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petermr / CEVOpen

Contentmining of Open phytochemical literature for medicinal activities
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Error while doing ami_gui.py #96

Open 950vasant opened 3 years ago

950vasant commented 3 years ago 
C:\Users\vasan\openDiagram\physchem\python>python ami_gui.py
<class 'str'> C:\Users\vasan\openDiagram\physchem\python\section_templates.json
dict_keys(['abstract', 'acknowledge', 'affiliation', 'author', 'conclusion', 'discussion', 'ethics', 'fig_caption', 'front', 'introduction', 'jrnl_title', 'keyword', 'method', 'octree', 'pdfimage', 'pub_date', 'publisher', 'reference', 'results_discuss', 'search_results', 'sections', 'svg', 'table', 'title'])
SECTION LIST {'abstract': {'_DESC': 'abstract(s) usually in front; sometimes duplicated', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '*article-meta', 'FILE': '*abstract', 'SUFFIX': 'xml', '_MAKE': ['AmiSection.makeSections']}, 'acknowledge': {'_DESC': 'acknowledgments (may include funders)', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_back', 'SUBSUB': '_NULL', 'FILE': '*ack', 'SUFFIX': 'xml'}, 'affiliation': {'_DESC': 'author affiliations, usually institutiom and country; aometimes structured', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '*article-meta', 'FILE': '*aff', 'SUFFIX': 'xml'}, 'author': {'_DESC': 'authors, maybe with affiliation links (e.g. #aff1 etc.)', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '*article-meta', 'FILE': '*contrib-group', 'SUFFIX': 'xml'}, 'conclusion': {'_DESC': 'conclusion (might overlap with discussion)', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': '**', 'SUBSECT': '*conclusion*', 'SUBSUB': '**', 'FILE': '*p', 'SUFFIX': 'xml'}, 'discussion': {'_DESC': 'discussion', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': '**', 'SUBSECT': '*discussion*', 'SUBSUB': '**', 'FILE': '*p', 'SUFFIX': 'xml'}, 'ethics': {'_DESC': 'ethics statements; often in methods but found elsewhere', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '**', 'SUBSUB': '*ethic*', 'FILE': '*p*', 'SUFFIX': 'xml'}, 'fig_caption': {'_DESC': 'captions of figures', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': 'figures', 'SUBSUB': '_NULL', 'FILE': '*figure*', 'SUFFIX': 'xml'}, 'front': {'_DESC': 'ALL front matter; recommend constraining with SUBSUB and FILE', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '**', 'FILE': '_REQD', 'SUFFIX': 'xml'}, 'introduction': {'_DESC': 'introduction or background; looks for these words anywhere in file titles', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': '**', 'SUBSECT': ['*introduction*', '*background*'], 'SUBSUB': '**', 'FILE': '*', 'SUFFIX': 'xml'}, 'jrnl_title': {'_DESC': 'journal title (may contain alternatives)', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '*journal-meta', 'FILE': '*journal-title-group', 'SUFFIX': 'xml'}, 'keyword': {'_DESC': 'publisher or author keywords', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '*article-meta', 'FILE': '*kwd-group', 'SUFFIX': 'xml'}, 'method': {'_DESC': 'methods and/or materials; looks for these words anywhere in file titles', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': '**', 'SUBSECT': ['*method*', '*material*'], 'SUBSUB': '**', 'FILE': '*p', 'SUFFIX': 'xml'}, 'octree': {'_DESC': 'octree colour channels; requires octree to have been run', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'pdfimages', 'SUBSECT': 'image*', 'SUBSUB': '*octree', 'FILE': 'channel*', 'SUFFIX': 'png'}, 'pdfimage': {'_DESC': 'images extracted from PDF; default raw.png; requires ami pdfbox to have been run', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'pdfimages', 'SUBSECT': 'image*', 'SUBSUB': '_NULL', 'FILE': 'raw', 'SUFFIX': 'png'}, 'pub_date': {'_DESC': 'publication date(s); front; a variety of types and granularity', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '*article-meta', 'FILE': '*pub-date', 'SUFFIX': 'xml'}, 'publisher': {'_DESC': 'publisher; journal', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '*journal-meta', 'FILE': '*publisher', 'SUFFIX': 'xml'}, 'reference': {'_DESC': 'references often called citations; semi-structured or structured', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_back', 'SUBSUB': '*ref-list', 'FILE': '*ref', 'SUFFIX': 'xml'}, 'results_discuss': {'_DESC': 'results and/or discussion ', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': '**', 'SUBSECT': ['*results*', '*discussion*'], 'SUBSUB': '**', 'FILE': '*p', 'SUFFIX': 'xml'}, 'search_results': {'_DESC': 'result of AMI search (search|word) * (result|empty); ami search should have been run (will update for pyamisearch)', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'results', 'SUBSECT': ['search', 'word'], 'SUBSUB': '**', 'FILE': ['results', 'empty'], 'SUFFIX': 'xml'}, 'sections': {'_DESC': 'ALL *.xml under sections/; often constrained with SUBSECT/ and SUBSET/', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '**', 'SUBSUB': '**', 'FILE': '*', 'SUFFIX': 'xml'}, 'svg': {'_DESC': 'svg pages extracted from PDF; after running ami pdfbox', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'svg', 'SUBSECT': '_NULL', 'SUBSUB': '_NULL', 'FILE': 'fulltext-page*', 'SUFFIX': 'svg'}, 'table': {'_DESC': 'tables including caption; extracted from floats-group', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': 'tables', 'SUBSUB': '_NULL', 'FILE': '*table*', 'SUFFIX': 'xml'}, 'title': {'_DESC': 'article title (may contain alternatives)', 'PROJ': '_REQD', 'TREE': '*', 'SECTS': 'sections', 'SUBSECT': '*_front', 'SUBSUB': '*article-meta', 'FILE': '*title-group', 'SUFFIX': 'xml'}}
project files not available for  C:\Users\vasan\openDiagram\python\diagrams\satish\cct
project files not available for  C:\Users\vasan\openVirus\miniproject\disease\1-part
project files not available for  C:\Users\vasan\worcester\synthesis
project files not available for  C:\Users\vasan\worcester\explosion
Traceback (most recent call last):
  File "C:\Users\vasan\openDiagram\physchem\python\ami_gui.py", line 1109, in <module>
    app = AmiGui(master=root)
  File "C:\Users\vasan\openDiagram\physchem\python\ami_gui.py", line 77, in __init__
    self.create_all_widgets(root)
  File "C:\Users\vasan\openDiagram\physchem\python\ami_gui.py", line 88, in create_all_widgets
    self.create_display_frame(master)
  File "C:\Users\vasan\openDiagram\physchem\python\ami_gui.py", line 155, in create_display_frame
    if self.show_html_frame:
AttributeError: 'AmiGui' object has no attribute 'show_html_frame'