json
+import logging
+import os
+import pprint
+import secrets
+import string
+import requests
+from requests.packages import urllib3
+# Multiple inheritence for pretty printing of help text.
+class MultiArgFormatClasses(
+argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter
+):
+pass
+# Basic checks
+def check_file_extension(folder_path) -> os.PathLike:
+if not os.path.isdir(folder_path):
+logging.error(f"The provided path: '{folder_path}' is not a valid directory.")
+exit(1)
+tree_and_metadata_files = [
+file
+for file in os.listdir(folder_path)
+if file.endswith(".nwk") or file.endswith(".csv")
+]
+if len(tree_and_metadata_files) != 2:
+logging.error(
+"We need exactly one .nwk file and one metadata "
++ "file in CSV (.csv) format."
+)
+exit(1)
+for file in tree_and_metadata_files:
+file_path = os.path.join(folder_path, file)
+if os.path.isfile(file_path):
+extension = os.path.splitext(file)
+if extension[1] not in [".csv", ".nwk"]:
+logging.error(f"{file} is not the correct extension: .nwk or .csv")
+exit(1)
+if file_path.endswith(".nwk"):
+nwk_file = file_path
+return nwk_file
+# Checking the CSV file
+def uppercase_headers(folder_path) -> list:
+for filename in os.listdir(folder_path):
+if filename.endswith(".csv"):
+filepath = os.path.join(folder_path, filename)
+with open(filepath, "r", newline="") as file:
+reader = csv.reader(file)
+headers = next(reader)
+if all(header.isupper() for header in headers):
+pass
+else:
+headers = [header.upper() for header in headers]
+with open(filepath, "w", newline="") as file:
+writer = csv.writer(file)
+writer.writerow(headers)
+for row in reader:
+writer.writerow(row)
+file.close()
+file.close()
+return headers
+def check_csv(folder_path) -> os.PathLike:
+for filename in os.listdir(folder_path):
+if filename.endswith(".csv"):
+filepath = os.path.join(folder_path, filename)
+with open(filepath, "r", newline="") as file:
+reader = csv.reader(file)
+# Checking for headers and first column named "ID"
+headers = next(reader, None)
+if headers is None:
+logging.error("Error: CSV file has no column headers.")
+exit(1)
+if headers[0] != "ID":
+logging.error("Error: First column header is not 'ID'.")
+exit(1)
+# Check if all values in "ID" column are unique
+col_values = set()
+for row in reader:
+id_value = row[0].strip()
+if id_value in col_values:
+logging.error(f"Duplicate ID found: {id_value}")
+exit(1)
+col_values.add(id_value)
+# Checking that columns are equal across all rows
+num_columns = None
+for i, row in enumerate(reader):
+if num_columns is None:
+num_columns = len(row)
+elif len(row) != num_columns:
+logging.error(
+f"Error: Unequal number of columns in row {i + 1}"
+)
+exit(1)
+file.close()
+return filepath
+# Encode files to base64 for uploading
+def encode_file(file) -> str:
+with open(file, "r") as f:
+file = f.read()
+file_64 = base64.b64encode(file.encode()).decode()
+f.close()
+return file_64
+# Creating the .microreact JSON file
+def gen_ran_string(length=4) -> str:
+letters = string.ascii_letters
+return "".join(secrets.choice(letters) for i in range(length))
+# Microreact JSON template
+def create_json(
+metadata_csv, tree_path, metadata_64, tree_64, ProjectName, folder_path
+) -> os.PathLike:
+file_csv = gen_ran_string()
+file_tree = gen_ran_string()
+csv_size = os.path.getsize(metadata_csv)
+tree_size = os.path.getsize(tree_path)
+headers = uppercase_headers(folder_path)
+columns = [{"field": "ID", "fixed": False}]
+for header in headers[1:]:
+columns.append({"field": header, "fixed": False})
+microreact_data = {
+"charts": {},
+"datasets": {
+"dataset-1": {"id": "dataset-1", "file": file_csv, "idFieldName": "ID"}
+},
+"files": {
+file_csv: {
+"blob": f"data:text/csv;base64,{metadata_64}",
+"format": "text/csv",
+"id": file_csv,
+"name": os.path.basename(metadata_csv),
+"size": csv_size,
+"type": "data",
+},
+file_tree: {
+"blob": f"data:application/octet-stream;base64,{tree_64}",
+"format": "text/x-nh",
+"id": file_tree,
+"name": os.path.basename(tree_path),
+"size": tree_size,
+"type": "tree",
+},
+},
+"filters": {
+"dataFilters": [],
+"chartFilters": [],
+"searchOperator": "includes",
+"searchValue": "",
+"selection": [],
+"selectionBreakdownField": None,
+},
+"maps": {},
+"meta": {"name": ProjectName},
+"trees": {
+"tree-1": {
+"alignLabels": False,
+"blockHeaderFontSize": 13,
+"blockPadding": 0,
+"blocks": ["MLST_SEQUENCE_TYPE", "ISOLATION_SOURCE"],
+"blockSize": 14,
+"branchLengthsDigits": 4,
+"controls": True,
+"fontSize": 16,
+"hideOrphanDataRows": False,
+"ids": None,
+"internalLabelsFilterRange": [0, 100],
+"internalLabelsFontSize": 13,
+"lasso": False,
+"nodeSize": 14,
+"path": None,
+"roundBranchLengths": True,
+"scaleLineAlpha": True,
+"showBlockHeaders": True,
+"showBlockLabels": False,
+"showBranchLengths": False,
+"showEdges": True,
+"showInternalLabels": False,
+"showLabels": True,
+"showLeafLabels": True,
+"showPiecharts": True,
+"showShapeBorders": True,
+"showShapes": True,
+"styleLeafLabels": False,
+"styleNodeEdges": False,
+"subtreeIds": None,
+"type": "rc",
+"title": "Tree",
+"labelField": "ID",
+"file": file_tree,
+}
+},
+"tables": {
+"table-1": {
+"displayMode": "cosy",
+"hideUnselected": False,
+"title": "Metadata",
+"paneId": "table-1",
+"columns": columns,
+"file": file_csv,
+}
+},
+"views": [],
+"schema": "https://microreact.org/schema/v1.json",
+}
+micro_path = os.path.join(os.getcwd(), ProjectName + ".microreact")
+with open(micro_path, "w") as microreact_file:
+json.dump(microreact_data, microreact_file, indent=2)
+microreact_file.close()
+microreact_file.close()
+return micro_path
+# Main
+def main() -> None:
+"""
+Will take as input a folder containing 2 files, a tree file and a metadata CSV file
+and upload it to a new project named "Cronology" and get a publicly shareable link from
+microreact.org once the upload is successful
+"""
+# Debug print.
+ppp = pprint.PrettyPrinter(width=55)
+# Set logging.
+logging.basicConfig(
+format="\n"
++ "=" * 55
++ "\n%(asctime)s - %(levelname)s\n"
++ "=" * 55
++ "\n%(message)s\n\n",
+level=logging.DEBUG,
+)
+# Turn off SSL warnings
+urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
+prog_name = os.path.basename(inspect.stack()[0].filename)
+parser = argparse.ArgumentParser(
+prog=prog_name, description=main.__doc__, formatter_class=MultiArgFormatClasses
+)
+# Add required arguments
+required = parser.add_argument_group("required arguments")
+required.add_argument(
+"-dir",
+dest="dir",
+default=False,
+required=True,
+help="UNIX path to diretory containing the tree and all other\ndataset and annotation files."
++ " Your tree file and metadata files must\nhave the extension .nwk and .csv",
+)
+required.add_argument(
+"-atp",
+dest="AccessTokenPath",
+default=False,
+required=True,
+help="The path to your API Access Token needed for uploading.\n"
++ "File must be a .txt file.",
+)
+parser.add_argument(
+"-name",
+dest="ProjectName",
+default="Project",
+required=False,
+help="Name for the project you want to upload",
+)
+# Define defaults
+args = parser.parse_args()
+upload_url = "https://microreact.org/api/projects/create"
+folder_path = args.dir
+ProjectName = args.ProjectName
+micro_url_info_path = os.path.join(os.getcwd(), "microreact_url.txt")
+with open(args.AccessTokenPath, "r") as token:
+atp = token.readline()
+token.close()
+tree_path = check_file_extension(folder_path)
+metadata_csv = check_csv(folder_path)
+metadata_64 = encode_file(metadata_csv)
+tree_64 = encode_file(tree_path)
+# Prepare the data to be sent in the request
+micro_path = create_json(
+metadata_csv, tree_path, metadata_64, tree_64, ProjectName, folder_path
+)
+f = open(micro_path)
+data = json.load(f)
+f.close()
+# Additional parameters, including the MicroReact API key
+headers = {"Content-type": "application/json; charset=UTF-8", "Access-Token": atp}
+# Make the POST request to Microreact
+r = requests.post(upload_url, json=data, headers=headers, verify=False)
+if not r.ok:
+if r.status_code == 400:
+logging.error("Microreact API call failed with response " + r.text + "\n")
+else:
+logging.error(
+"Microreact API call failed with unknown response code "
++ str(r.status_code)
++ "\n"
+)
+exit(1)
+if r.status_code == 200:
+r_json = json.loads(r.text)
+with open(micro_url_info_path, "w") as out_fh:
+out_fh.write(
+f"Uploaded successfully!\n\nYour project URL:\n{r_json['url']}"
+)
+out_fh.close()
+if __name__ == "__main__":
+main()

Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/bin/microreact_post.py @ 0:9e8b1c747a6a draft default tip