writing: Restructure module layout per-program
Similarly to the qutebrowser module we change the layout to have a program name at the top-level and all required files for that specific program within, whether they reside within .config, .local or anywhere else. We use dotter mappings to achieve this.
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19 changed files with 8 additions and 2 deletions
74
writing/papis/config
Normal file
74
writing/papis/config
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[settings]
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default-library = main
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formater = bbt
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local-config-file = .papis.config
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opentool = sioyek
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picktool = papis-tui
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mark-opener-format = sioyek --page {mark[value]}
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file-browser = vifm
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# edit info.yaml as new papers are added
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add-edit = True
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# ref-format = {doc[author_list][0][family]}{doc[year]}
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ref-format = bbt
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add-folder-name = {doc[author_list][0][family]}-{doc[title]}
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add-file-name = {doc[author_list][0][family]}{doc[year]}
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header-format-file = ~/.config/papis/headerformat
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extra-bibtex-keys = ["tags", "readstatus", "priority"]
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database-backend = whoosh
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whoosh-schema-fields = ["doi", "ref", "author", "year", "title", "publisher", "tags", "readstatus", "date", "isbn", "type", "keyword", "qualityassured", "priority"]
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# to make whoosh list everything by default
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default-query-string = *
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notes-name = notes.md
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notes-template = {doc[author_list][0][family]}{doc[year]}--{doc[title]}
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[tui]
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editmore = vi
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[main]
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dir = ~/documents/library
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# My personal reading
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[personal]
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dir = ~/documents/library/personal
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# Sustainable supply chain logistics, especially procurement
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[litrev-rahman]
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dir = ~/documents/library/litrev-rahman
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# Addressing Inequalities in World of Work research
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[ilo]
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dir = ~/documents/library/ilo-wow
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# fediverse-related academia, from
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# https://www.zotero.org/groups/5490166/fediverse_research
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[fedi]
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dir = ~/documents/library/fediverse
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# General computer science reading
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[cs]
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dir = ~/documents/library/cs
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# Electrical engineering reading
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[ee]
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dir = ~/documents/library/ee
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# All my university programme readings
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[emgs]
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dir = ~/documents/library/emgs
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# General research reading
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[academia]
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dir = ~/documents/library/academia
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[plugins.extract]
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tags = {"red": "important", "green": "extra", "blue": "toread"}
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[plugins.bbt-formatter]
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full-year = True
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title-words = 2
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title-chars = 20
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3
writing/papis/config.py
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3
writing/papis/config.py
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# from papis import config
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#
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# config.set("ref-format", f"{doc[author].split()[0] if 'author' in doc else 'Unknown'}{doc[year] if 'year' in doc else '0000'}")
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3
writing/papis/headerformat
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3
writing/papis/headerformat
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{doc.html_escape[title]}
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<ansigreen>{doc.html_escape[author]}</ansigreen>
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<ansiblue>({doc.html_escape[year]})</ansiblue> [<ansiyellow>{doc.html_escape[tags]}</ansiyellow>] [<ansired>{doc.html_escape[readstatus]}</ansired>]
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203
writing/papis/papistui.yaml
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203
writing/papis/papistui.yaml
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# current issues/requests
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# - [ ] call arbitrary shell command
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# - [ ] non-blocking opening of files
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# - [ ] distinguish in config between aliases for multiline/table
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# - [ ] update view after more operations
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# - if I call an 'update' command (e.g. set new tag or read status), it will not update in list until 'edit' command invoked and rebuilding the list
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# - two selection additions:
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# - [ ] select all in view
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# - [ ] limit view to currently selected
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#
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# for papis itself:
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# - [ ] I can not search custom numeric fields in whoosh? i.e. 'priority:1' will not give results. 'priority:high' will
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base:
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vimflavour: nvim
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documentlist:
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defaultstyle: multiline
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marked-icon: ""
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multilinestyle:
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rows:
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# TODO: show if already note attached; have info window display note content?
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- "{' ' if 'priority' not in doc or doc['priority'] == 'low' else '<red> </red>' if doc['priority'] == 'high' else '<yellow> </yellow>'}<cyan>{doc.alias('type')} {doc['ref']}</cyan> {doc.alias('readstatus')} {' ' if doc['notes'] else ''}"
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- "<white><bold>{doc.html_escape['title']}</bold></white>"
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- "<blue>{doc.html_escape['author']}</blue>"
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- "{doc.foreach('tags', '<lightgray>(</lightgray><gray><dim>{}</dim></gray><lightgray>)</lightgray>', split = ', ', sep = ' ')}"
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tablestyle:
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separator: " "
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headerstyle: "underline|bold"
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rowstyle: "white_bg"
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cursorrowstyle: "black_white|bold"
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columns:
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- {
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header: "",
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content: "{'' if 'priority' not in doc or doc['priority'] == 'low' else '' if doc['priority'] == 'high' else ''}",
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width: 1,
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}
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- {
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header: "",
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content: "{'' if doc['readstatus'] == 'read' else '' if doc['readstatus'] == 'skimmed' else ' '}",
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width: 1,
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}
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- {
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header: "",
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content: "{'' if doc['notes'] else '' if doc['note'] else ' '}",
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width: 1,
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}
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- {
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header: "",
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content: "{doc.alias('type')}",
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width: 1,
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}
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- { header: "Authors", content: "{doc['author']}", width: 25 }
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- { header: "Year", content: "{str(doc['year'])}", width: 4 }
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- { header: "Title", content: "{doc['title']}", width: 125 }
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- { header: "Reference", content: "{doc['ref']}", width: 15 }
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- {
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header: "",
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content: "{str(len(doc.get_files()) if len(doc.get_files()) > 0 else '')}",
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width: 1,
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}
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- { header: "Tags", content: "{doc['tags'] if isinstance(doc['tags'], str) else doc.foreach('tags', '{}', sep=', ')}", width: 35 }
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aliases:
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type:
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{
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article: "",
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book: "",
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inbook: "",
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incollection: "",
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software: "",
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presentation: "",
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thesis: "",
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techreport: "",
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_default_: "",
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}
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readstatus:
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{
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read: "<green></green>",
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skimmed: "<yellow></yellow>"
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}
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keymappings:
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q: quit
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"?": help
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T: toggle_style
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S: cmd "sort "
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/: search_mode
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<key_down>: scroll_down
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<key_up>: scroll_up
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<ctrl-f>: page_down
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<ctrl-b>: page_up
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G: jump_to_bottom
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gg: jump_to_top
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j: scroll_down
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k: scroll_up
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o: open -r "pdf$"
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O: open -d
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b: browse
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B: papis browse -k doi papis_id:{doc['papis_id']}
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R: view_reset
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<c-r>: reload
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e:
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- edit
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- edit info
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n:
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- papis edit -n papis_id:{doc['papis_id']}
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- edit notes
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"'n":
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- search "notes:.+"
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- limit to entries with notes
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"'u":
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- search "readstatus:read OR readstatus:skimmed"
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- limit to read entries
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"'r":
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- search "NOT readstatus:read AND NOT readstatus:skimmed"
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- limit to unread entries
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" ": mark_selected
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mm: mark_selected
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M: mark_down
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J: mark_down
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mu: unmark_all
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mv: mark_view
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",t": cmd "tag "
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",r":
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- papis update -s readstatus read papis_id:{doc['papis_id']}
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- set readstatus read
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",k":
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- papis update -s readstatus skimmed papis_id:{doc['papis_id']}
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- set readstatus skimmed
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",u":
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- papis update -s readstatus "" papis_id:{doc['papis_id']}
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- set readstatus unread
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",ph":
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- papis update -s priority high papis_id:{doc['papis_id']}
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- set priority high
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",pm":
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- papis update -s priority medium read papis_id:{doc['papis_id']}
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- set priority medium
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",pl":
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- papis update -s priority low read papis_id:{doc['papis_id']}
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- set priority low
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i:
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- info_toggle
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- "Toggle info window"
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I:
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- info_cycle
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- "Cycle info windows"
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<ctrl-p>: info_scroll_up
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<ctrl-n>: info_scroll_down
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# all require 'clip' script to be available on PATH
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yy:
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- copy_to_clipboard "[@{doc['ref']}]"
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- yank pandoc-styled reference
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ss:
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- vim_send "[@{doc['ref']}]"
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- send vim pandoc-styled reference
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yl:
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- copy_to_clipboard "\\cite\{{doc['ref']}\}"
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- yank latex-styled reference
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sl:
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- vim_send "\\cite\{{doc['ref']}\}"
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- send vim latex-styled reference
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yr:
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- copy_to_clipboard "{format_reference(doc,style='apa')}"
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- yank apa-styled reference
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sr:
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- vim_send "{format_reference(doc,style='apa')}"
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- send vim apa-styled reference
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yt:
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- copy_to_clipboard "{doc['title']}"
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- yank title
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yu:
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- copy_to_clipboard "{doc['url']}"
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- yank url
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yd:
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- copy_to_clipboard "{doc['doi']}"
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- yank doi
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# TODO look into https://github.com/supersambo/papis-tui vim-send mappings
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infowindow:
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default_on: False
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views:
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doc:
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content: "author: {doc['author'].strip()}\n title: {doc['title'].strip()}\n tags:{doc['tags'] if isinstance(doc['tags'], str) else doc.foreach('tags', '{}', sep=', ')}"
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height: 8
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apa:
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content: "{format_reference(doc,style='apa')}"
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abstract:
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content: "{doc['abstract']}"
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linewrap: True
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height: 8
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commandline:
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search:
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keyword_aliases: { a: "author:", t: "title:", y: "year:", k: "tags:" }
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statusbar:
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left:
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default: "<black_green><bold> {info['mode_upper']} </black_green></bold><green_bg></green_bg>"
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normal: "<black_green><bold> {info['mode_upper']} </black_green></bold><green_bg></green_bg>"
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command: "<black_cyan><bold> {info['mode_upper']} </black_cyan></bold><cyan_bg></cyan_bg>"
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select: "<black_red><bold> {info['mode_upper']} </black_red></bold><red_bg></red_bg>"
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search: "<black_magenta><bold> {info['mode_upper']} </black_magenta></bold><magenta_bg></magenta_bg>"
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right:
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default: "<green>{info['sortkeys']} </green><cyan_bg></cyan_bg><black_cyan> {info['idx']} < {info['marked']} < {info['view']} < {info['items']} </black_cyan>"
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163
writing/papis/scripts/papis-marvin
Executable file
163
writing/papis/scripts/papis-marvin
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@ -0,0 +1,163 @@
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#!/usr/bin/env python
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# papis-short-help: Import iOS Marvin exported csv annotations
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#
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# This script can be used to import your highlights and notes from
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# the iOS application 'Marvin Reader'. In the app, export your
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# annotations as 'csv' format and then point the script to the
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# resulting file.
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# https://git.martyoeh.me/Marty/papis-marvin
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import os
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import sys
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import re
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import logging
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from typing import Dict
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import papis.api
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import papis.pick
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import papis.format
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import papis.commands.edit
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import papis.commands.list
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import papis.commands.add
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import papis.notes
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import papis.config
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import papis.database
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import isbnlib
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import papis.isbn
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logger = logging.getLogger("marvin")
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logger.setLevel(logging.DEBUG)
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DEFAULT_CSV_PATH = "/home/marty/Nextcloud/Personal/Backups/Journal.csv"
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def main(fpath, db):
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with open(fpath) as f:
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import csv
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csv = csv.DictReader(f)
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notes = get_all_annotations(db, csv)
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write_to_files(notes)
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def get_all_annotations(db, csv) -> Dict:
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notes = {}
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note_file = ""
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for row in csv:
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# switch to next book
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if not is_same_book(row["Title"]):
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doc = get_document(db, row["Author"], row["Title"])
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if not doc:
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continue
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note_file = get_notefile(db, doc)
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text = format_entry(row)
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if note_file and text:
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if note_file not in notes.keys():
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notes[note_file] = []
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notes[note_file].append(text)
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return notes
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def get_document(db, author, title):
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res = query_document(db, author, title)
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if not res:
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add_to_database(author, title)
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res = query_document(db, author, title)
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if not res:
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logger.warning(f"Nothing found for {author}: {title}.\nPlease create manually.")
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return
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return res
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# TODO warn user/ let him pick with picker if multiple docs found
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def query_document(db, author, title):
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title = strip_string(title)
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for query in [f"author:({author}) title:({title})"]:
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print(f"query: {query}")
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res = db.query(query)
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if len(res) >= 1:
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return res[0]
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def add_to_database(author, title, confirm=True, edit=False):
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logger.info(f"Searching - '{title} {author}'")
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data = None
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try:
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data = papis.isbn.get_data(f"{title}")
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except isbnlib.ISBNLibException as e:
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logger.error(e)
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else:
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logger.warning(f"Found: {data}")
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if data:
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papis_data = papis.isbn.data_to_papis(data[0])
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papis.commands.add.run([], data=papis_data, confirm=confirm, edit=edit)
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def get_notefile(db, document) -> str | None:
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if not document.has("notes"):
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notes_name = papis.config.getstring("notes-name")
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document["notes"] = papis.format.format(notes_name, document)
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document.save()
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db.update(document)
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notes_path = os.path.join(str(document.get_main_folder()), document["notes"])
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if not os.path.exists(notes_path):
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# TODO reimplement logger: logger.debug("Creating '%s'", notes_path)
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papis.notes.notes_path_ensured(document)
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return notes_path
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# TODO implement custom formatting (akin to pubs-extract)
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def format_entry(row) -> str:
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text = f"> {row['HighlightText']}"
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if row["EntryText"]:
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if text:
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text += "\n"
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else:
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text = "> "
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text += f"{row['EntryText']}"
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return text
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_old_title = ""
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def is_same_book(title):
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global _old_title
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same = _old_title == title
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_old_title = title
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if same:
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return True
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return False
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def write_to_files(notes: Dict):
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# write to notes
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for f, entries in notes.items():
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if f:
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with open(f, "a") as note:
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logger.info(f"Editing {f}...")
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num_added = 0
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for entry in entries:
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with open(f) as noteread:
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if entry not in noteread.read():
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note.write(f"{entry}\n\n")
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num_added += 1
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logger.info(f"Added {num_added} entries to it.")
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strip_pattern = re.compile(r"([^\s\w]|_)+\w*")
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def strip_string(title) -> str:
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return strip_pattern.sub("", title)
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if __name__ == "__main__":
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# use argument passed to command as file or default file here
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fpath = sys.argv[1] if len(sys.argv) > 1 else DEFAULT_CSV_PATH
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main(fpath, papis.database.get())
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28
writing/papis/scripts/papis-reload
Executable file
28
writing/papis/scripts/papis-reload
Executable file
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#!/usr/bin/env python
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# papis-short-help: Manually rebuild cache for all libraries
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#
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# This tiny script updates all libraries by rebuilding their caches.
|
||||
# Useful to invoke after manual edits in one of your library folders
|
||||
# if you have many 'sub-libraries' (one library location with sub-
|
||||
# directories).
|
||||
# You don't have to think about which library you changed stuff in
|
||||
# and just get everything updated. Might take a little time but
|
||||
# should generally be a quick process ().
|
||||
|
||||
import papis.api
|
||||
from argparse import ArgumentParser
|
||||
|
||||
parser = ArgumentParser()
|
||||
_ = parser.add_argument(
|
||||
"--all", "-a", help="reload all libraries not just current", action="store_true"
|
||||
)
|
||||
args = parser.parse_args()
|
||||
|
||||
if args.all:
|
||||
libs = papis.api.get_libraries()
|
||||
else:
|
||||
libs = [papis.api.get_lib_name()]
|
||||
|
||||
for lib in libs:
|
||||
papis.api.clear_lib_cache(lib)
|
||||
_ = papis.api.get_all_documents_in_lib()
|
||||
116
writing/papis/scripts/papis-show
Executable file
116
writing/papis/scripts/papis-show
Executable file
|
|
@ -0,0 +1,116 @@
|
|||
#!/usr/bin/env python
|
||||
# papis-short-help: Display pretty human-readable document overview
|
||||
#
|
||||
# Takes a query and displays the metadata of the results. Uses
|
||||
# python-rich to display pretty panels if it exists in the environment,
|
||||
# otherwise displays regular text.
|
||||
# Can be invoked with -s to display single-line results better for
|
||||
# pasting into other documents.
|
||||
|
||||
import argparse
|
||||
from importlib.util import find_spec
|
||||
from papis import database
|
||||
from papis.database.base import Database
|
||||
from papis.document import Document
|
||||
from dataclasses import dataclass, field
|
||||
|
||||
parser = argparse.ArgumentParser()
|
||||
parser.add_argument(
|
||||
"--short", "-s", help="only display single-line quick info", action="store_true"
|
||||
)
|
||||
parser.add_argument(
|
||||
"--url",
|
||||
dest="identifier",
|
||||
help="display identifier (doi, isbn, url) or not",
|
||||
action=argparse.BooleanOptionalAction,
|
||||
default=True,
|
||||
)
|
||||
parser.add_argument("query", nargs="*", help="the query to search for")
|
||||
args = parser.parse_args()
|
||||
|
||||
|
||||
@dataclass
|
||||
class DocInfo:
|
||||
author: str = ""
|
||||
title: str = ""
|
||||
year: str = ""
|
||||
journal: str = ""
|
||||
volume: str = ""
|
||||
issue: str = ""
|
||||
pages: str = ""
|
||||
publisher: str = ""
|
||||
tags: list = field(default_factory=lambda: [])
|
||||
dtype: str = ""
|
||||
identifier: str = ""
|
||||
doi: str = ""
|
||||
|
||||
@staticmethod
|
||||
def from_Document(doc: Document):
|
||||
t: list[str] | str = doc.get("tags", "")
|
||||
tags = (
|
||||
t.replace(";", ",").replace(" ", "").split(",") if isinstance(t, str) else t
|
||||
)
|
||||
return DocInfo(
|
||||
author=doc.get("author", ""),
|
||||
title=doc.get("title", ""),
|
||||
year=doc.get("year", ""),
|
||||
journal=doc.get("journal", ""),
|
||||
volume=doc.get("volume", ""),
|
||||
issue=doc.get("issue", ""),
|
||||
pages=doc.get("pages", ""),
|
||||
publisher=doc.get("publisher", ""),
|
||||
tags=tags,
|
||||
dtype=doc.get("type", ""),
|
||||
identifier=doc.get("doi", doc.get("isbn", doc.get("url", ""))),
|
||||
)
|
||||
|
||||
|
||||
def main(db: Database, args) -> None:
|
||||
query = " ".join(args.query)
|
||||
docs: list[Document] = db.query(query)
|
||||
for doc in docs:
|
||||
info = DocInfo.from_Document(doc)
|
||||
if args.short:
|
||||
print_short(info, with_identifier=args.identifier)
|
||||
else:
|
||||
print_info(info, with_identifier=args.identifier)
|
||||
|
||||
|
||||
def print_short(doc: DocInfo, with_identifier: bool = True) -> None:
|
||||
print(
|
||||
f"{doc.author} ({doc.year}). {doc.title}. "
|
||||
f"{doc.identifier if with_identifier else ''}\n"
|
||||
)
|
||||
|
||||
|
||||
def print_info(doc: DocInfo, with_identifier: bool = True) -> None:
|
||||
if find_spec("rich"):
|
||||
from rich import print as richprint
|
||||
from rich.panel import Panel
|
||||
|
||||
info: str = (
|
||||
f"[red]{doc.author}[/red] ({doc.year}) "
|
||||
f"[steel_blue]\\[{doc.dtype}][/steel_blue]\n"
|
||||
f"[bold]{doc.title}[/bold]\n"
|
||||
f"{doc.journal} ({doc.volume}/{doc.issue}){doc.pages} - {doc.publisher}\n"
|
||||
f"[grey69]{[tag for tag in doc.tags]} "
|
||||
)
|
||||
if with_identifier:
|
||||
info += f"[link={doc.identifier}]{doc.identifier}[/link][/grey69]"
|
||||
richprint(Panel(info, expand=False))
|
||||
else:
|
||||
info: str = (
|
||||
f"{doc.author} ({doc.year}) "
|
||||
f"[{doc.dtype}]\n"
|
||||
f"{doc.title}\n"
|
||||
f"{doc.journal} ({doc.volume}/{doc.issue}){doc.pages} - {doc.publisher}\n"
|
||||
f"{[tag for tag in doc.tags]} "
|
||||
f"{doc.identifier}"
|
||||
if with_identifier
|
||||
else ""
|
||||
)
|
||||
print(f"{info}\n---")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main(database.get(), args)
|
||||
57
writing/papis/scripts/papis-tags
Executable file
57
writing/papis/scripts/papis-tags
Executable file
|
|
@ -0,0 +1,57 @@
|
|||
#!/usr/bin/env python
|
||||
# papis-short-help: List all tags occuring in query items
|
||||
#
|
||||
# Takes a query and spits out a sorted list of all tags contained therein,
|
||||
# nothing more.
|
||||
# Can be very useful for things like picking a tag or two and listing all
|
||||
# items that contain it:
|
||||
# $ papis tags "*" | fzf | xargs papis show "tags:{}"
|
||||
|
||||
import argparse
|
||||
from papis import database
|
||||
from papis.database.base import Database
|
||||
|
||||
from papis.document import Document
|
||||
|
||||
parser = argparse.ArgumentParser()
|
||||
parser.add_argument(
|
||||
"--count", "-c", help="the query to search for", action="store_true"
|
||||
)
|
||||
parser.add_argument("query", nargs="*", help="the query to search for", default="*")
|
||||
args = parser.parse_args()
|
||||
|
||||
|
||||
def main(db: Database, args) -> None:
|
||||
query = " ".join(args.query)
|
||||
docs: list[Document] = db.query(query)
|
||||
|
||||
all_tags: dict[str, int] = {}
|
||||
for doc in docs:
|
||||
t: list[str] | str = doc.get("tags", "")
|
||||
tags = (
|
||||
t.replace(";", ",").replace(" ", "").split(",") if isinstance(t, str) else t
|
||||
)
|
||||
|
||||
for tag in tags:
|
||||
if tag == '':
|
||||
continue
|
||||
all_tags[tag] = all_tags.get(tag, 0) + 1
|
||||
|
||||
if args.count:
|
||||
print_tags_and_counts(all_tags)
|
||||
else:
|
||||
print_tags_only(all_tags)
|
||||
|
||||
def print_tags_only(all_tags):
|
||||
for tag in sorted(all_tags):
|
||||
print(tag)
|
||||
|
||||
def print_tags_and_counts(all_tags):
|
||||
for tag, count in sorted(all_tags.items(), key=lambda d: d[1], reverse=True):
|
||||
if args.count:
|
||||
print(tag, count)
|
||||
else:
|
||||
print(tag)
|
||||
|
||||
if __name__ == "__main__":
|
||||
main(database.get(), args)
|
||||
Loading…
Add table
Add a link
Reference in a new issue