def showAbfParent(pathUrl):
"""
Display the ABF list and data for a parent ABF.
- also processes changes to cells.txt
- also deletes graphs for child ABFs
- also marks ABFs as ignored
- also analyzes new ABFs
- also marks ABFs as ignored
"""
showRequest(pathUrl, request)
pathLocal = abfBrowse.getLocalPath(pathUrl)
if os.path.isfile(pathLocal):
if ('colorCode' in request.form.keys()):
print("Processing a change to cells.txt...")
cellsFile = abfBrowse.CellsFile(request.form['abfFolderPath'])
cellsFile.modify(request.form['abfID'], request.form['colorCode'],
request.form['comment'],
abfBrowse.AUTOANALYSIS_FOLDER_NAME)
if ('deleteGraphsForChildren' in request.args.keys()):
print("Deleting graphs for children...")
abfFldr = abfBrowse.AbfFolder(os.path.dirname(pathLocal))
abfFldr.deleteChildGraphs(os.path.basename(pathLocal))
print("complete.")
if ('ignoreABF' in request.args.keys()):
ignoreAbf = request.args['ignoreABF']
ignoreAbfPath = os.path.join(os.path.dirname(pathLocal), ignoreAbf)
print(f"ignoring ABF: {ignoreAbfPath}")
os.rename(ignoreAbfPath, ignoreAbfPath + ".ignored")
return abfBrowse.pages.parent.generateHtml(pathLocal)
else:
return f"ERROR: does not exist: [{pathLocal}.abf]"
def generateHtml(pathLocal):
abfFolder = abfBrowse.AbfFolder(pathLocal)
html = ""
html += readOriginCommandScript()
html += specialHtml
if len(abfFolder.abfList.abfIDs):
html += getJavaBlock(abfFolder)
else:
html += "this is not an ABF folder..."
html = f"<div style='margin: 10px;'>{html}</div>"
return abfBrowse.htmlTools.htmlPageWrap(html)
def generateHtml(pathLocal):
abfFolder = abfBrowse.AbfFolder(pathLocal)
html = "<div class='title' style='font-size: 150%;'>Experiment Notes</div>"
if len(abfFolder.abfList.abfIDs):
html += getNotesForm(pathLocal)
else:
html += '<i>this is not an ABF folder</i>'
html = f"<div style='padding: 20px;'>{html}</div>"
return abfBrowse.htmlTools.htmlPageWrap(html)
def generateHtml(pathLocal):
"""
This is a file browser menu which displays electrophysiology
data if ABFs are present in the current folder.
"""
abfFolder = abfBrowse.AbfFolder(pathLocal)
html = ""
# html += "<style>body {background-color: #FAFAFA;}</style>"
html += menuDirectoryNavigator(abfFolder.path)
if len(abfFolder.abfList.fileNamesAbf):
html += menuParentCellList(abfFolder)
html += menuFolderContents(abfFolder)
return abfBrowse.htmlTools.htmlPageWrap(html)
def generateHtml(pathLocal):
"""
This page shows all child data for a parent ABF.
All child images are shown.
Options are available to edit comments for this parent.
"""
if not os.path.exists(pathLocal):
return f"ERROR: file does not exist: [{pathLocal}]"
pathFolder = os.path.dirname(pathLocal)
parentAbfFileName = os.path.basename(pathLocal)
parentAbfId = os.path.splitext(parentAbfFileName)[0]
abfFolder = abfBrowse.AbfFolder(pathFolder)
if not parentAbfId and len(abfFolder.abfList.family):
parentAbfId = list(abfFolder.abfList.family.keys())[0]
if not parentAbfId in abfFolder.abfList.family.keys():
html = f"ERROR: [{pathLocal}] is not a parent ABF"
return abfBrowse.htmlTools.htmlPageWrap(html)
cellsFile = abfBrowse.CellsFile(abfFolder.path)
parentNote = cellsFile.getNoteForAbf(parentAbfId)
abfFolder.convertTifsOfParent(parentAbfId)
html = ""
html += pageParentHeader(abfFolder, parentNote)
html += pageParentNotes(abfFolder, parentNote)
html += pageParentChildAbfList(abfFolder, parentNote)
html += pageFolderActions(abfFolder, parentNote)
html += pageParentImages(abfFolder, parentNote)
html = abfBrowse.htmlTools.htmlPageWrap(html)
return html
def test_json_abfFolder(folderPath):
print(f"creating JSON for abf folder: {folderPath}")
abfFolder = abfBrowse.AbfFolder(folderPath)
print()
print(abfFolder.toJSON())