def pageFolderActions(abfFolder, parentNote):
abfPath = os.path.join(abfFolder.path, parentNote.abfID) + ".abf"
urlParent = "/ABFparent" + abfBrowse.getUrl(abfPath)
urlAnalyze = "/ABFanalyze" + abfBrowse.getUrl(abfFolder.path)
urlExperiment = "/ABFexperiment" + abfBrowse.getUrl(abfFolder.path)
html = ""
html += "<div style='background-color: #F6F6F6; padding: .5em; color: gray'>"
html += "<code>"
unanalyzedAbfs = abfFolder.abfsRequiringAnalysis()
if len(unanalyzedAbfs):
with open(abfBrowse.AUTOANALYSIS_COMMAND_FILE) as f:
commandText = f.read()
html += f"Folder contains {len(unanalyzedAbfs)} unanalyzed ABFs | "
if abfFolder.path in commandText:
html += "this folder is in the auto-analysis list | "
else:
html += f"<a href='{urlAnalyze}' class='abfAnalysisNeeded'>auto-analyze this folder</a> | "
#html += f"<span class='abfAnalysisNeeded'>Auto-analysis disabled (COVID-19). Analyze with pyABFauto.</span> | "
else:
html += f"<a href='{urlAnalyze}' style='color: gray;'>No ABFs require analysis</a> | "
html += f"<a href='{urlParent}?deleteGraphsForChildren' class='' style='color: gray;'>delete graphs</a> | "
html += f"<a href='{urlExperiment}' class=''>experiment notes</a>"
html += "</code>"
html += "</div>"
return html
def getHtmlForImageFilePaths(abfFolder, filePaths):
html = ""
for imagePath in filePaths:
imagePath = abfFolder.analysisFolder+"/"+imagePath
imageUrl = abfBrowse.getUrl(imagePath)
html += f"<a href='{imageUrl}'><img src='{imageUrl}' class='analysisImage'></a> "
return html
def getNotesForm(pathLocal):
expNotes = abfBrowse.experimentNotes.ExperimentNotes(pathLocal)
xDriveFilePath = abfBrowse.getXdrivePath(expNotes.path)
experimentText = expNotes.getText()
if not experimentText:
experimentText = "## Experiment Notes ##\n"
experimentText += "Goal: \n"
experimentText += "Animal: \n"
experimentText += "Internal: \n"
experimentText += "Bath: \n"
experimentText += "Drugs: \n"
url = "/ABFexperiment" + abfBrowse.getUrl(pathLocal)
url = url.replace("X:/", "/X/")
html = ""
html += f"<div style='font-size: 80%; font-family: consolas, monospace;'>{xDriveFilePath}</div>"
html += f"<div style='color: #ccc; font-size: 80%;'><i>{expNotes.getEditDateString()}</i></div>"
# add warnings here
html += f"<form action='{url}' method='post' style='margin: 0px;'>"
html += f"<textarea name='experimentText' class='editBox' style='margin-top: 20px;'>{experimentText}</textarea>"
html += f"<input class='submitButton' type='submit' value='SAVE' style='margin-top: 20px;'>"
html += f"</form>"
return html
def menuParentCellList(abfFolder):
urlExperiment = "/ABFexperiment" + abfBrowse.getUrl(abfFolder.path)
urlOrigin = "/ABForigin" + abfBrowse.getUrl(abfFolder.path)
html = ""
html += "<div class='menuEphysProject'>"
html += "<span class='title'>Electrophysiology Project</span><br>"
html += f"<div><a href='{urlExperiment}' target='content'>Experiment Notes</a></div>"
html += f"<div><a href='{urlOrigin}' target='content'>Origin Commands</a></div>"
html += "</div>"
cells = abfBrowse.CellsFile(abfFolder.path)
unknownCells = cells.getUnknownCells(abfFolder.abfList.family.keys())
activeCellMarkerId = 0
if len(cells.cellNotes):
html += "<div class='menuCellList'>"
for line in cells.cellNotes:
if isinstance(line, str):
html += f"<br><div class='title'><b>{line}</b></div>"
elif isinstance(line, abfBrowse.CellNote):
abfUrl = abfBrowse.getUrl(abfFolder.path + "/" + line.abfID +
".abf")
activeCellMarkerId += 1
abfLink = f"<a href='/ABFparent{abfUrl}' target='content' onclick='setClicked({activeCellMarkerId})' style='background-color: {line.color};'>{line.abfID}</a>"
if line.abfID in abfFolder.abfList.family:
abfCount = f"({len(abfFolder.abfList.family[line.abfID])})"
else:
abfCount = f"(?)"
abfComment = f"<span class='menuCellComments'>{line.comment}</span>"
activeCellMarker = f"<span class='abftick' style='visibility: hidden' id='{activeCellMarkerId}'>»</span>"
html += f"<div>{activeCellMarker}{abfLink} {abfCount} {abfComment}</div>"
html += "</div>"
if len(unknownCells):
html += "<div class='menuCellList'>"
html += f"<div class='title'><b>Unlabeled:</b></div>"
for unknownCellID in unknownCells:
abfUrl = abfBrowse.getUrl(abfFolder.path + "/" + unknownCellID +
".abf")
abfCount = len(abfFolder.abfList.family[unknownCellID])
activeCellMarkerId += 1
activeCellMarker = f"<span class='abftick' style='visibility: hidden' id='{activeCellMarkerId}'>»</span>"
html += f"<div>{activeCellMarker}<a href='/ABFparent{abfUrl}' target='content' onclick='setClicked({activeCellMarkerId})'>{unknownCellID}</a> ({abfCount})</div>"
html += "</div>"
return html
def pageParentNotes(abfFolder, parentNote):
assert isinstance(abfFolder, abfBrowse.AbfFolder)
assert isinstance(parentNote, abfBrowse.cellsFile.CellNote)
abfPath = os.path.join(abfFolder.path, parentNote.abfID) + ".abf"
url = "/ABFparent" + abfBrowse.getUrl(abfPath)
urlMenu = "/ABFmenu" + abfBrowse.getUrl(os.path.dirname(abfPath))
html = ""
html += f"<form action='{url}' method='post' style='margin: 0px;'>"
html += f"<input type='hidden' name='abfFolderPath' value='{abfFolder.path}' />"
html += f"<input type='hidden' name='abfID' value='{parentNote.abfID}' />"
html += f"<div style='background-color: #DDD; padding: .5em;'>"
html += getColorBoxesHTML(parentNote.colorCode)
html += f"<input style='margin-top: 8px;' type='text' size='35' name='comment' value='{parentNote.comment}'> "
html += f"<input type='submit' value='Submit'> "
html += f"<a href='{urlMenu}' target='menu'>refresh menu</a>"
html += "</div>"
html += "</form>"
return html
def menuFolderContents(abfFolder):
subFolders = glob.glob(abfFolder.path + "/*/")
fileNames = abfFolder.abfList.fileNamesOther
fileNames = [x for x in fileNames if not x.lower().endswith(".tif")]
fileNames = [x for x in fileNames if not x.lower().endswith(".ignored")]
fileNames = [x for x in fileNames if "." in x]
html = ""
if len(subFolders) or len(fileNames):
html += "<div class='menuFileBrowser'>"
html += "<div class='title'>Folder Contents:</div>"
for subFolder in subFolders:
subFolder = os.path.basename(subFolder[:-1])
# TODO: make this top level
url = abfBrowse.getUrl(os.path.join(abfFolder.path, subFolder))
html += f"<div><a href='/ABFviewer{url}' target='_top'>{subFolder}/</a></div>"
for fileName in fileNames:
url = abfBrowse.getUrl(abfFolder.path + "/" + fileName)
html += f"<div><a href='{url}' target='content'>{fileName}</a></div>"
html += "</div>"
return html
def menuDirectoryNavigator(currentPath):
"""
Given a filesystem path, return HTML links where each subfolder
is on a new line and nested by depth.
"""
allPaths = [currentPath]
baseNames = [os.path.basename(currentPath)]
while baseNames[-1]:
shorterPath = os.path.dirname(allPaths[-1])
allPaths.append(shorterPath)
baseNames.append(os.path.basename(shorterPath))
allPaths.reverse()
baseNames.reverse()
# remove root drive letter
baseNames.pop(0)
allPaths.pop(0)
# remove folder (server only)
if baseNames[0] == "X_Drive":
baseNames.pop(0)
allPaths.pop(0)
html = "<div class='menuFileBrowser'>"
html += "<span class='title'>Project Browser</span><br>"
html += "<div style='color: blue;'>X:</div>"
for i in range(len(allPaths)):
padding = " " * (i + 1)
url = abfBrowse.getUrl(allPaths[i])
html += f"<div>{padding}<a href='/ABFviewer{url}' target='_top'>{baseNames[i]}</a></div>"
html += "<hr>"
html += abfBrowse.htmlTools.copyButton(
"copy path", abfBrowse.getXdrivePath(allPaths[i]))
html += abfBrowse.htmlTools.refreshButton()
html += "</div>"
return html