# **************************************************************************
# *
# * Authors: Carlos Oscar S. Sorzano (coss@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
import os
import glob
import pyworkflow as pw
import pyworkflow.protocol.params as params
import pyworkflow.utils as pwutils
from pwem.protocols import EMProtocol
PDFLATEX = "pdflatex"
[docs]class ProtPDFReport(EMProtocol):
"""
Produce a pdf report from the files in a given directory.
Supported file formats: *.tex, *.txt, *.jpg, *.png, *.pdf
Files in the directory are sorted by name alphabetically,
so if you want them to have the right order a possibility is to name them as
0010-myText.txt
0020-aFigure.png
0030-anotherFigure.jpg
0040-aPaper.pdf
0050-anotherText.tex
...
when these files are sorted, they will be sorted by the number in front.
"""
_label = 'pdf report'
_lastUpdateVersion = pw.VERSION_1_1
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('filesPath', params.PathParam,
label="Files directory",
help="Directory with the input files. \n"
"Check protocol help for more details.")
# --------------------------- INSERT steps functions ----------------------
def _insertAllSteps(self):
self._insertFunctionStep('createReport')
# --------------------------- STEPS functions -----------------------------
[docs] def createReport(self):
fnTex = "report.tex"
fhTex = open(self._getExtraPath(fnTex), "w")
template = """
\\documentclass[12pt]{article}
\\usepackage{amsmath,amsthm,amssymb,amsfonts}
\\usepackage{graphicx}
\\usepackage{pdfpages}
\\DeclareGraphicsExtensions{.pdf,.png,.jpg}
\\begin{document}
\\title{User Report}
\\author{Created by Scipion}
\\maketitle
"""
fhTex.write(template)
fnDir = self.filesPath.get()
if not os.path.isdir(fnDir):
fnDir = os.path.basename(fnDir)
for fileName in sorted(glob.glob(os.path.join(fnDir, "*"))):
fnDest = os.path.basename(fileName).lower()
fnDest = fnDest.replace(" ", "_")
fnDest = fnDest.replace(":", "_")
fnDest = fnDest.replace(";", "_")
pwutils.copyFile(fileName, self._getExtraPath(fnDest))
if fnDest.endswith(".tex") or fnDest.endswith(".txt"):
fhTex.write("\\input{%s}\n" % fnDest)
fhTex.write("\n")
elif fnDest.endswith(".png") or fnDest.endswith(".jpg"):
fhTex.write("\\begin{center}\n")
fhTex.write("\\includegraphics[width=14cm]{%s}\n" % fnDest)
fhTex.write("\\end{center}\n")
fhTex.write("\n")
elif fnDest.endswith(".pdf"):
fhTex.write("\\includepdf[pages=-]{%s}\n" % fnDest)
fhTex.write("\\clearpage\n")
fhTex.write("\n")
template = """
\\end{document}
"""
fhTex.write(template)
fhTex.close()
args = "-interaction=nonstopmode " + fnTex
self.runJob(PDFLATEX, args, cwd=self._getExtraPath())
fnPDF = self._getExtraPath("report.pdf")
if os.path.exists(fnPDF):
pwutils.moveFile(fnPDF, self._getPath("report.pdf"))
else:
raise Exception("PDF file was not produced.")
# --------------------------- INFO functions ------------------------------
def _summary(self):
summary = []
summary.append("Input directory: %s" % self.filesPath.get())
summary.append("Output report: %s" % self._getPath("report.pdf"))
return summary
[docs] @classmethod
def validateInstallation(cls):
""" This function will be used to check if PDFto latex is available. """
missingPaths = []
from pyworkflow.utils import commandExists
if not (commandExists(PDFLATEX)):
missingPaths.append("%s not found in the system" % PDFLATEX)
if missingPaths:
return ["Missing variables:"] + missingPaths
else:
return [] # No errors