pybiolib 1.2.1022__py3-none-any.whl → 1.2.1030__py3-none-any.whl

biolib/_internal/templates/gui_template/Dockerfile

@@ -23,4 +23,4 @@ COPY run.py .
 
 RUN mkdir output
 
-COPY --from=gui_builder /home/biolib/dist/index.html gui.html
+COPY --from=gui_builder /home/biolib/dist/index.html result.html

biolib/_internal/templates/init_template/.biolib/config.yml

@@ -10,6 +10,7 @@ modules:
         output_files:
             - COPY /home/biolib/output/ /
 
+BIOLIB_REPLACE_GUI_CONFIG
 arguments:
     -
         key: --input

biolib/_internal/templates/init_template/run.sh

@@ -1,3 +1,4 @@
 #!/bin/bash
 set -e
+BIOLIB_REPLACE_GUI_MV_COMMAND
 python3 run.py "$@"

biolib/biolib_api_client/app_types.py

@@ -68,6 +68,12 @@ class LargeFileSystemMapping(TypedDict):
     uuid: str
 
 
+class PortMapping(TypedDict):
+    from_port: int
+    to_port: int
+    mapping_priority: int
+
+
 class _Module(TypedDict):
     command: str
     environment: Literal['biolib-app', 'biolib-custom', 'biolib-ecr']
@@ -78,6 +84,7 @@ class _Module(TypedDict):
     large_file_systems: List[LargeFileSystemMapping]
     name: str
     output_files_mappings: List[FilesMapping]
+    port_mappings: List[PortMapping]
     source_files_mappings: List[FilesMapping]
     working_directory: str
 

biolib/cli/init.py

@@ -98,6 +98,12 @@ def init() -> None:
                         )
                         new_content = new_content.replace('BIOLIB_REPLACE_APP_NAME', replace_app_name)
 
+                        gui_config = "main_output_file: '/result.html'\n" if include_gui else ''
+                        new_content = new_content.replace('BIOLIB_REPLACE_GUI_CONFIG\n', gui_config)
+
+                        gui_mv_command = 'mv result.html output/result.html\n' if include_gui else ''
+                        new_content = new_content.replace('BIOLIB_REPLACE_GUI_MV_COMMAND\n', gui_mv_command)
+
                         with open(destination_file, 'w') as f:
                             f.write(new_content)
                     except UnicodeDecodeError:

biolib/compute_node/job_worker/job_worker.py

@@ -250,6 +250,13 @@ class JobWorker:
         job = job_wrapper['job']
         self._jobs[job['public_id']] = job
 
+        app_version = job['app_version']
+        modules = app_version.get('modules', [])
+        port_mappings = []
+        for module in modules:
+            port_mappings.extend(module.get('port_mappings', []))
+        logger_no_user_data.debug(f"Port mappings for job {job['public_id']}: {port_mappings}")
+
         if job['app_version'].get('modules') is not None and BiolibDockerClient.is_docker_running():
             self._start_network_and_remote_host_proxies(job)
 

{pybiolib-1.2.1022.dist-info → pybiolib-1.2.1030.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.1022
+Version: 1.2.1030
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.1022.dist-info → pybiolib-1.2.1030.dist-info}/RECORD

@@ -29,20 +29,20 @@ biolib/_internal/templates/copilot_template/.github/prompts/biolib_onboard_repo.
 biolib/_internal/templates/copilot_template/.github/prompts/biolib_run_apps.prompt.md,sha256=-t1bmGr3zEFa6lKHaLcI98yq4Sg1TCMW8xbelNSHaOA,696
 biolib/_internal/templates/gui_template/.yarnrc.yml,sha256=Rz5t74b8A2OBIODAHQyLurCVZ3JWRg-k6nY-XUaX8nA,25
 biolib/_internal/templates/gui_template/App.tsx,sha256=hh_r7P4Pn4HLaE8C1PoECawd81yoC4MfWPu7Op02kWg,509
-biolib/_internal/templates/gui_template/Dockerfile,sha256=8-V5rcram1Ip21rMKKgzAKEKNiYkLJzdY42gy2jXrlg,446
+biolib/_internal/templates/gui_template/Dockerfile,sha256=C_2vCYPu8JtJRhwviwwI7jq8767G7nGE8naYvNzej4E,449
 biolib/_internal/templates/gui_template/index.css,sha256=WYds1xQY2of84ebHhRW9ummbw0Bg9N-EyfmBzJKigck,70
 biolib/_internal/templates/gui_template/index.html,sha256=EM5xzJ9CsJalgzL-jLNkAoP4tgosw0WYExcH5W6DOs8,403
 biolib/_internal/templates/gui_template/index.tsx,sha256=YrdrpcckwLo0kYIA-2egtzlo0OMWigGxnt7mNN4qmlU,234
 biolib/_internal/templates/gui_template/package.json,sha256=iyYYUC0zKGWvZcH8YxN-3w-0N68W5vx-0WPlluMn6Y4,621
 biolib/_internal/templates/gui_template/tsconfig.json,sha256=T3DJIzeLQ2BL8HLfPHI-IvHtJhnMXdHOoRjkmQlJQAw,541
 biolib/_internal/templates/gui_template/vite.config.mts,sha256=Bf1bgRReU3XFsR6rX9yylW2IAxy2cDQI1FHBMjRnyQ4,271
-biolib/_internal/templates/init_template/.biolib/config.yml,sha256=y4ndTgbFvUE1UiGcIOqogT2Wm8jahGffeyU5rlCEltQ,427
+biolib/_internal/templates/init_template/.biolib/config.yml,sha256=gxMVd1wjbsDvMv4byc8fKEdJFby4qgi6v38mO5qmhoY,453
 biolib/_internal/templates/init_template/.github/workflows/biolib.yml,sha256=sphjoiycV_oc4VbaA8wbUEokSMpnrdB6N-bYju_5Ibo,522
 biolib/_internal/templates/init_template/.gitignore,sha256=dR_jhtT0boUspgk3S5PPUwuO0o8gKGIbdwu8IH638CY,20
 biolib/_internal/templates/init_template/Dockerfile,sha256=Wv2r9aiazkL1wOf_BT1f5Kx_-txfrqSkYTtWI8HGdL8,169
 biolib/_internal/templates/init_template/requirements.txt,sha256=2GnBHsKg4tX5F06Z4YeLuId6jQO3-HGTITsaVBTDG0Y,42
 biolib/_internal/templates/init_template/run.py,sha256=oat-Vzcz4XZilrTtgy8CzfltBAa5v6iduGof4Tuulhg,402
-biolib/_internal/templates/init_template/run.sh,sha256=CF25MYW8vNcZee6_Lydg0o5JDWG0YbrSvFHhMJ5I6x0,39
+biolib/_internal/templates/init_template/run.sh,sha256=ncvInHCn_PgjXmvaa5oBU0vC3dgFJQ6k7fUJKJzpOh4,69
 biolib/_internal/templates/templates.py,sha256=ni0euP0KD5NHkxJPIt__i2WvXxYIcC8qugQEoT9oIJQ,308
 biolib/_internal/tree_utils.py,sha256=_Q_6_NDtIiROcefymqxEVddjqti6Mt3OZ4U0GcDW61s,3904
 biolib/_internal/types/__init__.py,sha256=WvtlSHh77QhYVTLeRpoPAzqvByLzbEPf_ZqYGHFlQug,247
@@ -70,7 +70,7 @@ biolib/app/app.py,sha256=E4PuwMWiWujQQzHQcq7MfVEZV-q6uKAbwBLr0ZPY5Dk,11825
 biolib/app/search_apps.py,sha256=K4a41f5XIWth2BWI7OffASgIsD0ko8elCax8YL2igaY,1470
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
 biolib/biolib_api_client/api_client.py,sha256=IONzXeFCHl4wuct6fqOC_7NiTv_zFy6ys0hsAtvLzTA,7578
-biolib/biolib_api_client/app_types.py,sha256=1sXz9XnLRKNALMglNdTbew7AL6OkcUan0MPdj4xQLis,2456
+biolib/biolib_api_client/app_types.py,sha256=-L7d22CdqORy_e21qtIwNeZL72EKU1lAnzKUovaashA,2587
 biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
 biolib/biolib_api_client/biolib_app_api.py,sha256=DdE_kRfDgVa876Cdl_D1P0lBoaghFomEyy-ZP8K7SoY,5177
 biolib/biolib_api_client/biolib_job_api.py,sha256=3Hzv5Os4d377pKrCzg3i7c5xiy9FiqeVssub690GLdA,7423
@@ -98,7 +98,7 @@ biolib/cli/__init__.py,sha256=IHC2bEyA27pvgp-18SGfFVJOP456elanz7suDP8D084,1316
 biolib/cli/auth.py,sha256=p9ZGY6ld2rnMbpsuRskvIQJNUHlSgYgcLTDsYGyUwyw,1407
 biolib/cli/data_record.py,sha256=t8DfJK2EZ_SNZ9drDA_N5Jqy8DNwf9f5SlFrIaOvtv0,3501
 biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5LRos,483
-biolib/cli/init.py,sha256=BZ3MF9bvtyiFdc2VXIaUtQwLVc6wG508oO5WRgVNK5Y,5429
+biolib/cli/init.py,sha256=mRi3gw36QPPCvxjhEQPnNJI8qpsK9HxdhXiGzZgW0Qw,5840
 biolib/cli/lfs.py,sha256=z2qHUwink85mv9yDgifbVKkVwuyknGhMDTfly_gLKJM,4151
 biolib/cli/push.py,sha256=J8BswMYVeTacZBHbm4K4a2XbS_I8kvfgRZLoby2wi3I,1695
 biolib/cli/run.py,sha256=RAAXbIx8Bi-4fNkEoz2ODJ0fEtyS7VxD3dkc2fVZwjY,2150
@@ -121,7 +121,7 @@ biolib/compute_node/job_worker/executors/types.py,sha256=wbjWZZ2f9FttjqUCCOeZmn7
 biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py,sha256=_cvEiZbOwfkv6fYmfrvdi_FVviIEYr_dSClQcOQaUWM,1198
 biolib/compute_node/job_worker/job_max_runtime_timer_thread.py,sha256=K_xgz7IhiIjpLlXRk8sqaMyLoApcidJkgu29sJX0gb8,1174
 biolib/compute_node/job_worker/job_storage.py,sha256=J6B5wkBo3cqmT1AV-qJnm2Lt9Qmcp3qn-1AabjO9m60,4686
-biolib/compute_node/job_worker/job_worker.py,sha256=3m6_ZzsSbuygbh9UmQ2RQrPZgJVsjcSR5V57ddECcqo,29139
+biolib/compute_node/job_worker/job_worker.py,sha256=Lutt80H-_KQFfgkRWx-cbJZeDrE2UHZIqlAD11oW9Nw,29450
 biolib/compute_node/job_worker/large_file_system.py,sha256=XXqRlVtYhs-Ji9zQGIk5KQPXFO_Q5jJH0nnlw4GkeMY,10461
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
 biolib/compute_node/job_worker/utilization_reporter_thread.py,sha256=7tm5Yk9coqJ9VbEdnO86tSXI0iM0omwIyKENxdxiVXk,8575
@@ -155,8 +155,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.1022.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1022.dist-info/METADATA,sha256=tI9lo-BlqyBDLv8qDJbqIxmWyJAUKL32ZuRVO0j4GH0,1571
-pybiolib-1.2.1022.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pybiolib-1.2.1022.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1022.dist-info/RECORD,,
+pybiolib-1.2.1030.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1030.dist-info/METADATA,sha256=9RhdSN_Tz_gIIygI29KWrceSwaurkwgRRwOKScoIw-U,1571
+pybiolib-1.2.1030.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pybiolib-1.2.1030.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1030.dist-info/RECORD,,