From 931a8aa1fc4af75d49e108dc2c10f327a278367a Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Sat, 17 Aug 2024 08:07:21 -0500
Subject: [PATCH 1/9] add bbmap tool

---
 .github/workflows/build-push-bbmap-image.yml  | 31 ++++++++++++
 src/loaders/compute_tools/bbmap/Dockerfile    | 31 ++++++++++++
 src/loaders/compute_tools/bbmap/bbmap.py      | 50 +++++++++++++++++++
 src/loaders/compute_tools/bbmap/versions.yaml |  5 ++
 src/loaders/jobs/taskfarmer/task_generator.py |  2 +-
 5 files changed, 118 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/build-push-bbmap-image.yml
 create mode 100644 src/loaders/compute_tools/bbmap/Dockerfile
 create mode 100644 src/loaders/compute_tools/bbmap/bbmap.py
 create mode 100644 src/loaders/compute_tools/bbmap/versions.yaml

diff --git a/.github/workflows/build-push-bbmap-image.yml b/.github/workflows/build-push-bbmap-image.yml
new file mode 100644
index 00000000..0a27c123
--- /dev/null
+++ b/.github/workflows/build-push-bbmap-image.yml
@@ -0,0 +1,31 @@
+name: Build & Push BBMap Image to GHCR
+
+on:
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+    paths:
+      - 'src/loaders/compute_tools/bbmap/versions.yaml'
+      - '.github/workflows/build-push-bbmap-image.yml'
+      - '.github/workflows/build-push-tool-images.yml'
+
+  push:
+    branches:
+      - main
+      - master
+      - develop
+    paths:
+      - 'src/loaders/compute_tools/bbmap/versions.yaml'
+      - '.github/workflows/build-push-bbmap-image.yml'
+      - '.github/workflows/build-push-tool-images.yml'
+
+jobs:
+  trigger-build-push:
+    uses: ./.github/workflows/build-push-tool-images.yml
+    with:
+      tool_name: bbmap
+      version_file: 'src/loaders/compute_tools/bbmap/versions.yaml'
+    secrets: inherit
\ No newline at end of file
diff --git a/src/loaders/compute_tools/bbmap/Dockerfile b/src/loaders/compute_tools/bbmap/Dockerfile
new file mode 100644
index 00000000..56f2923b
--- /dev/null
+++ b/src/loaders/compute_tools/bbmap/Dockerfile
@@ -0,0 +1,31 @@
+FROM continuumio/miniconda3:24.5.0-0
+
+# NOTE: If the tool version changes, ensure the metadata information saved after running the tool in the _run_bbmap_single method is updated
+ARG BBMAP_VER=39.06
+ENV CONDA_ENV bbmap-$BBMAP_VER
+
+# Add Bioconda and Conda-Forge channels
+RUN conda config --add channels bioconda
+RUN conda config --add channels conda-forge
+
+# Install BBMap
+ARG PYTHON_VER=3.11
+RUN conda create -n $CONDA_ENV python=$PYTHON_VER bbmap=$BBMAP_VER
+
+# Activate the environment
+RUN echo "source activate $CONDA_ENV" >> ~/.bashrc
+
+# Set up directories
+RUN mkdir -p /app
+COPY ./ /app/collections
+RUN rm -r /app/collections/.git
+
+
+ENV PYTHONPATH /app/collections
+WORKDIR /app
+
+ENV PY_SCRIPT=/app/collections/src/loaders/compute_tools/bbmap/bbmap.py
+
+RUN chmod -R 777 /app/collections
+
+ENTRYPOINT ["/app/collections/src/loaders/compute_tools/entrypoint.sh"]
diff --git a/src/loaders/compute_tools/bbmap/bbmap.py b/src/loaders/compute_tools/bbmap/bbmap.py
new file mode 100644
index 00000000..e6796afe
--- /dev/null
+++ b/src/loaders/compute_tools/bbmap/bbmap.py
@@ -0,0 +1,50 @@
+"""
+Run BBMap tool on a set of faa files.
+
+This tool serves a distinct purpose separate from collection tools; instead, it is suited for CDM work.
+Therefore, the parser program is not compatible with data generated by this tool.
+
+"""
+from pathlib import Path
+
+from src.loaders.common.loader_common_names import TOOL_METADATA
+from src.loaders.compute_tools.tool_common import ToolRunner, run_command, create_tool_metadata
+
+
+def _run_bbmap_single(
+        tool_safe_data_id: str,
+        data_id: str,
+        source_file: Path,
+        output_dir: Path,
+        threads_per_tool_run: int,
+        debug: bool) -> None:
+
+    metadata_file = output_dir / TOOL_METADATA
+    if metadata_file.exists():
+        print(f"Skipping {source_file} as it has already been processed.")
+        return
+
+    command = [
+        'stats.sh',
+        'in=' + str(source_file),
+        'out=' + str(output_dir / 'result.json'),
+    ]
+
+    run_command(command, output_dir if debug else None)
+
+    # Save run info to a metadata file in the output directory for parsing later
+    metadata = {'tool_name': 'bbmap',
+                'version': '39.06',
+                'command': command,
+                'data_id': data_id,
+                'source_file': str(source_file),}
+    create_tool_metadata(output_dir, metadata)
+
+
+def main():
+    runner = ToolRunner("bbmap")
+    runner.parallel_single_execution(_run_bbmap_single, unzip=True)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/src/loaders/compute_tools/bbmap/versions.yaml b/src/loaders/compute_tools/bbmap/versions.yaml
new file mode 100644
index 00000000..8c38d4c5
--- /dev/null
+++ b/src/loaders/compute_tools/bbmap/versions.yaml
@@ -0,0 +1,5 @@
+versions:
+  - version: 0.1.0
+    date: 2024-08-16
+    notes: |
+      - initial BBMap implementation
\ No newline at end of file
diff --git a/src/loaders/jobs/taskfarmer/task_generator.py b/src/loaders/jobs/taskfarmer/task_generator.py
index 444c39fe..35231696 100644
--- a/src/loaders/jobs/taskfarmer/task_generator.py
+++ b/src/loaders/jobs/taskfarmer/task_generator.py
@@ -41,7 +41,7 @@
                         
 '''
 
-TOOLS_AVAILABLE = ['gtdb_tk', 'checkm2', 'microtrait', 'mash', 'eggnog']
+TOOLS_AVAILABLE = ['gtdb_tk', 'checkm2', 'microtrait', 'mash', 'eggnog', 'bbmap']
 
 NODE_TIME_LIMIT_DEFAULT = 5  # hours
 # Used as THREADS variable in the batch script which controls the number of parallel tasks per node

From 94f23208a59a1ca4712e46a9075178ecec3d43f1 Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Sat, 17 Aug 2024 08:23:13 -0500
Subject: [PATCH 2/9] add release notes

---
 RELEASE_NOTES.md      | 8 ++++++++
 src/common/version.py | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 2f49cb1c..a5ede7ff 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,5 +1,13 @@
 # KBase Collections Release Notes
 
+## 0.1.3
+
+* Added BBMap tool to the CDM pipeline.
+* Included metadata file generation after each tool's execution.
+* Updated Python library dependencies to the latest versions.
+* Standardized thread management logic across all tools.
+* Pass `job_id` to the tool container and remove `node_id`.
+
 ## 0.1.2
 
 * Fixed a bug that caused requests with filters to fail for filter keys containing colons.
diff --git a/src/common/version.py b/src/common/version.py
index ed49400a..2f787825 100644
--- a/src/common/version.py
+++ b/src/common/version.py
@@ -2,4 +2,4 @@
 The version of the KBase collections software.
 '''
 
-VERSION = "0.1.2"
+VERSION = "0.1.3"

From e6f60df4bc750117c322f6829104e8a6c2f80603 Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Sat, 17 Aug 2024 09:27:44 -0500
Subject: [PATCH 3/9] forget to add JSON format

---
 src/loaders/compute_tools/bbmap/bbmap.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/loaders/compute_tools/bbmap/bbmap.py b/src/loaders/compute_tools/bbmap/bbmap.py
index e6796afe..a97da0e7 100644
--- a/src/loaders/compute_tools/bbmap/bbmap.py
+++ b/src/loaders/compute_tools/bbmap/bbmap.py
@@ -18,7 +18,6 @@ def _run_bbmap_single(
         output_dir: Path,
         threads_per_tool_run: int,
         debug: bool) -> None:
-
     metadata_file = output_dir / TOOL_METADATA
     if metadata_file.exists():
         print(f"Skipping {source_file} as it has already been processed.")
@@ -28,6 +27,8 @@ def _run_bbmap_single(
         'stats.sh',
         'in=' + str(source_file),
         'out=' + str(output_dir / 'result.json'),
+        'format=8',  # output in JSON format
+        'overwrite=true'
     ]
 
     run_command(command, output_dir if debug else None)
@@ -37,7 +38,8 @@ def _run_bbmap_single(
                 'version': '39.06',
                 'command': command,
                 'data_id': data_id,
-                'source_file': str(source_file),}
+                'source_file': str(source_file),
+                }
     create_tool_metadata(output_dir, metadata)
 
 

From eb6cf1d6a0ee190ab2d5891271f60b2e8e0990a7 Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Sat, 17 Aug 2024 10:34:06 -0500
Subject: [PATCH 4/9] add lib to the img

---
 src/loaders/compute_tools/bbmap/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/loaders/compute_tools/bbmap/Dockerfile b/src/loaders/compute_tools/bbmap/Dockerfile
index 56f2923b..e74df2b6 100644
--- a/src/loaders/compute_tools/bbmap/Dockerfile
+++ b/src/loaders/compute_tools/bbmap/Dockerfile
@@ -11,6 +11,7 @@ RUN conda config --add channels conda-forge
 # Install BBMap
 ARG PYTHON_VER=3.11
 RUN conda create -n $CONDA_ENV python=$PYTHON_VER bbmap=$BBMAP_VER
+RUN conda install -n $CONDA_ENV pandas=2.2.2 jsonlines=4.0.0
 
 # Activate the environment
 RUN echo "source activate $CONDA_ENV" >> ~/.bashrc

From 4fcf0bd4669aeeec41d6f157dbefe55315cb8267 Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Tue, 20 Aug 2024 10:41:03 -0500
Subject: [PATCH 5/9] using the updated create_metadata method

---
 src/loaders/compute_tools/bbmap/bbmap.py | 30 +++++++++++++++++-------
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/src/loaders/compute_tools/bbmap/bbmap.py b/src/loaders/compute_tools/bbmap/bbmap.py
index a97da0e7..6faa7fe5 100644
--- a/src/loaders/compute_tools/bbmap/bbmap.py
+++ b/src/loaders/compute_tools/bbmap/bbmap.py
@@ -1,10 +1,11 @@
 """
-Run BBMap tool on a set of faa files.
+Run BBMap tool on a set of fna files.
 
 This tool serves a distinct purpose separate from collection tools; instead, it is suited for CDM work.
 Therefore, the parser program is not compatible with data generated by this tool.
 
 """
+import time
 from pathlib import Path
 
 from src.loaders.common.loader_common_names import TOOL_METADATA
@@ -18,6 +19,9 @@ def _run_bbmap_single(
         output_dir: Path,
         threads_per_tool_run: int,
         debug: bool) -> None:
+    start = time.time()
+    print(f'Start executing BBMap for {data_id}')
+
     metadata_file = output_dir / TOOL_METADATA
     if metadata_file.exists():
         print(f"Skipping {source_file} as it has already been processed.")
@@ -33,14 +37,24 @@ def _run_bbmap_single(
 
     run_command(command, output_dir if debug else None)
 
+    end_time = time.time()
+    run_time = end_time - start
+    print(
+        f'Used {round(run_time / 60, 2)} minutes to execute BBMap for {data_id}')
+
     # Save run info to a metadata file in the output directory for parsing later
-    metadata = {'tool_name': 'bbmap',
-                'version': '39.06',
-                'command': command,
-                'data_id': data_id,
-                'source_file': str(source_file),
-                }
-    create_tool_metadata(output_dir, metadata)
+    additional_metadata = {
+        'source_file': str(source_file),
+        'data_id': data_id,
+    }
+    create_tool_metadata(
+        output_dir,
+        tool_name="bbmap",
+        version="39.06",
+        command=command,
+        run_time=round(run_time, 2),
+        batch_size=1,
+        additional_metadata=additional_metadata)
 
 
 def main():

From eab560943e48dfa928a58cbea2f323ed008f79e4 Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Tue, 20 Aug 2024 11:10:02 -0500
Subject: [PATCH 6/9] upgrade aiohttp

---
 Pipfile      |   2 +-
 Pipfile.lock | 339 ++++++++++++++++++++++++++++-----------------------
 2 files changed, 185 insertions(+), 156 deletions(-)

diff --git a/Pipfile b/Pipfile
index 98151633..c6bd18f4 100644
--- a/Pipfile
+++ b/Pipfile
@@ -8,7 +8,7 @@ fastapi = "==0.112.1"
 uvicorn = {version = "==0.30.6", extras = ["standard"]}
 jsonlines = "==4.0.0"
 cacheout = "==0.16.0"
-aiohttp = "==3.10.3"
+aiohttp = "==3.10.5"
 requests = "==2.32.3"
 jinja-cli = "==1.2.2"
 pandas = "==2.2.2"
diff --git a/Pipfile.lock b/Pipfile.lock
index 84f18c3b..1b6419a8 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "75018eac1a10153ad9c2164bf95cfc19d54acb08c6639ba11cc4f1fbdd0c1c20"
+            "sha256": "ed18b574bba0a525372bfad99b9ffaeea39442d9f3832ee7465cbe668c86f401"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -26,94 +26,109 @@
         },
         "aiohappyeyeballs": {
             "hashes": [
-                "sha256:337ce4dc0e99eb697c3c5a77d6cb3c52925824d9a67ac0dea7c55b8a2d60b222",
-                "sha256:e794cd29ba6a14078092984e43688212a19081de3a73b6796c2fdeb3706dd6ce"
+                "sha256:55a1714f084e63d49639800f95716da97a1f173d46a16dfcfda0016abb93b6b2",
+                "sha256:7ce92076e249169a13c2f49320d1967425eaf1f407522d707d59cac7628d62bd"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==2.3.7"
+            "version": "==2.4.0"
         },
         "aiohttp": {
             "hashes": [
-                "sha256:05d66203a530209cbe40f102ebaac0b2214aba2a33c075d0bf825987c36f1f0b",
-                "sha256:08bd0754d257b2db27d6bab208c74601df6f21bfe4cb2ec7b258ba691aac64b3",
-                "sha256:0974f3b5b0132edcec92c3306f858ad4356a63d26b18021d859c9927616ebf27",
-                "sha256:09bc79275737d4dc066e0ae2951866bb36d9c6b460cb7564f111cc0427f14844",
-                "sha256:123e5819bfe1b87204575515cf448ab3bf1489cdeb3b61012bde716cda5853e7",
-                "sha256:13031e7ec1188274bad243255c328cc3019e36a5a907978501256000d57a7201",
-                "sha256:166de65e2e4e63357cfa8417cf952a519ac42f1654cb2d43ed76899e2319b1ee",
-                "sha256:214277dcb07ab3875f17ee1c777d446dcce75bea85846849cc9d139ab8f5081f",
-                "sha256:21650e7032cc2d31fc23d353d7123e771354f2a3d5b05a5647fc30fea214e696",
-                "sha256:24fade6dae446b183e2410a8628b80df9b7a42205c6bfc2eff783cbeedc224a2",
-                "sha256:2a5d0ea8a6467b15d53b00c4e8ea8811e47c3cc1bdbc62b1aceb3076403d551f",
-                "sha256:2b0f670502100cdc567188c49415bebba947eb3edaa2028e1a50dd81bd13363f",
-                "sha256:2bbc55a964b8eecb341e492ae91c3bd0848324d313e1e71a27e3d96e6ee7e8e8",
-                "sha256:32007fdcaab789689c2ecaaf4b71f8e37bf012a15cd02c0a9db8c4d0e7989fa8",
-                "sha256:3461d9294941937f07bbbaa6227ba799bc71cc3b22c40222568dc1cca5118f68",
-                "sha256:3731a73ddc26969d65f90471c635abd4e1546a25299b687e654ea6d2fc052394",
-                "sha256:38d91b98b4320ffe66efa56cb0f614a05af53b675ce1b8607cdb2ac826a8d58e",
-                "sha256:3a9dcdccf50284b1b0dc72bc57e5bbd3cc9bf019060dfa0668f63241ccc16aa7",
-                "sha256:434b3ab75833accd0b931d11874e206e816f6e6626fd69f643d6a8269cd9166a",
-                "sha256:43b09f38a67679e32d380fe512189ccb0b25e15afc79b23fbd5b5e48e4fc8fd9",
-                "sha256:44bb159b55926b57812dca1b21c34528e800963ffe130d08b049b2d6b994ada7",
-                "sha256:48665433bb59144aaf502c324694bec25867eb6630fcd831f7a893ca473fcde4",
-                "sha256:50544fe498c81cb98912afabfc4e4d9d85e89f86238348e3712f7ca6a2f01dab",
-                "sha256:5337cc742a03f9e3213b097abff8781f79de7190bbfaa987bd2b7ceb5bb0bdec",
-                "sha256:56fb94bae2be58f68d000d046172d8b8e6b1b571eb02ceee5535e9633dcd559c",
-                "sha256:59c489661edbd863edb30a8bd69ecb044bd381d1818022bc698ba1b6f80e5dd1",
-                "sha256:5ba2e838b5e6a8755ac8297275c9460e729dc1522b6454aee1766c6de6d56e5e",
-                "sha256:61ccb867b2f2f53df6598eb2a93329b5eee0b00646ee79ea67d68844747a418e",
-                "sha256:671efce3a4a0281060edf9a07a2f7e6230dca3a1cbc61d110eee7753d28405f7",
-                "sha256:673bb6e3249dc8825df1105f6ef74e2eab779b7ff78e96c15cadb78b04a83752",
-                "sha256:6ae9ae382d1c9617a91647575255ad55a48bfdde34cc2185dd558ce476bf16e9",
-                "sha256:6c51ed03e19c885c8e91f574e4bbe7381793f56f93229731597e4a499ffef2a5",
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-                "sha256:7f9159ae530297f61a00116771e57516f89a3de6ba33f314402e41560872b50a",
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-                "sha256:b84857b66fa6510a163bb083c1199d1ee091a40163cfcbbd0642495fed096204",
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-                "sha256:ba562736d3fbfe9241dad46c1a8994478d4a0e50796d80e29d50cabe8fbfcc3f",
-                "sha256:bac352fceed158620ce2d701ad39d4c1c76d114255a7c530e057e2b9f55bdf9f",
-                "sha256:baec1eb274f78b2de54471fc4c69ecbea4275965eab4b556ef7a7698dee18bf2",
-                "sha256:bc8e9f15939dacb0e1f2d15f9c41b786051c10472c7a926f5771e99b49a5957f",
-                "sha256:bf75716377aad2c718cdf66451c5cf02042085d84522aec1f9246d3e4b8641a6",
-                "sha256:c124b9206b1befe0491f48185fd30a0dd51b0f4e0e7e43ac1236066215aff272",
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-                "sha256:ffefa1374cd508d633646d51a8e9277763a9b78ae71324183693959cf94635a7"
-            ],
-            "version": "==12.0"
+                "sha256:02cc9bb1a887dac0e08bf657c5d00aa3fac0d03215d35a599130c2034ae6663a",
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+                "sha256:851fd0afb3bc0b73f7c5b5858975d42769a5fdde5314f4ef2c106aec63100687",
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+                "sha256:a00e1e587c655749afb5b135d8d3edcfe84ec6db864201e40a882e64168610b3",
+                "sha256:a1ab8f0e0cadc5be5f3f9fa11a663957fecbf483d434762c8dfb8aa44948944a",
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+                "sha256:a7fbf2a8fe7556a8f4e68cb3e736884af7bf93653e79f6219f17ebb75e97d8f0",
+                "sha256:ad4fa707ff9e2ffee019e946257b5300a45137a58f41fbd9a4db8e684ab61528",
+                "sha256:ad818cdac37c0ad4c58e51cb4964eae4f18b43c4a83cb37170b0d90c31bd80cf",
+                "sha256:addf0a16e4983280efed272d8cb3b2e05f0051755372461e7d966b80a6554e16",
+                "sha256:ae7a519a56a714f64c3445cabde9fc2fc927e7eae44f413eae187cddd9e54178",
+                "sha256:b32f38bc81170fd56d0482d505b556e52bf9078b36819a8ba52624bd6667e39e",
+                "sha256:b5407c34776b9b77bd89a5f95eb0a34aaf91889e3f911c63f13035220eb50107",
+                "sha256:b7bf950234a482b7461afdb2ec99eee3548ec4d53f418c7990bb79c620476602",
+                "sha256:b89849171b590107f6724a7b0790736daead40926ddf47eadf998b4ff51d6414",
+                "sha256:bcea3eb58c09c3a31cc83b45c06d5907f02ddaf10920aaa6443975310f699b95",
+                "sha256:bd4ba86513430513e2aa25a441bb538f6f83734dc368a2c5d18afdd39097aa33",
+                "sha256:bf8eb5dca4f484a60f5327b044e842e0d7f7cdbf02ea6dc4a4f811259f1f1f0b",
+                "sha256:c026ee729c4ce55708a14b839ba35086dfae265fc12813b62d34ce33f4980c1c",
+                "sha256:c210d1460dc8d326ffdef9703c2f83269b7539a1690ad11ae04162bc1878d33d",
+                "sha256:c8feb8e19ef65c9994e652c5b0324abd657bedd0abeb946fb4f5163012c1e730",
+                "sha256:cbac2eb7ce0fac755fb983c9247c4a60c4019bcde4c0e4d167aeb17520cc7ef1",
+                "sha256:cbfe82a07596a044de78bb7a62519e71690c5812c26c5f1d4b877e64e4f46309",
+                "sha256:d3f3d2e20c442b58dbac593cb1e02bc02d149a86056cc4126d977ad902472e3b",
+                "sha256:d42a818e634f789350cd8fb413a3f5eec1cf0400a53d02062534c41519f5125c",
+                "sha256:d4b83cf7354cbbc058e97b3e545dceb75b8d9cf17fd5a19db419c319ddbaaf7a",
+                "sha256:d9726d2c9bd6aed8cb994d89b3910ca0079406edce3670886ec828a73e7bdd53",
+                "sha256:da7e501e59857e8e3e9d10586139dc196b80445a591451ca9998aafba1af5278",
+                "sha256:da7e918d82e7bdfc6f66d31febe1b2e28a1ca3387315f918de26f5e367f61572",
+                "sha256:dbbac01e80aee253d44c4f098ab3cc17c822518519e869b284cfbb8cd16cc9de",
+                "sha256:df5c0eff91f61b8205a6c9f7b255ff390cdb77b61c7b41f79ca10afcbb22b6cb",
+                "sha256:e07e76c49f39c5b45cbd7362b94f001ae209a3ea4905ae9a09cfd53b3c76373d",
+                "sha256:e1e10b3fbed7be4a59831d3a939900e50fcd34d93716e433d4193a4d0d1d335d",
+                "sha256:e39d393e0ab5b8bd01717cc26f2922026050188947ff54fe6a49dc489f7750b7",
+                "sha256:e5ba5e9b332267d0f2c33ede390061850f1ac3ee6cd1bdcf4c5ea33ead971966",
+                "sha256:e7a1963302947332c3039e3f66209ec73b1626f8a0191649e0713c391e9f5b0d",
+                "sha256:e7fcad070dcd9ad37a09d89a4cbc2a5e3e45080b88977c0da87b3090f9f55ead",
+                "sha256:eae368cac85adc4c7dc3b0d5f84ffcca609d658db6447387300478e44db70796",
+                "sha256:ede95125a30602b1691a4b1da88946bf27dae283cf30f22cd2cb8ca4b2e0d119",
+                "sha256:f5737c53eb2c8ed8f64b50d3dafd3c1dae739f78aa495a288421ac1b3de82717",
+                "sha256:f5f9d23fbbf96eefde836d9692670bfc89e2d159f456d499c5efcf6a6281c1af",
+                "sha256:f66e00e42f25ca7e91076366303e11c82572ca87cc5aae51e6e9c094f315ab41",
+                "sha256:f9af457ed593e35f467140d8b61d425495b127744a9d65d45a366f8678449a23",
+                "sha256:fa0839f35322f7b038d8adcf679e2698c3a483688cc92e3bd15ee4fb06669e9a",
+                "sha256:fd038bc9e2c134847f1e0ce3191797fad110756e690c2fdd9702ed34e7a43abb"
+            ],
+            "version": "==13.0"
         },
         "xmltodict": {
             "hashes": [

From 2068f47b55b50ed739465e3d52e15c9ccdacdb88 Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Tue, 20 Aug 2024 12:28:35 -0500
Subject: [PATCH 7/9] no need to unpack

---
 src/loaders/compute_tools/bbmap/bbmap.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/loaders/compute_tools/bbmap/bbmap.py b/src/loaders/compute_tools/bbmap/bbmap.py
index 6faa7fe5..9356f7c5 100644
--- a/src/loaders/compute_tools/bbmap/bbmap.py
+++ b/src/loaders/compute_tools/bbmap/bbmap.py
@@ -59,7 +59,7 @@ def _run_bbmap_single(
 
 def main():
     runner = ToolRunner("bbmap")
-    runner.parallel_single_execution(_run_bbmap_single, unzip=True)
+    runner.parallel_single_execution(_run_bbmap_single)
 
 
 if __name__ == "__main__":

From dd6d7392f1dee0b6ca70a8fc5fbb9c6b48c620ea Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Wed, 21 Aug 2024 08:57:55 -0500
Subject: [PATCH 8/9] address comments

---
 RELEASE_NOTES.md                               | 3 +++
 src/loaders/compute_tools/bbmap/versions.yaml  | 3 +++
 src/loaders/compute_tools/eggnog/versions.yaml | 3 +++
 3 files changed, 9 insertions(+)

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index a5ede7ff..d2833b9d 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -7,6 +7,9 @@
 * Updated Python library dependencies to the latest versions.
 * Standardized thread management logic across all tools.
 * Pass `job_id` to the tool container and remove `node_id`.
+* Converted Data IDs to string format to ensure proper comparison with associated folder names
+* Fix `kbase_id` formate for biolog parser script
+* Added a guide for process from KBase Genome to Collections.
 
 ## 0.1.2
 
diff --git a/src/loaders/compute_tools/bbmap/versions.yaml b/src/loaders/compute_tools/bbmap/versions.yaml
index 8c38d4c5..39038287 100644
--- a/src/loaders/compute_tools/bbmap/versions.yaml
+++ b/src/loaders/compute_tools/bbmap/versions.yaml
@@ -1,3 +1,6 @@
+# This tool serves a distinct purpose separate from collection tools; instead, it is suited for CDM work.
+# Therefore, the parser program is not compatible with data generated by this tool.
+
 versions:
   - version: 0.1.0
     date: 2024-08-16
diff --git a/src/loaders/compute_tools/eggnog/versions.yaml b/src/loaders/compute_tools/eggnog/versions.yaml
index e9db90c4..fdad8f2e 100644
--- a/src/loaders/compute_tools/eggnog/versions.yaml
+++ b/src/loaders/compute_tools/eggnog/versions.yaml
@@ -1,3 +1,6 @@
+# This tool serves a distinct purpose separate from collection tools; instead, it is suited for CDM work.
+# Therefore, the parser program is not compatible with data generated by this tool.
+
 versions:
   - version: 0.1.0
     date: 2024-03-13

From 8e9138288dbf5ceeac37287c6f732b9cd28e2d20 Mon Sep 17 00:00:00 2001
From: Tianhao-Gu <tgu@anl.gov>
Date: Wed, 21 Aug 2024 14:03:37 -0500
Subject: [PATCH 9/9] add more release notes

---
 RELEASE_NOTES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index d2833b9d..920d0d7a 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -10,6 +10,7 @@
 * Converted Data IDs to string format to ensure proper comparison with associated folder names
 * Fix `kbase_id` formate for biolog parser script
 * Added a guide for process from KBase Genome to Collections.
+* The task generator now asks for confirmation before submitting a job.
 
 ## 0.1.2