| Previous changeset 44:23ad2924bf78 (2020-08-16) Next changeset 46:f8700bed1e17 (2020-08-18) |
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Commit message:
trying to get a workflow to do something interesting |
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added:
TF_example_wf.ga toolfactory/.github/workflows/commit.yml toolfactory/.gitignore toolfactory/.shed.yml toolfactory/html_dir.py toolfactory/testtf.sh |
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removed:
toolfactory/TF_example_wf.ga |
| b |
| diff -r 23ad2924bf78 -r 668c37cc8962 TF_example_wf.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TF_example_wf.ga Sun Aug 16 20:05:19 2020 -0400 |
| [ |
| b'@@ -0,0 +1,458 @@\n+{\n+ "a_galaxy_workflow": "true",\n+ "annotation": "",\n+ "format-version": "0.1",\n+ "name": "TF examples",\n+ "steps": {\n+ "0": {\n+ "annotation": "a fasta file - gc ratio will be estimated",\n+ "content_id": null,\n+ "errors": null,\n+ "id": 0,\n+ "input_connections": {},\n+ "inputs": [\n+ {\n+ "description": "a fasta file - gc ratio will be estimated",\n+ "name": "phiX.fasta"\n+ }\n+ ],\n+ "label": "phiX.fasta",\n+ "name": "Input dataset",\n+ "outputs": [],\n+ "position": {\n+ "bottom": 231,\n+ "height": 61,\n+ "left": 393,\n+ "right": 593,\n+ "top": 170,\n+ "width": 200,\n+ "x": 393,\n+ "y": 170\n+ },\n+ "tool_id": null,\n+ "tool_state": "{\\"optional\\": false}",\n+ "tool_version": null,\n+ "type": "data_input",\n+ "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33",\n+ "workflow_outputs": [\n+ {\n+ "label": null,\n+ "output_name": "output",\n+ "uuid": "f5ce2386-b80c-4691-a0a7-abeec8854461"\n+ }\n+ ]\n+ },\n+ "1": {\n+ "annotation": "Any text file to be reversed lots of times and bjorked once.",\n+ "content_id": null,\n+ "errors": null,\n+ "id": 1,\n+ "input_connections": {},\n+ "inputs": [\n+ {\n+ "description": "Any text file to be reversed lots of times and bjorked once.",\n+ "name": "rgToolFactory2.py"\n+ }\n+ ],\n+ "label": "rgToolFactory2.py",\n+ "name": "Input dataset",\n+ "outputs": [],\n+ "position": {\n+ "bottom": 371,\n+ "height": 81,\n+ "left": 393,\n+ "right": 593,\n+ "top": 290,\n+ "width": 200,\n+ "x": 393,\n+ "y": 290\n+ },\n+ "tool_id": null,\n+ "tool_state": "{\\"optional\\": false}",\n+ "tool_version": null,\n+ "type": "data_input",\n+ "uuid": "f530b390-2424-4aae-8bd9-dd9d30277561",\n+ "workflow_outputs": [\n+ {\n+ "label": null,\n+ "output_name": "output",\n+ "uuid": "3d2a1699-50af-46e1-8981-dc6c3de2cf6c"\n+ }\n+ ]\n+ },\n+ "2": {\n+ "annotation": "",\n+ "content_id": "rgTF2",\n+ "errors": null,\n+ "id": 2,\n+ "input_connections": {\n+ "ppass|history_inputs_0|input_files": {\n+ "id": 0,\n+ "output_name": "output"\n+ }\n+ },\n+ "inputs": [],\n+ "label": null,\n+ "name": "toolfactory",\n+ "outputs": [\n+ {\n+ "name": "TF_run_report",\n+ "type": "input"\n+ },\n+ {\n+ "name": "new_tool",\n+ "type": "tgz"\n+ }\n+ ],\n+ "position": {\n+ "bottom": 372,\n+ "height": 202,\n+ "left": 613,\n+ "right": 813,\n+ "top": 170,\n+ "width": 200,\n+ "x": 613,\n+ "y": 170\n+ },\n+ "post_job_actions": {},\n+ "tool_id": "rgTF2",\n+ "tool_state": "{\\"__input_ext\\": \\"input\\", \\"chromInfo\\": \\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\\", \\"interexe\\": {\\"interpreter\\": \\"perl\\", \\"__current_case__\\": 4, \\"interpreter_version\\": \\"\\'..b'\n+ "height": 242,\n+ "left": 833,\n+ "right": 1033,\n+ "top": 170,\n+ "width": 200,\n+ "x": 833,\n+ "y": 170\n+ },\n+ "post_job_actions": {},\n+ "tool_id": "rgTF2",\n+ "tool_state": "{\\"__input_ext\\": \\"input\\", \\"chromInfo\\": \\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\\", \\"interexe\\": {\\"interpreter\\": \\"python\\", \\"__current_case__\\": 2, \\"interpreter_version\\": \\"\\", \\"exe_package_version\\": \\"\\", \\"dynScript\\": \\"import argparse\\\\nimport tarfile\\\\nimport os\\\\nimport tempfile\\\\nimport subprocess\\\\n\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\n\\\\nparser = argparse.ArgumentParser()\\\\na = parser.add_argument\\\\na(\'--tooltgz\',default=\'\')\\\\na(\'--report\',default=None)\\\\na(\'--toolout\',default=None)\\\\na(\'--galaxy_root\',default=None)\\\\nargs = parser.parse_args()\\\\ntoolname = args.toolout.split(os.sep)[-1]\\\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\\\ntf = tarfile.open(args.tooltgz,\\\\\\"r:gz\\\\\\")\\\\ntf.extractall(toolpath)\\\\ncl = \\\\\\"planemo test --skip_venv --galaxy_root %s %s\\\\\\" % (args.galaxy_root,toolpath)\\\\ncll = cl.split(\' \')\\\\nsto = open(args.report, \'w\')\\\\np = subprocess.run(cll, shell=False, stdout=sto)\\\\nretval = p.returncode\\\\nsto.close()\\\\n\\"}, \\"makeMode\\": {\\"make_Tool\\": \\"yes\\", \\"__current_case__\\": 0, \\"tool_version\\": \\"0.01\\", \\"tool_desc\\": \\"Tool to test toolshed tool archives generated by the tool factory.\\", \\"help_text\\": \\"**What it Does**\\\\n\\\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\\\nIt was generated using the tool factory.\\", \\"citations\\": []}, \\"ppass\\": {\\"parampass\\": \\"argparse\\", \\"__current_case__\\": 0, \\"history_inputs\\": [{\\"__index__\\": 0, \\"input_files\\": {\\"__class__\\": \\"ConnectedValue\\"}, \\"input_formats\\": [\\"tgz\\"], \\"input_label\\": \\"tool toolshed tgz archive from history\\", \\"input_help\\": \\"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\\", \\"input_CL\\": \\"tooltgz\\"}], \\"history_outputs\\": [{\\"__index__\\": 0, \\"history_name\\": \\"report\\", \\"history_format\\": \\"txt\\", \\"history_CL\\": \\"report\\"}], \\"edit_params\\": \\"yes\\", \\"additional_parameters\\": [{\\"__index__\\": 0, \\"param_name\\": \\"toolout\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"tools/toolmakers/planemotest\\", \\"param_label\\": \\"output path under galaxy root\\", \\"param_help\\": \\"This is where the tgz file will be extracted and tested by planemo\\", \\"param_CL\\": \\"toolout\\", \\"param_CLprefixed\\": \\"\\"}, {\\"__index__\\": 1, \\"param_name\\": \\"galaxy_root\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"/home/ross/galaxy\\", \\"param_label\\": \\"Galaxy source root directory to use for running planemo\\", \\"param_help\\": \\"This will form the galaxy_root parameter for rnning planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that rootu\\", \\"param_CL\\": \\"galaxy_root\\", \\"param_CLprefixed\\": \\"\\"}]}, \\"tool_name\\": \\"planemotest\\", \\"__page__\\": null, \\"__rerun_remap_job_id__\\": null}",\n+ "tool_version": "2.00",\n+ "type": "tool",\n+ "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc",\n+ "workflow_outputs": [\n+ {\n+ "label": null,\n+ "output_name": "TF_run_report",\n+ "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b"\n+ },\n+ {\n+ "label": null,\n+ "output_name": "new_tool",\n+ "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978"\n+ }\n+ ]\n+ }\n+ },\n+ "tags": [],\n+ "uuid": "321a7f9f-c287-453c-807a-43afd948770e",\n+ "version": 1\n+}\n' |
| b |
| diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/.github/workflows/commit.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.github/workflows/commit.yml Sun Aug 16 20:05:19 2020 -0400 |
| [ |
| @@ -0,0 +1,68 @@ +name: Galaxy Tool Linting and Tests for PR +# run planemo on a git repository containing a single tool +# as a github action. Does NOT run flake8. So, bite me. +# ross lazarus august 2020 +on: [pull_request,push] +env: + GALAXY_REPO: https://github.com/galaxyproject/galaxy + GALAXY_RELEASE: release_20.05 +jobs: + setup: + name: setup environment and python + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.7] + steps: + - name: Print github context properties + run: | + echo 'event: ${{ github.event_name }}' + echo 'sha: ${{ github.sha }}' + echo 'ref: ${{ github.ref }}' + echo 'head_ref: ${{ github.head_ref }}' + echo 'base_ref: ${{ github.base_ref }}' + echo 'event.before: ${{ github.event.before }}' + echo 'event.after: ${{ github.event.after }}' + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - uses: actions/checkout@v2 + with: + # planemo does not seem to want to install the requirement galaxyxml + # into the venv it manages at tool testing so do it the old skool way + repository: 'galaxyproject/galaxy' + path: 'galaxy' + - name: make venv ready for this galaxy and planemo + run: | + python3 -m venv $GITHUB_WORKSPACE/galaxy/.venv + . $GITHUB_WORKSPACE/galaxy/.venv/bin/activate + pip install --upgrade pip + pip install wheel + pip install -r $GITHUB_WORKSPACE/galaxy/requirements.txt + # pip install galaxyxml # currently includes a patched working version awaiting PR merge + - name: Upgrade pip + run: pip install --upgrade pip + # Install the `wheel` package so that when installing other packages which + # are not available as wheels, pip will build a wheel for them, which can be cached. + - name: Install wheel + run: pip install wheel + - name: Install Planemo and flake8 + run: pip install planemo flake8 flake8-import-order + # galaxyxml temporarily removed until PR accepted + - uses: actions/checkout@v2 + with: + fetch-depth: 1 + - name: flake8 + run: flake8 --ignore=E2,E3,E4,E5,W3,W505 + - name: Planemo lint + run: planemo lint . + - name: Planemo test tool + run: planemo test --galaxy_root $GITHUB_WORKSPACE/galaxy --test_output tool_test_output.html --skip_venv --test_output_json tool_test_output.json --galaxy_python_version ${{ matrix.python-version }} . + - name: Copy artifacts into place + run: | + mkdir upload + mv tool_test_output.json tool_test_output.html upload/ + - uses: actions/upload-artifact@v2.0.1 + with: + name: 'All tool test results' + path: upload |
| b |
| diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.gitignore Sun Aug 16 20:05:19 2020 -0400 |
| [ |
| @@ -0,0 +1,129 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ |
| b |
| diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.shed.yml Sun Aug 16 20:05:19 2020 -0400 |
| b |
| @@ -0,0 +1,13 @@ +name: toolfactory +owner: fubar +description: ToolFactory - tool to make Galaxy tools ready for the toolshed +homepage_url: https://github.com/fubar2/toolfactory +long_description: | + ToolFactory - turn executable packages and R/python/perl/bash scripts into ordinary Galaxy tools + + Creating re-usable tools from scripts: The Galaxy Tool Factory Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team + Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 +remote_repository_url: https://github.com/fubar2/toolfactory +type: tool_dependency_definition +categories: +- Tool Generators |
| b |
| diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/TF_example_wf.ga --- a/toolfactory/TF_example_wf.ga Sun Aug 16 08:51:49 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,458 +0,0 @@\n-{\n- "a_galaxy_workflow": "true",\n- "annotation": "",\n- "format-version": "0.1",\n- "name": "TF examples",\n- "steps": {\n- "0": {\n- "annotation": "a fasta file - gc ratio will be estimated",\n- "content_id": null,\n- "errors": null,\n- "id": 0,\n- "input_connections": {},\n- "inputs": [\n- {\n- "description": "a fasta file - gc ratio will be estimated",\n- "name": "phiX.fasta"\n- }\n- ],\n- "label": "phiX.fasta",\n- "name": "Input dataset",\n- "outputs": [],\n- "position": {\n- "bottom": 231,\n- "height": 61,\n- "left": 393,\n- "right": 593,\n- "top": 170,\n- "width": 200,\n- "x": 393,\n- "y": 170\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "f5ce2386-b80c-4691-a0a7-abeec8854461"\n- }\n- ]\n- },\n- "1": {\n- "annotation": "Any text file to be reversed lots of times and bjorked once.",\n- "content_id": null,\n- "errors": null,\n- "id": 1,\n- "input_connections": {},\n- "inputs": [\n- {\n- "description": "Any text file to be reversed lots of times and bjorked once.",\n- "name": "rgToolFactory2.py"\n- }\n- ],\n- "label": "rgToolFactory2.py",\n- "name": "Input dataset",\n- "outputs": [],\n- "position": {\n- "bottom": 371,\n- "height": 81,\n- "left": 393,\n- "right": 593,\n- "top": 290,\n- "width": 200,\n- "x": 393,\n- "y": 290\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "f530b390-2424-4aae-8bd9-dd9d30277561",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "3d2a1699-50af-46e1-8981-dc6c3de2cf6c"\n- }\n- ]\n- },\n- "2": {\n- "annotation": "",\n- "content_id": "rgTF2",\n- "errors": null,\n- "id": 2,\n- "input_connections": {\n- "ppass|history_inputs_0|input_files": {\n- "id": 0,\n- "output_name": "output"\n- }\n- },\n- "inputs": [],\n- "label": null,\n- "name": "toolfactory",\n- "outputs": [\n- {\n- "name": "TF_run_report",\n- "type": "input"\n- },\n- {\n- "name": "new_tool",\n- "type": "tgz"\n- }\n- ],\n- "position": {\n- "bottom": 372,\n- "height": 202,\n- "left": 613,\n- "right": 813,\n- "top": 170,\n- "width": 200,\n- "x": 613,\n- "y": 170\n- },\n- "post_job_actions": {},\n- "tool_id": "rgTF2",\n- "tool_state": "{\\"__input_ext\\": \\"input\\", \\"chromInfo\\": \\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\\", \\"interexe\\": {\\"interpreter\\": \\"perl\\", \\"__current_case__\\": 4, \\"interpreter_version\\": \\"\\'..b'\n- "height": 242,\n- "left": 833,\n- "right": 1033,\n- "top": 170,\n- "width": 200,\n- "x": 833,\n- "y": 170\n- },\n- "post_job_actions": {},\n- "tool_id": "rgTF2",\n- "tool_state": "{\\"__input_ext\\": \\"input\\", \\"chromInfo\\": \\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\\", \\"interexe\\": {\\"interpreter\\": \\"python\\", \\"__current_case__\\": 2, \\"interpreter_version\\": \\"\\", \\"exe_package_version\\": \\"\\", \\"dynScript\\": \\"import argparse\\\\nimport tarfile\\\\nimport os\\\\nimport tempfile\\\\nimport subprocess\\\\n\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\n\\\\nparser = argparse.ArgumentParser()\\\\na = parser.add_argument\\\\na(\'--tooltgz\',default=\'\')\\\\na(\'--report\',default=None)\\\\na(\'--toolout\',default=None)\\\\na(\'--galaxy_root\',default=None)\\\\nargs = parser.parse_args()\\\\ntoolname = args.toolout.split(os.sep)[-1]\\\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\\\ntf = tarfile.open(args.tooltgz,\\\\\\"r:gz\\\\\\")\\\\ntf.extractall(toolpath)\\\\ncl = \\\\\\"planemo test --skip_venv --galaxy_root %s %s\\\\\\" % (args.galaxy_root,toolpath)\\\\ncll = cl.split(\' \')\\\\nsto = open(args.report, \'w\')\\\\np = subprocess.run(cll, shell=False, stdout=sto)\\\\nretval = p.returncode\\\\nsto.close()\\\\n\\"}, \\"makeMode\\": {\\"make_Tool\\": \\"yes\\", \\"__current_case__\\": 0, \\"tool_version\\": \\"0.01\\", \\"tool_desc\\": \\"Tool to test toolshed tool archives generated by the tool factory.\\", \\"help_text\\": \\"**What it Does**\\\\n\\\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\\\nIt was generated using the tool factory.\\", \\"citations\\": []}, \\"ppass\\": {\\"parampass\\": \\"argparse\\", \\"__current_case__\\": 0, \\"history_inputs\\": [{\\"__index__\\": 0, \\"input_files\\": {\\"__class__\\": \\"ConnectedValue\\"}, \\"input_formats\\": [\\"tgz\\"], \\"input_label\\": \\"tool toolshed tgz archive from history\\", \\"input_help\\": \\"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\\", \\"input_CL\\": \\"tooltgz\\"}], \\"history_outputs\\": [{\\"__index__\\": 0, \\"history_name\\": \\"report\\", \\"history_format\\": \\"txt\\", \\"history_CL\\": \\"report\\"}], \\"edit_params\\": \\"yes\\", \\"additional_parameters\\": [{\\"__index__\\": 0, \\"param_name\\": \\"toolout\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"tools/toolmakers/planemotest\\", \\"param_label\\": \\"output path under galaxy root\\", \\"param_help\\": \\"This is where the tgz file will be extracted and tested by planemo\\", \\"param_CL\\": \\"toolout\\", \\"param_CLprefixed\\": \\"\\"}, {\\"__index__\\": 1, \\"param_name\\": \\"galaxy_root\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"/home/ross/galaxy\\", \\"param_label\\": \\"Galaxy source root directory to use for running planemo\\", \\"param_help\\": \\"This will form the galaxy_root parameter for rnning planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that rootu\\", \\"param_CL\\": \\"galaxy_root\\", \\"param_CLprefixed\\": \\"\\"}]}, \\"tool_name\\": \\"planemotest\\", \\"__page__\\": null, \\"__rerun_remap_job_id__\\": null}",\n- "tool_version": "2.00",\n- "type": "tool",\n- "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "TF_run_report",\n- "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b"\n- },\n- {\n- "label": null,\n- "output_name": "new_tool",\n- "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978"\n- }\n- ]\n- }\n- },\n- "tags": [],\n- "uuid": "321a7f9f-c287-453c-807a-43afd948770e",\n- "version": 1\n-}\n' |
| b |
| diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/html_dir.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/html_dir.py Sun Aug 16 20:05:19 2020 -0400 |
| [ |
| b'@@ -0,0 +1,180 @@\n+\n+class tooloutHTMLifyer(self):\n+\n+ def compressPDF(self,inpdf=None,thumbformat=\'png\'):\n+ """need absolute path to pdf\n+ note that GS gets confoozled if no $TMP or $TEMP\n+ so we set it\n+ """\n+ assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)\n+ hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))\n+ sto = open(hlog,\'a\')\n+ our_env = os.environ.copy()\n+ our_tmp = our_env.get(\'TMP\',None)\n+ if not our_tmp:\n+ our_tmp = our_env.get(\'TEMP\',None)\n+ if not (our_tmp and os.path.exists(our_tmp)):\n+ newtmp = os.path.join(self.opts.output_dir,\'tmp\')\n+ try:\n+ os.mkdir(newtmp)\n+ except:\n+ sto.write(\'## WARNING - cannot make %s - it may exist or permissions need fixing\\n\' % newtmp)\n+ our_env[\'TEMP\'] = newtmp\n+ if not self.temp_warned:\n+ sto.write(\'## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\\n\' % newtmp)\n+ self.temp_warned = True \n+ outpdf = \'%s_compressed\' % inpdf\n+ cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]\n+ x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)\n+ retval1 = x.wait()\n+ sto.close()\n+ if retval1 == 0:\n+ os.unlink(inpdf)\n+ shutil.move(outpdf,inpdf)\n+ os.unlink(hlog)\n+ hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))\n+ sto = open(hlog,\'w\')\n+ outpng = \'%s.%s\' % (os.path.splitext(inpdf)[0],thumbformat)\n+ if self.useGM: \n+ cl2 = [\'gm\', \'convert\', inpdf, outpng]\n+ else: # assume imagemagick\n+ cl2 = [\'convert\', inpdf, outpng]\n+ x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)\n+ retval2 = x.wait()\n+ sto.close()\n+ if retval2 == 0:\n+ os.unlink(hlog)\n+ retval = retval1 or retval2\n+ return retval\n+\n+\n+ def getfSize(self,fpath,outpath):\n+ """\n+ format a nice file size string\n+ """\n+ size = \'\'\n+ fp = os.path.join(outpath,fpath)\n+ if os.path.isfile(fp):\n+ size = \'0 B\'\n+ n = float(os.path.getsize(fp))\n+ if n > 2**20:\n+ size = \'%1.1f MB\' % (n/2**20)\n+ elif n > 2**10:\n+ size = \'%1.1f KB\' % (n/2**10)\n+ elif n > 0:\n+ size = \'%d B\' % (int(n))\n+ return size\n+\n+ def makeHtml(self):\n+ """ Create an HTML file content to list all the artifacts found in the output_dir\n+ """\n+\n+ galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> \n+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> \n+ <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> \n+ <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> \n+ <title></title> \n+ <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> \n+ </head> \n+ <body> \n+ <div class="toolFormBody"> \n+ """ \n+ galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" \n+ galhtmlpostfix = """</div></body></html>\\n"""\n+\n+ flist = os.listdir(self.opts.output_dir)\n+ flist = [x for x in flist if x != \'Rplots.pdf\']\n+ flist.sort()\n+ html = []\n+ html.append(galhtmlprefix % progname)\n+ html.append(\'<div class="infomessage">Galaxy T'..b'% (fname,fname,sfsize))\n+ else:\n+ fhtml.append(\'<tr><td><a href="%s">%s</a></td><td>%s</td></tr>\' % (fname,fname,sfsize))\n+ for logfname in logfiles: # expect at least tlog - if more\n+ if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later\n+ sectionname = \'All tool run\'\n+ if (len(logfiles) > 1):\n+ sectionname = \'Other\'\n+ ourpdfs = pdflist\n+ else:\n+ realname = os.path.basename(logfname)\n+ sectionname = os.path.splitext(realname)[0].split(\'_\')[0] # break in case _ added to log\n+ ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split(\'_\')[0] == sectionname]\n+ pdflist = [x for x in pdflist if os.path.basename(x[0]).split(\'_\')[0] != sectionname] # remove\n+ nacross = 1\n+ npdf = len(ourpdfs)\n+\n+ if npdf > 0:\n+ nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))\n+ if int(nacross)**2 != npdf:\n+ nacross += 1\n+ nacross = int(nacross)\n+ width = min(400,int(1200/nacross))\n+ html.append(\'<div class="toolFormTitle">%s images and outputs</div>\' % sectionname)\n+ html.append(\'(Click on a thumbnail image to download the corresponding original PDF image)<br/>\')\n+ ntogo = nacross # counter for table row padding with empty cells\n+ html.append(\'<div><table class="simple" cellpadding="2" cellspacing="2">\\n<tr>\')\n+ for i,paths in enumerate(ourpdfs): \n+ fname,thumb = paths\n+ s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" \n+ alt="Image called %s"/></a></td>\\n""" % (fname,thumb,fname,width,fname)\n+ if ((i+1) % nacross == 0):\n+ s += \'</tr>\\n\'\n+ ntogo = 0\n+ if i < (npdf - 1): # more to come\n+ s += \'<tr>\'\n+ ntogo = nacross\n+ else:\n+ ntogo -= 1\n+ html.append(s)\n+ if html[-1].strip().endswith(\'</tr>\'):\n+ html.append(\'</table></div>\\n\')\n+ else:\n+ if ntogo > 0: # pad\n+ html.append(\'<td> </td>\'*ntogo)\n+ html.append(\'</tr></table></div>\\n\')\n+ logt = open(logfname,\'r\').readlines()\n+ logtext = [x for x in logt if x.strip() > \'\']\n+ html.append(\'<div class="toolFormTitle">%s log output</div>\' % sectionname)\n+ if len(logtext) > 1:\n+ html.append(\'\\n<pre>\\n\')\n+ html += logtext\n+ html.append(\'\\n</pre>\\n\')\n+ else:\n+ html.append(\'%s is empty<br/>\' % logfname)\n+ if len(fhtml) > 0:\n+ fhtml.insert(0,\'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\\n\')\n+ fhtml.append(\'</table></div><br/>\')\n+ html.append(\'<div class="toolFormTitle">All output files available for downloading</div>\\n\')\n+ html += fhtml # add all non-pdf files to the end of the display\n+ else:\n+ html.append(\'<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>\' % self.opts.interpreter)\n+ html.append(galhtmlpostfix)\n+ htmlf = file(self.opts.output_html,\'w\')\n+ htmlf.write(\'\\n\'.join(html))\n+ htmlf.write(\'\\n\')\n+ htmlf.close()\n+ self.html = html\n+\n+\n' |
| b |
| diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/testtf.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/testtf.sh Sun Aug 16 20:05:19 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo + |