def writeReadme(): """ Extract readme file from readme path in config. If not specified file containing <readme> in scriptsPath with be chosen""" conf = Config() scriptsPath = conf.get("scriptsPath") snakeroot = conf.snakeroot try: filename_readme = conf.get("readmePath") #### should be .md file except AttributeError as e: filename_readme = "" onlyfiles = [ f for f in os.listdir(snakeroot) if os.path.isfile(os.path.join(snakeroot, f)) ] for f in onlyfiles: if ("readme" in f) and f.endswith(".md"): filename_readme = f filename_readme = filename_readme.replace(".md", ".html") readmeString = '<li><a href="javascript:navigate(' + " '{}'".format( filename_readme) + ');">Readme</a></li> ' readmeIframeString = '<iframe id="Iframe" src="' + filename_readme + '" width=100% height=95% ></iframe> ' readmeFilename = ' "{}" '.format(filename_readme) return readmeString, readmeIframeString, readmeFilename
def writeDependencyFile(): """ Entry point for writing .wBuild.depend. """ # if not wbuildVersionIsCurrent(): # print(bcolors.WARNING + "Version of the project's static .wBuild lib is not the same as the dynamically loaded " # "wBuild" # "version. It is strongly recommended to update .wBuild lib using \'wbuild update\'; " # "otherwise, the consistency of the build can not be guaranteed." + bcolors.ENDC) logger.info("Structuring dependencies...") conf = Config() htmlOutputPath = conf.get("htmlOutputPath") logger.debug("Loaded config.\n html output path (key htmlOutputPath): " + htmlOutputPath + "\n") scriptsPath = conf.get("scriptsPath") readmePath = conf.get("readmePath") wbData = parseWBInfosFromRFiles(script_dir=scriptsPath, htmlPath=htmlOutputPath) mdData = parseMDFiles(script_dir=scriptsPath, htmlPath=htmlOutputPath, readmePath=readmePath) dependFile = tempfile.NamedTemporaryFile('w', delete=False) with dependFile as f: #start off with the header f.write('######\n') f.write('#This is a autogenerated snakemake file by wBuild\n') f.write('#wBuild by Leonhard Wachutka\n') f.write('######\n') # write build index rule writeIndexRule(wbData, mdData, f) logger.info("Dependencies file generated at: {}\n".format(dependFile.name)) return dependFile.name
def writeDepSVG(): """ Search for rule graph. If path not specified in config, take default dep.svg in snakeroot path""" conf = Config() scriptsPath = conf.get("scriptsPath") htmlOutputPath = conf.get("htmlOutputPath") snakeroot = conf.snakeroot foldername = snakeroot.split("/")[-1] try: filename_SVG = conf.get("ruleGraphPath") #### should be .md file except AttributeError as e: ### try with default name "dep.svg" if os.path.isfile(os.path.join(htmlOutputPath, "dep.svg")): filename_SVG = "dep.svg" else: ### search for files containing "svg" and foldername filename_SVG = "" onlyfiles = [ f for f in os.listdir(htmlOutputPath) if os.path.isfile(os.path.join(htmlOutputPath, f)) ] for f in onlyfiles: if (foldername in f) and f.endswith(".svg"): filename_SVG = f svgString = '<li><a href="javascript:navigate(' + "'{}'".format( filename_SVG) + ');">Dependency</a></li>' return svgString
def writeIndexHTMLMenu(scriptsPath=None, index_name=None): """ Scan for files involved in the current HTML rendering and fill the HTML quick access toolbar correspondingly """ conf = Config() if scriptsPath is None: scriptsPath = conf.get("scriptsPath") htmlOutputPath = conf.get("htmlOutputPath") pageTitle = conf.get("projectTitle") snakeroot = conf.snakeroot wbData = parseWBInfosFromRFiles(script_dir=scriptsPath, htmlPath=htmlOutputPath) mdData = parseMDFiles(script_dir=scriptsPath, htmlPath=htmlOutputPath) wbData += mdData temp = [] # for all of the scanned files, collect their paths for r in wbData: # this is needed so the relative path to "../wbuild/Snakefile" is not # part of the html sub menu r['file'] = removeFilePrefix(r['file'], snakeroot) temp.append(pathlib.PurePath(r['file']).parts[1]) menuString = "" for top in sorted(set(temp)): menuString += ( '<li class="dropdown">\n' + # write the current directory's name to the main ("top") toolbar tab ' <a href="#" class="dropdown-toggle" data-toggle="dropdown" ' + 'role="button" aria-haspopup="true" aria-expanded="false">' + top + '<span class="caret"></span></a>\n' ' <ul class="dropdown-menu multi-level" role="menu">\n' + # write sub-directories to the dropdown list of the "top" tabs writeSubMenu(top, wbData, 2) + ' </ul>\n' + '</li>\n') _, output, graphPath, readmePath = createIndexRule(scriptsPath, index_name) readmeString, readmeIframeString, readmeFilename = writeReadme(readmePath) depSVGString = writeDepSVG(graphPath) # fill the HTML template with the constructed tag structure wbuildPath = pathlib.Path(wbuild.__file__).parent template = open(str(wbuildPath / "html/template.html")).read() template = Template(template).substitute(menu=menuString, title=pageTitle, rf=getRecentMenu(), readme=readmeString, readmeIframe=readmeIframeString, readmeFilename=readmeFilename, depSVG=depSVGString) f = open(output, 'w') f.write(template) f.close()
def writeIndexRule(wbRRows, wbMDrows, file): """ Write the rule of mapping the R and md wbData to the index.html. :param wbRRows: info dict parsed from R wB files :param wbMDrows: info dict parsed from MD wB files :param file: file to print the index rule to """ inputFiles = [] for r in wbRRows: #ignore if the file is script or noindex if getYamlParam(r, 'type') == 'script' or getYamlParam( r, 'type') == 'noindex': continue inputFiles.append(r['outputFile']) for r in wbMDrows: inputFiles.append(r['outputFile']) conf = Config() htmlOutputPath = conf.get("htmlOutputPath") try: filename_index = conf.get("htmlIndex") except AttributeError as e: filename_index = "index.html" try: indexWithFolderName = conf.get("indexWithFolderName") except: indexWithFolderName = False if indexWithFolderName: scriptsPath = conf.get("scriptsPath") abs_path = str(os.path.abspath(scriptsPath)) name = abs_path.split("/")[-2] filename_index = name + "_" + filename_index file.write('\n') file.write('rule Index:\n') file.write(' input: \n "' + '",\n "'.join(inputFiles) + '"\n') file.write(' output: "' + htmlOutputPath + '/' + filename_index + '" \n') # file.write(' script: ".wBuild/createIndex.py"\n') file.write(' run:\n') file.write(' import wbuild.createIndex\n') file.write(' wbuild.createIndex.ci()\n') file.write('\n')
def getRecentMenu(): """ Support recently edited files list to the HTML web output. :return: HTML string: "Recently viewed" menu contents """ conf = Config() htmlOutputPath = conf.get("htmlOutputPath") rFiles = sorted([ join(htmlOutputPath, f) for f in listdir(htmlOutputPath) if isfile(join(htmlOutputPath, f)) ], key=os.path.getmtime, reverse=True) ## delete all files containing the word "index from html menu " rFiles = [f for f in rFiles if "index" not in f] rFiles = rFiles[:10] # open recent Files in new tab menuString = "" for f in rFiles: fo = pathlib.PurePath(f).name # Open in a new tab #menuString += ('<p><a href='+ fo + ' target="_blank">' + fo.replace('_', ' ').replace('.html', '') + # '</a></p>\n') # Open in same tab menuString += ('<p><a href="javascript:navigate(\'' + fo + '\');" >' + fo.replace('_', ' ').replace('.html', '') + '</a></p>\n') return menuString
def insertPlaceholders(dest, source): """ Infer placeholders' substitutions. :param dest: string to replace placeholders in :param source: file; from its path we infer the placeholders values :return: dest with replaced placeholders """ path = pathlib.Path(source) #get the path to the file conf = Config() processedDataPath = conf.get("processedDataPath") PD = pathlib.Path(processedDataPath) PP = path.parts[-2] dest = dest.replace("{wbPD}", str(PD)) dest = dest.replace("{wbPP}", str(PP)) if len(path.parts) <= 2 and bool(re.search('{wbP(D_P*)?}', source)): print("If using placeholders please make sure you have the right", " directory structure.") if len(path.parts) > 2: P = path.parts[-3] dest = dest.replace("{wbPD_P}", str(PD / P)) dest = dest.replace("{wbPD_PP}", str(PD / P / PP)) dest = dest.replace("{wbP}", str(P)) return dest
def autolink(config): conf = Config() scriptsPath = conf.get("scriptsPath") S = Path(scriptsPath) tasks = load(open(config)) for filename in glob.iglob(scriptsPath + '/**/*.ln.R', recursive=True): os.remove(filename) for task in tasks: print(task) if task['dst'] is None: continue if task['src'] is None: continue for dst in task['dst']: if dst is None: continue if not os.path.exists(str(S / dst)): os.makedirs(str(S / dst)) for src in task['src']: if src is None: continue link(str(S / Path(src)), str(S / Path(dst) / Path(src).stem) + '.ln.R')
def writeIndexRule(wbData, mdData, file, ignoreMD=False, dump=False): """ Write the rule of mapping the R and md wbData to the index.html. :param wbRRows: info dict parsed from R wB files :param wbMDrows: info dict parsed from MD wB files :param file: file to print the index rule to """ conf = Config() htmlOutputPath = conf.get("htmlOutputPath") for r in wbData: writeRule(r, file, dump) if not ignoreMD: for r in mdData: writeMdRule(r, file) input, output, graphPath, _ = wbuild.createIndex.createIndexRule( wbData=wbData, mdData=mdData) # write rule file.write('\n') file.write('rule Index:\n') file.write(' input: \n "' + '",\n "'.join(input) + '"\n') file.write(' output: \n') file.write(' index = "' + output + '", \n') file.write(' graph = "' + graphPath + '" \n') # file.write(' script: ".wBuild/createIndex.py"\n') file.write(' run:\n') file.write(' import wbuild.createIndex\n') file.write(' wbuild.createIndex.ci()\n') file.write( ' shell("snakemake --rulegraph | dot -Tsvg -Grankdir=RL > {output.graph}")\n' ) file.write('\n')
def createIndexName(scriptsPath, default=None): if default is not None: return default name = "" conf = Config() indexWithFolderName = conf.get("indexWithFolderName") if indexWithFolderName: abs_path = str(os.path.abspath(scriptsPath)) name = abs_path.split("/")[-2] return name
def ci(): writeIndexHTMLMenu() conf = Config() htmlOutputPath = conf.get("htmlOutputPath") libDir = htmlOutputPath + "/lib" if os.path.exists(libDir): shutil.rmtree(libDir) wbuildPath = pathlib.Path(wbuild.__file__).parent shutil.copytree(str(wbuildPath) + "/html/lib", libDir)
def writeWBParseDependencyFile(filename): """ Entry point for writing .wBuild.depend. for the wbParseFunction in R """ conf = Config() htmlOutputPath = conf.get("htmlOutputPath") wbData = parseWBInfosFromRFile(filename=filename, htmlPath=htmlOutputPath) with open('.wBuild.depend', 'w') as f: #start off with the header f.write('######\n') f.write('#This is a autogenerated snakemake file by wBuild\n') f.write('#wBuild by Leonhard Wachutka\n') f.write('######\n') # write rules for r in wbData: writeRule(r, f, True) writeIndexRule(wbData, list(), f) logger.info("Dependencies file generated.\n")
def ci(scriptsPath=None, index_name=None): """ Write HTML index file :param scriptsPath: relative scripts path. If not specified, use the default scripts path from the config. :param index_name: prefix of the index file name `<index_name>_index.html` """ conf = Config() htmlOutputPath = conf.get("htmlOutputPath") writeIndexHTMLMenu(scriptsPath, index_name) libDir = htmlOutputPath + "/lib" # if os.path.exists(libDir): # shutil.rmtree(libDir) if not os.path.exists(libDir): wbuildPath = pathlib.Path(wbuild.__file__).parent shutil.copytree(str(wbuildPath) + "/html/lib", libDir)
def createIndexRule(scriptsPath=None, index_name=None, wbData=None, mdData=None): """ Create the input and output files necessary for an HTML index rule. :param scriptsPath: relative scripts path. If not specified, use the default scripts path from the config. :param index_name: prefix of the index file name `<index_name>_index.html` :param wbData: wBuild rule data from parsed R scripts :param mdData: wBuild rule data from parsed markdown files :return: + **inputFiles** - list of output HTML files from the `scriptsPath`, comprising the input of the index rule + **indexPath** - index html file name, equates to the output + **graphPath** - dependency graph image file name for HTML template (graph is needs to be written to this file) + **readmePath** - readme HTML name for HTML template (takes readme from the `scriptsPath`) """ conf = Config() if scriptsPath is None or scriptsPath == conf.get("scriptsPath"): readmePath = conf.get("readmePath") scriptsPath = conf.get("scriptsPath") else: # find readme file readmePath = findFirstFile(scriptsPath, ".*readme.*", "md", re.I) if readmePath is None: readmePath = scriptsPath + "/readme.md" open(readmePath, "a").close() htmlOutputPath = conf.get("htmlOutputPath") htmlIndex = conf.get("htmlIndex") index_name = createIndexName(scriptsPath, index_name) # gather index input files inputFiles = [] if wbData is None: wbData = parseWBInfosFromRFiles(script_dir=scriptsPath, htmlPath=htmlOutputPath) if mdData is None: mdData = parseMDFiles(script_dir=scriptsPath, htmlPath=htmlOutputPath, readmePath=readmePath) for r in wbData: # ignore if the file is script or noindex if getYamlParam(r, 'type') == 'script' or getYamlParam( r, 'type') == 'noindex': continue inputFiles.append(r['outputFile']) for r in mdData: inputFiles.append(r['outputFile']) if len(index_name) > 0: index_name = index_name + "_" # separator for distinct index_name indexPath = "/".join([htmlOutputPath, index_name + htmlIndex]) graphPath = "/".join([htmlOutputPath, index_name + "dep.svg"]) # readme html readmePath = htmlOutputPath + "/" + pathsepsToUnderscore( os.path.splitext(readmePath)[0]) + ".html" return inputFiles, indexPath, graphPath, readmePath