Mercurial > repos > fubar > tool_factory_2
changeset 45:668c37cc8962 draft
trying to get a workflow to do something interesting
| author | fubar |
|---|---|
| date | Sun, 16 Aug 2020 20:05:19 -0400 |
| parents | 23ad2924bf78 |
| children | f8700bed1e17 |
| files | TF_example_wf.ga toolfactory/.github/workflows/commit.yml toolfactory/.gitignore toolfactory/.shed.yml toolfactory/TF_example_wf.ga toolfactory/html_dir.py toolfactory/testtf.sh |
| diffstat | 7 files changed, 850 insertions(+), 458 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TF_example_wf.ga Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,458 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "TF examples", + "steps": { + "0": { + "annotation": "a fasta file - gc ratio will be estimated", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "a fasta file - gc ratio will be estimated", + "name": "phiX.fasta" + } + ], + "label": "phiX.fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 231, + "height": 61, + "left": 393, + "right": 593, + "top": 170, + "width": 200, + "x": 393, + "y": 170 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f5ce2386-b80c-4691-a0a7-abeec8854461" + } + ] + }, + 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'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}", + "tool_version": "2.00", + "type": "tool", + "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc", + "workflow_outputs": [ + { + "label": null, + "output_name": "TF_run_report", + "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978" + } + ] + } + }, + "tags": [], + "uuid": "321a7f9f-c287-453c-807a-43afd948770e", + "version": 1 +}
--- /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 ${{ matrix.python-version }} . + - name: Copy artifacts into place + run: | + mkdir upload + mv tool_test_output.json tool_test_output.html upload/ + - uses: actions/upload-artifact@v2.0.1 + with: + name: 'All tool test results' + path: upload
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.gitignore Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,129 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$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/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.shed.yml Sun Aug 16 20:05:19 2020 -0400 @@ -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
--- a/toolfactory/TF_example_wf.ga Sun Aug 16 08:51:49 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,458 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "TF examples", - "steps": { - "0": { - "annotation": "a fasta file - gc ratio will be estimated", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "a fasta file - gc ratio will be estimated", - "name": "phiX.fasta" - } - ], - "label": "phiX.fasta", - "name": "Input dataset", - "outputs": [], - "position": { - "bottom": 231, - "height": 61, - "left": 393, - "right": 593, - "top": 170, - "width": 200, - "x": 393, - "y": 170 - }, - "tool_id": null, - "tool_state": "{\"optional\": false}", - "tool_version": null, - "type": "data_input", - "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "f5ce2386-b80c-4691-a0a7-abeec8854461" - } - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/html_dir.py Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,180 @@ + +class tooloutHTMLifyer(self): + + def compressPDF(self,inpdf=None,thumbformat='png'): + """need absolute path to pdf + note that GS gets confoozled if no $TMP or $TEMP + so we set it + """ + assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) + hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'a') + our_env = os.environ.copy() + our_tmp = our_env.get('TMP',None) + if not our_tmp: + our_tmp = our_env.get('TEMP',None) + if not (our_tmp and os.path.exists(our_tmp)): + newtmp = os.path.join(self.opts.output_dir,'tmp') + try: + os.mkdir(newtmp) + except: + sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp) + our_env['TEMP'] = newtmp + if not self.temp_warned: + sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp) + self.temp_warned = True + outpdf = '%s_compressed' % inpdf + cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] + x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval1 = x.wait() + sto.close() + if retval1 == 0: + os.unlink(inpdf) + shutil.move(outpdf,inpdf) + os.unlink(hlog) + hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'w') + outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) + if self.useGM: + cl2 = ['gm', 'convert', inpdf, outpng] + else: # assume imagemagick + cl2 = ['convert', inpdf, outpng] + x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval2 = x.wait() + sto.close() + if retval2 == 0: + os.unlink(hlog) + retval = retval1 or retval2 + return retval + + + def getfSize(self,fpath,outpath): + """ + format a nice file size string + """ + size = '' + fp = os.path.join(outpath,fpath) + if os.path.isfile(fp): + size = '0 B' + n = float(os.path.getsize(fp)) + if n > 2**20: + size = '%1.1f MB' % (n/2**20) + elif n > 2**10: + size = '%1.1f KB' % (n/2**10) + elif n > 0: + size = '%d B' % (int(n)) + return size + + def makeHtml(self): + """ Create an HTML file content to list all the artifacts found in the output_dir + """ + + galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + """ + 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/>""" + galhtmlpostfix = """</div></body></html>\n""" + + flist = os.listdir(self.opts.output_dir) + flist = [x for x in flist if x != 'Rplots.pdf'] + flist.sort() + html = [] + html.append(galhtmlprefix % progname) + html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow())) + fhtml = [] + if len(flist) > 0: + logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections + logfiles.sort() + logfiles = [x for x in logfiles if os.path.abspath(x) != os.path.abspath(self.tlog)] + logfiles.append(os.path.abspath(self.tlog)) # make it the last one + pdflist = [] + npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) + for rownum,fname in enumerate(flist): + dname,e = os.path.splitext(fname) + sfsize = self.getfSize(fname,self.opts.output_dir) + if e.lower() == '.pdf' : # compress and make a thumbnail + thumb = '%s.%s' % (dname,self.thumbformat) + pdff = os.path.join(self.opts.output_dir,fname) + retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) + if retval == 0: + pdflist.append((fname,thumb)) + else: + pdflist.append((fname,fname)) + if (rownum+1) % 2 == 0: + fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + else: + fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + for logfname in logfiles: # expect at least tlog - if more + if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later + sectionname = 'All tool run' + if (len(logfiles) > 1): + sectionname = 'Other' + ourpdfs = pdflist + else: + realname = os.path.basename(logfname) + sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log + ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] + pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove + nacross = 1 + npdf = len(ourpdfs) + + if npdf > 0: + nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) + if int(nacross)**2 != npdf: + nacross += 1 + nacross = int(nacross) + width = min(400,int(1200/nacross)) + html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname) + html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>') + ntogo = nacross # counter for table row padding with empty cells + html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') + for i,paths in enumerate(ourpdfs): + fname,thumb = paths + s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" + alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) + if ((i+1) % nacross == 0): + s += '</tr>\n' + ntogo = 0 + if i < (npdf - 1): # more to come + s += '<tr>' + ntogo = nacross + else: + ntogo -= 1 + html.append(s) + if html[-1].strip().endswith('</tr>'): + html.append('</table></div>\n') + else: + if ntogo > 0: # pad + html.append('<td> </td>'*ntogo) + html.append('</tr></table></div>\n') + logt = open(logfname,'r').readlines() + logtext = [x for x in logt if x.strip() > ''] + html.append('<div class="toolFormTitle">%s log output</div>' % sectionname) + if len(logtext) > 1: + html.append('\n<pre>\n') + html += logtext + html.append('\n</pre>\n') + else: + html.append('%s is empty<br/>' % logfname) + if len(fhtml) > 0: + 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') + fhtml.append('</table></div><br/>') + html.append('<div class="toolFormTitle">All output files available for downloading</div>\n') + html += fhtml # add all non-pdf files to the end of the display + else: + html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) + html.append(galhtmlpostfix) + htmlf = file(self.opts.output_html,'w') + htmlf.write('\n'.join(html)) + htmlf.write('\n') + htmlf.close() + self.html = html + +