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Merge pull request #55 from genomic-medicine-sweden/doodads
Search improvments and refactoring
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| #!/usr/bin/env python | ||
| """ | ||
| Module for interactive usage. | ||
| """ | ||
| import os | ||
| import sys | ||
| import time | ||
|
|
||
| from pathlib import Path | ||
|
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| from NGPIris import log, TIMESTAMP | ||
| from NGPIris.preproc import preproc | ||
|
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| class HCPInteracter: | ||
| def __init__(self, hcpmanager): | ||
| self.hcpm = hcpmanager | ||
|
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| def delete_interactive(self,query,force=False): | ||
| objs = self.hcpm.search_objects(query) # Get object with query | ||
| if len(objs) < 1: | ||
| log.info(f"File: {query} does not exist on {self.hcpm.bucket.name}") | ||
| else: | ||
| hits = list() | ||
| for obj in objs: | ||
| hits.append(obj.key) | ||
| log.info(f"Found {len(objs)} entries matching query '{query}':") | ||
| log.info(f"{hits}") | ||
| for obj in objs: | ||
| if not force: | ||
| sys.stdout.write(f"You are about to delete the file {obj.key} " \ | ||
| f"on {self.hcpm.bucket.name}, are you sure? [Y/N/Q]?\n") | ||
| sys.stdout.flush() | ||
| answer = sys.stdin.readline() | ||
| if answer[0].lower() == "y": | ||
| self.hcpm.delete_object(obj) # Delete file. | ||
| time.sleep(2) | ||
| log.info(f"Deleted file {obj.key} ") | ||
| elif answer[0].lower() == "q": | ||
| break | ||
| else: | ||
| log.info(f"Skipped deleting {obj.key} ") | ||
| elif force: | ||
| self.hcpm.delete_object(obj) # Delete file. | ||
| time.sleep(2) | ||
| log.info(f"Deleted file {obj.key} ") | ||
|
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||
|
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| def download_interactive(self, query, destination="", force=False, silent=False): | ||
| found_objs = self.hcpm.search_objects(query) | ||
|
|
||
| #Defaults destination to input name | ||
| if destination == "": | ||
| destination = os.path.basename(query) | ||
| #If destination is folder. Default file name to input name | ||
| elif destination[-1] in ["/","\\"]: | ||
| destination = os.path.join(destination, os.path.basename(query)) | ||
|
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||
|
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| if found_objs is None or len(found_objs) == 0: | ||
| log.info(f"File: {query} does not exist on {self.hcpm.bucket.name}") | ||
|
|
||
| elif len(found_objs) == 1: | ||
| obj = self.hcpm.get_object(query) # Get object with key. | ||
| self.hcpm.download_file(obj, destination, force=force, callback=(not silent)) # Downloads file. | ||
|
|
||
| elif len(found_objs) > 1: | ||
| for obj in found_objs: | ||
| log.info(f"Found {len(found_objs)} files matching query") | ||
| log.info(f"Download {obj}? [Y/N]") | ||
| sys.stdout.write(f"[--] Do you wish to download {obj.key} on {self.hcpm.bucket.name}? [Y/N]?\n") | ||
| sys.stdout.flush() | ||
| answer = sys.stdin.readline() | ||
| if answer[0].lower() == "y": | ||
| obj = self.hcpm.get_object(query) # Get object with key. | ||
| #Default destination name to key | ||
| if destination == "": | ||
| destination = obj.key | ||
| #If destination is folder. Default file name to obj.key | ||
| elif destination[-1] in ["/","\\"]: | ||
| destination = os.path.join(destination, obj.key) | ||
|
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| self.hcpm.download_file(obj, destination, force=force, callback=(not silent)) # Downloads file. | ||
| #log.info(f"Downloaded {obj.key}" | ||
|
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| def upload_interactive(self, source, destination="", fastq_only=False, metadata="", silent=False): | ||
| file_lst = [] | ||
| ###Sets destinations | ||
| #Defaults destination to source name | ||
| if destination == "": | ||
| destination = os.path.basename(source) | ||
| #If destination is folder. Default file name to source name | ||
| elif destination[-1] in ["/","\\"]: | ||
| destination = os.path.join(destination, os.path.basename(source)) | ||
|
|
||
| ###Verify fastq contents and metadata existence | ||
| if os.path.isdir(source) and fastq_only: | ||
| [file_lst, mdfile]=preproc.verify_upload_folder(source, metadata=metadata) | ||
| elif os.path.isdir(source): | ||
| [file_lst, mdfile]=preproc.folder_to_list(source, metadata=metadata) | ||
| elif fastq_only: | ||
| [file_lst, mdfile]=preproc.verify_upload_file(source, metadata=metadata) | ||
| if fastq_only and file_lst == []: | ||
| log.error(f"{source} could not be uploaded to NGPr. Try using an atypical (-a) upload") | ||
|
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||
| if os.path.isdir(source): | ||
| for file_pg in file_lst: | ||
| self.hcpm.upload_file(file_pg, destination, callback=(not silent)) | ||
| #time.sleep(2) | ||
| log.info(f"Uploaded: {file_pg}") | ||
| else: | ||
| self.hcpm.upload_file(file_lst, destination, callback=(not silent)) | ||
| #time.sleep(2) | ||
| log.info(f"Uploaded: {file_lst}") | ||
|
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||
| #Upload metadata | ||
| #dstfld = Path(destination) | ||
| #dstfld = dstfld.parent | ||
| #if dstfld.parts == (): | ||
| # dstfld = "" | ||
| #meta_fn = Path(mdfile).name | ||
| #ctx['hcpm'].upload_file(mdfile, os.path.join(dstfld, meta_fn), callback=(not silent)) |
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