Mercurial > repos > rhohensinner > galaxy_irods_interface
comparison main.py @ 3:d2be2eb8350f draft
"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
| author | rhohensinner |
|---|---|
| date | Mon, 19 Jul 2021 13:11:45 +0000 |
| parents | 0641ea2f75b1 |
| children |
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| 2:0641ea2f75b1 | 3:d2be2eb8350f |
|---|---|
| 2 ___created___ = "04.02.2021" | 2 ___created___ = "04.02.2021" |
| 3 ___last_modified___ = "20.05.2021" | 3 ___last_modified___ = "20.05.2021" |
| 4 | 4 |
| 5 # general imports | 5 # general imports |
| 6 import os, sys, json | 6 import os, sys, json |
| 7 import irods_upload | |
| 8 | 7 |
| 9 from shutil import copyfile | 8 from shutil import copyfile |
| 10 from datetime import datetime | 9 from datetime import datetime |
| 11 | 10 |
| 12 # irods-client imports | 11 # irods-client imports |
| 22 file_path_list = [] | 21 file_path_list = [] |
| 23 selected_file = "" | 22 selected_file = "" |
| 24 session_success = False | 23 session_success = False |
| 25 selection_success = False | 24 selection_success = False |
| 26 iRODSCredentials = {"host": "", "port": "", "user": "", "pw": "", "zone": ""} | 25 iRODSCredentials = {"host": "", "port": "", "user": "", "pw": "", "zone": ""} |
| 26 python_path = [] | |
| 27 | 27 |
| 28 | 28 |
| 29 ######################################################################################################################## | 29 ######################################################################################################################## |
| 30 # Main function of the iRODS tools | 30 # Main function of the iRODS tools |
| 31 # | 31 # |
| 438 python_command = params["galaxy_root"] + "/tools/data_source/upload.py" | 438 python_command = params["galaxy_root"] + "/tools/data_source/upload.py" |
| 439 arg1 = params["galaxy_root"] | 439 arg1 = params["galaxy_root"] |
| 440 arg2 = params["galaxy_datatypes"] | 440 arg2 = params["galaxy_datatypes"] |
| 441 arg3 = os.path.abspath(fileParams.name) | 441 arg3 = os.path.abspath(fileParams.name) |
| 442 arg4 = params["job_id"] + ":" + params["out_dir"] + ":" + params["out_file"] | 442 arg4 = params["job_id"] + ":" + params["out_dir"] + ":" + params["out_file"] |
| 443 arg5 = params["galaxy_root"] + "/lib/galaxy" | |
| 443 | 444 |
| 444 # copy sample registry.xml to working directory | 445 # copy sample registry.xml to working directory |
| 445 copyfile(reg_file, params["galaxy_datatypes"]) | 446 copyfile(reg_file, params["galaxy_datatypes"]) |
| 446 | 447 |
| 447 # activate environment for new process call and call the python upload command either both with | 448 # activate environment for new process call and call the python upload command either both with |
| 458 if upload_file != "": | 459 if upload_file != "": |
| 459 break | 460 break |
| 460 if upload_file != "": | 461 if upload_file != "": |
| 461 break | 462 break |
| 462 | 463 |
| 463 os.system("python " + upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4) | 464 global python_path |
| 465 python_path = sys.path | |
| 466 os.system(params["galaxy_root"] + "/.venv/bin/python " + upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4) | |
| 464 # close connection | 467 # close connection |
| 465 session.cleanup() | 468 session.cleanup() |
| 466 # -------------------------------------------------------------------------------------------------------------------- # | 469 # -------------------------------------------------------------------------------------------------------------------- # |
| 467 | 470 |
| 468 | 471 |