def add(self, document):
docs = self.get_documents()
self.logger.debug('adding ...')
docs.append(document)
assert (docs[-1].get_main_folder() == document.get_main_folder())
assert (os.path.exists(document.get_main_folder()))
self.save()
def main(self):
documents = self.get_db().query(self.args.search)
if self.args.json and self.args.folder or \
self.args.yaml and self.args.folder:
self.logger.warning("Only --folder flag will be considered")
if not self.args.all:
document = self.pick(documents)
if not document:
return 0
documents = [document]
if self.args.out and not self.get_args().folder \
and not self.args.file:
self.args.out = open(self.get_args().out, 'a+')
if not self.args.out and not self.get_args().folder \
and not self.args.file:
self.args.out = sys.stdout
ret_string = run(documents,
yaml=self.args.yaml,
bibtex=self.args.bibtex,
json=self.args.json,
text=self.args.text)
if ret_string is not None:
self.args.out.write(ret_string)
return 0
for document in documents:
if self.args.folder:
folder = document.get_main_folder()
outdir = self.args.out or document.get_main_folder_name()
if not len(documents) == 1:
outdir = os.path.join(outdir,
document.get_main_folder_name())
shutil.copytree(folder, outdir)
if not self.args.no_bibtex:
open(os.path.join(outdir, "info.bib"),
"a+").write(papis.document.to_bibtex(document))
elif self.args.file:
files = document.get_files()
if self.args.all:
files_to_open = files
else:
files_to_open = [
papis.api.pick(
files,
pick_config=dict(header_filter=lambda x: x.replace(
document.get_main_folder(), "")))
]
for file_to_open in filter(lambda x: x, files_to_open):
print(file_to_open)
shutil.copyfile(
file_to_open, self.args.out
or os.path.basename(file_to_open))
def cli(query: str,
doc_folder: str,
git: bool,
notes: bool,
_all: bool,
editor: Optional[str],
sort_field: Optional[str],
sort_reverse: bool) -> None:
"""Edit document information from a given library"""
logger = logging.getLogger('cli:edit')
if doc_folder:
documents = [papis.document.from_folder(doc_folder)]
else:
documents = papis.database.get().query(query)
if sort_field:
documents = papis.document.sort(documents, sort_field, sort_reverse)
if editor is not None:
papis.config.set('editor', editor)
if not _all:
documents = list(papis.pick.pick_doc(documents))
if len(documents) == 0:
logger.warning(papis.strings.no_documents_retrieved_message)
return
for document in documents:
if notes:
logger.debug("Editing notes")
if not document.has("notes"):
logger.warning(
"The document selected has no notes attached, \n"
"creating a notes files"
)
document["notes"] = papis.config.getstring("notes-name")
document.save()
notes_path = os.path.join(
str(document.get_main_folder()),
document["notes"]
)
if not os.path.exists(notes_path):
logger.info("Creating {0}".format(notes_path))
open(notes_path, "w+").close()
papis.api.edit_file(notes_path)
if git:
papis.git.add_and_commit_resource(
str(document.get_main_folder()),
str(document.get_info_file()),
"Update notes for '{0}'".format(
papis.document.describe(document)))
else:
run(document, git=git)
def cli(query, yaml, bibtex, json, folder, out, text, all, file):
"""Export a document from a given library"""
logger = logging.getLogger('cli:export')
documents = papis.database.get().query(query)
if json and folder or yaml and folder:
logger.warning("Only --folder flag will be considered")
if not all:
document = papis.api.pick_doc(documents)
if not document:
return 0
documents = [document]
ret_string = run(documents, yaml=yaml, bibtex=bibtex, json=json, text=text)
if ret_string is not None:
if out is not None:
logger.info("Dumping to {0}".format(out))
with open(out, 'w+') as fd:
fd.write(ret_string)
else:
logger.info("Dumping to stdout")
print(ret_string)
return 0
for document in documents:
if folder:
folder = document.get_main_folder()
outdir = out or document.get_main_folder_name()
if not len(documents) == 1:
outdir = os.path.join(outdir, document.get_main_folder_name())
shutil.copytree(folder, outdir)
elif file:
logger.info("Exporting file")
files = document.get_files()
assert (isinstance(files, list))
if not files:
logger.error('No files found for doc in {0}'.format(
document.get_main_folder()))
continue
files_to_open = [
papis.api.pick(
files,
pick_config=dict(header_filter=lambda x: x.replace(
document.get_main_folder(), "")))
]
files_to_copy = list(filter(lambda x: x, files_to_open))
for file_to_open in files_to_copy:
if out is not None and len(files_to_open) == 1:
out_file = out
else:
out_file = os.path.basename(file_to_open)
logger.info("copy {0} to {1}".format(file_to_open, out_file))
shutil.copyfile(file_to_open, out_file)
def add(self, document: papis.document.Document) -> None:
docs = self.get_documents()
self.logger.debug('adding ...')
docs.append(document)
assert(docs[-1].get_main_folder() == document.get_main_folder())
_folder = document.get_main_folder()
assert(_folder is not None)
assert(os.path.exists(_folder))
self.save()
def cli(query: str,
doc_folder: str,
sort_field: Optional[str],
sort_reverse: bool,
folder: str,
out: str,
fmt: str,
_all: bool) -> None:
"""Export a document from a given library"""
if doc_folder:
documents = [papis.document.from_folder(doc_folder)]
else:
documents = papis.database.get().query(query)
if fmt and folder:
logger.warning("Only --folder flag will be considered")
if not documents:
logger.warning(papis.strings.no_documents_retrieved_message)
return
if not _all:
documents = [d for d in papis.pick.pick_doc(documents)]
if not documents:
return
if sort_field:
documents = papis.document.sort(documents, sort_field, sort_reverse)
# Get the local folder of the document so that third-party apps
# can actually go to the folder without checking with papis
for d in documents:
d["_papis_local_folder"] = d.get_main_folder()
ret_string = run(documents, to_format=fmt)
if ret_string is not None and not folder:
if out is not None:
logger.info("Dumping to {0}".format(out))
with open(out, 'a+') as fd:
fd.write(ret_string)
else:
logger.info("Dumping to stdout")
print(ret_string)
return
for document in documents:
if folder:
_doc_folder = document.get_main_folder()
_doc_folder_name = document.get_main_folder_name()
outdir = out or _doc_folder_name
if not _doc_folder or not _doc_folder_name or not outdir:
raise Exception(papis.strings.no_folder_attached_to_document)
if not len(documents) == 1:
outdir = os.path.join(out, _doc_folder_name)
logger.info("Exporting doc {0} to {1}".format(
papis.document.describe(document), outdir
))
shutil.copytree(_doc_folder, outdir)
def cli(query, file, force):
"""Delete command for several objects"""
documents = papis.database.get().query(query)
logger = logging.getLogger('cli:rm')
if not documents:
logger.warning(papis.strings.no_documents_retrieved_message)
return 0
document = papis.api.pick_doc(documents)
if not document:
return
if file:
filepath = papis.api.pick(document.get_files())
if not filepath:
return
if not force:
tbar = 'The file {0} would be removed'.format(filepath)
if not papis.utils.confirm("Are you sure?", bottom_toolbar=tbar):
return
logger.info("Removing %s..." % filepath)
return run(document, filepath=filepath)
else:
if not force:
tbar = 'The folder {0} would be removed'.format(
document.get_main_folder())
logger.warning("This document will be removed, check it")
papis.utils.text_area(title=tbar,
text=papis.document.dump(document),
lexer_name='yaml')
if not papis.utils.confirm("Are you sure?", bottom_toolbar=tbar):
return
logger.info("Removing ...")
return run(document)
def run(document: papis.document.Document,
new_name: str,
git: bool = False) -> None:
db = papis.database.get()
logger = logging.getLogger('rename:run')
folder = document.get_main_folder()
if not folder:
raise Exception(papis.strings.no_folder_attached_to_document)
subfolder = os.path.dirname(folder)
new_folder_path = os.path.join(subfolder, new_name)
if os.path.exists(new_folder_path):
logger.warning("Path '%s' already exists", new_folder_path)
return
cmd = ['git', '-C', folder] if git else []
cmd += ['mv', folder, new_folder_path]
import subprocess
logger.debug(cmd)
subprocess.call(cmd)
if git:
papis.git.commit(new_folder_path,
"Rename from {} to '{}'".format(folder, new_name))
db.delete(document)
logger.debug("New document folder: '%s'", new_folder_path)
document.set_folder(new_folder_path)
db.add(document)
def cli(query, file, force):
"""Delete command for several objects"""
documents = papis.database.get().query(query)
document = papis.api.pick_doc(documents)
if not document:
return status.file_not_found
if file:
filepath = papis.api.pick(document.get_files())
if not filepath:
return status.file_not_found
if not force:
toolbar = 'The file {0} would be removed'.format(filepath)
if not papis.utils.confirm("Are you sure?",
bottom_toolbar=toolbar):
return status.success
click.echo("Removing %s..." % filepath)
return run(document, filepath=filepath)
else:
if not force:
toolbar = 'The folder {0} would be removed'.format(
document.get_main_folder())
if not papis.utils.confirm("Are you sure?",
bottom_toolbar=toolbar):
return status.success
click.echo("Removing ...")
return run(document)
def run(document: papis.document.Document,
filepath: Optional[str] = None,
git: bool = False) -> None:
"""Main method to the rm command
"""
db = papis.database.get()
_doc_folder = document.get_main_folder()
if not _doc_folder:
raise Exception(papis.strings.no_folder_attached_to_document)
if filepath is not None:
os.remove(filepath)
document['files'].remove(os.path.basename(filepath))
document.save()
db.update(document)
if git:
papis.git.rm(_doc_folder, filepath)
papis.git.add(_doc_folder, document.get_info_file())
papis.git.commit(_doc_folder, "Remove file '{0}'".format(filepath))
else:
if git:
_topfolder = os.path.dirname(os.path.abspath(_doc_folder))
papis.git.rm(_doc_folder, _doc_folder, recursive=True)
papis.git.commit(
_topfolder, "Remove document '{0}'".format(
papis.document.describe(document)))
else:
papis.document.delete(document)
db.delete(document)
def run(document: papis.document.Document,
filepaths: List[str],
git: bool = False) -> None:
logger = logging.getLogger('addto')
from string import ascii_lowercase
g = papis.utils.create_identifier(ascii_lowercase)
string_append = ''
_doc_folder = document.get_main_folder()
if not _doc_folder:
raise Exception("Document does not have a folder attached")
for i in range(len(document.get_files())):
string_append = next(g)
new_file_list = []
for i in range(len(filepaths)):
in_file_path = filepaths[i]
if not os.path.exists(in_file_path):
raise Exception("{} not found".format(in_file_path))
# Rename the file in the staging area
new_filename = papis.utils.clean_document_name(
papis.commands.add.get_file_name(papis.document.to_dict(document),
in_file_path,
suffix=string_append))
new_file_list.append(new_filename)
end_document_path = os.path.join(_doc_folder, new_filename)
string_append = next(g)
# Check if the absolute file path is > 255 characters
if len(os.path.abspath(end_document_path)) >= 255:
logger.warning('Length of absolute path is > 255 characters. '
'This may cause some issues with some pdf viewers')
if os.path.exists(end_document_path):
logger.warning("%s already exists, ignoring...", end_document_path)
continue
import shutil
logger.info("[CP] '%s' to '%s'", in_file_path, end_document_path)
shutil.copy(in_file_path, end_document_path)
if "files" not in document.keys():
document["files"] = []
document['files'] += new_file_list
document.save()
papis.database.get().update(document)
if git:
for r in new_file_list + [document.get_info_file()]:
papis.git.add(_doc_folder, r)
papis.git.commit(
_doc_folder,
"Add new files to '{}'".format(papis.document.describe(document)))
def edit_notes(document: papis.document.Document, git: bool = False) -> None:
logger = logging.getLogger('edit:notes')
logger.debug("Editing notes")
if not document.has("notes"):
document["notes"] = papis.config.getstring("notes-name")
document.save()
notes_path = os.path.join(str(document.get_main_folder()),
document["notes"])
if not os.path.exists(notes_path):
logger.debug("Creating {0}".format(notes_path))
open(notes_path, "w+").close()
papis.api.edit_file(notes_path)
if git:
papis.git.add_and_commit_resource(
str(document.get_main_folder()), str(document.get_info_file()),
"Update notes for '{0}'".format(papis.document.describe(document)))
def cli(query: str,
git: bool,
_file: bool,
force: bool,
_all: bool,
doc_folder: str,
sort_field: Optional[str],
sort_reverse: bool) -> None:
"""Delete a document or a file"""
if doc_folder:
documents = [papis.document.from_folder(doc_folder)]
else:
documents = papis.database.get().query(query)
if sort_field:
documents = papis.document.sort(documents, sort_field, sort_reverse)
logger = logging.getLogger('cli:rm')
if not documents:
logger.warning(papis.strings.no_documents_retrieved_message)
return
if not _all:
documents = list(papis.pick.pick_doc(documents))
if _file:
for document in documents:
filepaths = papis.pick.pick(document.get_files())
if not filepaths:
continue
filepath = filepaths[0]
if not force:
tbar = 'The file {0} would be removed'.format(filepath)
if not papis.tui.utils.confirm(
"Are you sure?", bottom_toolbar=tbar):
continue
logger.info("Removing '%s'...", filepath)
run(document, filepath=filepath, git=git)
else:
for document in documents:
if not force:
tbar = 'The folder {0} would be removed'.format(
document.get_main_folder())
logger.warning("This document will be removed, check it")
papis.tui.utils.text_area(
title=tbar,
text=papis.document.dump(document),
lexer_name='yaml')
if not papis.tui.utils.confirm(
"Are you sure?", bottom_toolbar=tbar):
continue
logger.warning("Removing ...")
run(document, git=git)
def _locate_document(self, document):
assert (isinstance(document, papis.document.Document))
result = list(
filter(
lambda d: d[1].get_main_folder() == document.get_main_folder(),
enumerate(self.get_documents())))
if len(result) == 0:
raise Exception(
'The document passed could not be found in the library')
return result
def get_id_value(self, document):
"""Get the value that is stored in the unique key identifier
of the documents in the database. In the case of papis this is
just the path of the documents.
:param document: Papis document
:type document: papis.document.Document
:returns: Path for the document
:rtype: str
"""
return document.get_main_folder()
def main(self):
# TODO: Try to recycle some of this code with command add.
documents = papis.api.get_documents_in_lib(self.get_args().lib,
self.get_args().search)
document = self.pick(documents)
if not document: return 0
data = dict()
if self.args.auto:
if 'doi' in document.keys() and not self.args.from_doi:
self.args.from_doi = document['doi']
if 'title' in document.keys() and not self.args.from_isbnplus:
self.args.from_isbnplus = document['title']
if self.args.from_yaml:
import yaml
data.update(yaml.load(open(self.args.from_yaml)))
if self.args.from_isbnplus:
doc = self.pick([
papis.document.Document(data=d)
for d in papis.isbn.get_data(query=self.args.from_isbnplus)
])
if doc:
data.update(doc.to_dict())
if self.args.from_bibtex:
bib_data = papis.bibtex.bibtex_to_dict(self.args.from_bibtex)
if len(bib_data) > 1:
self.logger.warning(
'Your bibtex file contains more than one entry,'
' I will be taking the first entry')
data.update(bib_data[0])
if self.args.from_url:
url_data = papis.downloaders.utils.get(self.args.from_url)
data.update(url_data["data"])
document_paths = url_data["documents_paths"]
if not len(document_paths) == 0:
document_path = document_paths[0]
old_doc = self.pick(document["files"])
if papis.utils.confirm("Really replace document %s?" %
old_doc):
new_path = os.path.join(document.get_main_folder(),
old_doc)
self.logger.debug("Moving %s to %s" %
(document_path, new_path))
shutil.move(document_path, new_path)
if self.args.from_doi:
self.logger.debug("Try using doi %s" % self.args.from_doi)
data.update(papis.utils.doi_to_data(self.args.from_doi))
document.update(data, self.args.force, self.args.interactive)
document.save()
def add_folder(template, doc_mgr, edit_flag=True, pick_flag=True):
# prepare logging
log_prefix = "add:{0}".format("folder")
logger = logging.getLogger(log_prefix)
doc_mgr_tmp = _lib_mgr.set_doc_item(query=template,
fun_item=task.get_item(task._task_dir),
pick=pick_flag)
if doc_mgr_tmp.is_empty():
logger.info(log.no_item_retrieved("documents")) # @log
return 1
document = doc_mgr.get_document()
document_tmp = doc_mgr_tmp.get_document()
import os.path
dirs = [
d for d in os.listdir(document_tmp.get_main_folder())
if os.path.isdir(os.path.join(document_tmp.get_main_folder(), d))
]
for d in dirs:
logger.info("[CP] '{0}' to '{1}'".format( # @log
os.path.join(document_tmp.get_main_folder(), d),
os.path.join(document.get_main_folder(), d)))
shutil.copytree(os.path.join(document_tmp.get_main_folder(), d),
os.path.join(document.get_main_folder(), d))
if edit_flag:
from papis.commands.open import run
doc_mgr = _lib_mgr.set_doc_item(doc_list=[document],
fun_item=task.get_item(
task._task_workspace),
fun_mark=None,
pick=False)
run(doc_mgr, open_task=task._task_workspace, verbose=False)
return
def run(document: papis.document.Document,
opener: Optional[str] = None,
folder: bool = False,
mark: bool = False) -> None:
logger = logging.getLogger('open:run')
if opener is not None:
papis.config.set("opentool", opener)
_doc_folder = document.get_main_folder()
if _doc_folder is None:
raise Exception(papis.strings.no_folder_attached_to_document)
if folder:
# Open directory
papis.api.open_dir(_doc_folder)
else:
if mark:
logger.debug("Getting document's marks")
marks = document[papis.config.getstring("mark-key-name")]
if marks:
logger.info("Picking marks")
_mark_fmt = papis.config.getstring("mark-header-format")
_mark_name = papis.config.getstring("mark-format-name")
_mark_opener = papis.config.getstring("mark-opener-format")
if not _mark_fmt:
raise Exception("No mark header format")
if not _mark_name:
raise Exception("No mark name format")
mark_dict = papis.api.pick(
marks,
header_filter=lambda x: papis.format.format(
_mark_fmt, x, doc_key=_mark_name),
match_filter=lambda x: papis.format.format(
_mark_fmt, x, doc_key=_mark_name))
if mark_dict:
if not _mark_opener:
raise Exception("mark-opener-format not set")
opener = papis.format.format(_mark_opener,
papis.document.from_data(
mark_dict[0]),
doc_key=_mark_name)
logger.info("Setting opener to '%s'", opener)
papis.config.set("opentool", opener)
files = document.get_files()
if len(files) == 0:
logger.error("The document chosen has no files attached")
return
files_to_open = papis.api.pick(files, header_filter=os.path.basename)
for file_to_open in files_to_open:
papis.api.open_file(file_to_open, wait=False)
def get_id_value(self, document: papis.document.Document) -> str:
"""Get the value that is stored in the unique key identifier
of the documents in the database. In the case of papis this is
just the path of the documents.
:param document: Papis document
:type document: papis.document.Document
:returns: Path for the document
:rtype: str
"""
_folder = document.get_main_folder()
if _folder is None:
raise Exception(papis.strings.no_folder_attached_to_document)
else:
return _folder
def run(document: papis.document.Document,
wait: bool = True,
git: bool = False) -> None:
database = papis.database.get()
info_file_path = document.get_info_file()
if not info_file_path:
raise Exception(papis.strings.no_folder_attached_to_document)
papis.utils.general_open(info_file_path, "editor", wait=wait)
document.load()
database.update(document)
if git:
papis.git.add_and_commit_resource(
str(document.get_main_folder()), info_file_path,
"Update information for '{0}'".format(
papis.document.describe(document)))
def run(document: papis.document.Document,
data: Dict[str, Any] = dict(),
git: bool = False) -> None:
# Keep the ref the same, otherwise issues can be caused when
# writing LaTeX documents and all the ref's change
data['ref'] = document['ref']
document.update(data)
_update_with_database(document)
folder = document.get_main_folder()
info = document.get_info_file()
if not folder or not info:
raise Exception(papis.strings.no_folder_attached_to_document)
if git:
papis.git.add_and_commit_resource(
folder, info, "Update information for '{0}'".format(
papis.document.describe(document)))
def run(document: papis.document.Document,
new_folder_path: str,
git: bool = False) -> None:
logger = logging.getLogger('mv:run')
folder = document.get_main_folder()
if not folder:
raise Exception(papis.strings.no_folder_attached_to_document)
cmd = ['git', '-C', folder] if git else []
cmd += ['mv', folder, new_folder_path]
db = papis.database.get()
logger.debug(cmd)
subprocess.call(cmd)
db.delete(document)
new_document_folder = os.path.join(new_folder_path,
os.path.basename(folder))
logger.debug("New document folder: {}".format(new_document_folder))
document.set_folder(new_document_folder)
db.add(document)
def cli(query, folder, out, format, all, **kwargs):
"""Export a document from a given library"""
documents = papis.database.get().query(query)
if format and folder:
logger.warning("Only --folder flag will be considered")
if not documents:
logger.warning(papis.strings.no_documents_retrieved_message)
return
if not all:
document = papis.api.pick_doc(documents)
if not document:
return 0
documents = [document]
ret_string = run(
documents,
to_format=format,
)
if ret_string is not None and not folder:
if out is not None:
logger.info("Dumping to {0}".format(out))
with open(out, 'a+') as fd:
fd.write(ret_string)
else:
logger.info("Dumping to stdout")
print(ret_string)
return 0
for document in documents:
if folder:
folder = document.get_main_folder()
outdir = out or document.get_main_folder_name()
if not len(documents) == 1:
outdir = os.path.join((out or ''),
document.get_main_folder_name())
logger.info("Exporting doc {0} to {1}".format(
papis.document.describe(document), outdir))
shutil.copytree(folder, outdir)
def run(document, filepaths):
logger = logging.getLogger('addto')
g = papis.utils.create_identifier(ascii_lowercase)
string_append = ''
for i in range(len(document.get_files())):
string_append = next(g)
new_file_list = []
for i in range(len(filepaths)):
in_file_path = filepaths[i]
if not os.path.exists(in_file_path):
raise Exception("{} not found".format(in_file_path))
# Rename the file in the staging area
new_filename = papis.utils.clean_document_name(
papis.commands.add.get_file_name(papis.document.to_dict(document),
in_file_path,
suffix=string_append))
new_file_list.append(new_filename)
endDocumentPath = os.path.join(document.get_main_folder(),
new_filename)
string_append = next(g)
# Check if the absolute file path is > 255 characters
if len(os.path.abspath(endDocumentPath)) >= 255:
logger.warning('Length of absolute path is > 255 characters. '
'This may cause some issues with some pdf viewers')
if os.path.exists(endDocumentPath):
logger.warning("%s already exists, ignoring..." % endDocumentPath)
continue
logger.debug("[CP] '%s' to '%s'" % (in_file_path, endDocumentPath))
shutil.copy(in_file_path, endDocumentPath)
if not "files" in document.keys():
document["files"] = []
document['files'] += new_file_list
document.save()
papis.database.get().update(document)
def run(document: papis.document.Document,
wait: bool = True,
git: bool = False) -> None:
logger = logging.getLogger('run:edit')
info_file_path = document.get_info_file()
if not info_file_path:
raise Exception(papis.strings.no_folder_attached_to_document)
_old_dict = papis.document.to_dict(document)
papis.utils.general_open(info_file_path, "editor", wait=wait)
document.load()
_new_dict = papis.document.to_dict(document)
# If nothing changed there is nothing else to be done
if _old_dict == _new_dict:
logger.debug("old and new are equal, doing nothing")
return
papis.database.get().update(document)
papis.hooks.run("on_edit_done")
if git:
papis.git.add_and_commit_resource(
str(document.get_main_folder()), info_file_path,
"Update information for '{0}'".format(
papis.document.describe(document)))
def main(self):
# TODO: Try to recycle some of this code with command add.
import papis.api
documents = papis.api.get_documents_in_lib(self.get_args().lib,
self.get_args().search)
data = dict()
if self.args.from_bibtex:
bib_data = papis.bibtex.bibtex_to_dict(self.args.from_bibtex)
# Then it means that the user wants to update all the information
# appearing in the bibtex file
if len(bib_data) > 1:
self.logger.warning(
'Your bibtex file contains more than one entry,')
self.logger.warning(
'It is supposed that you want to update all the'
'documents appearing inside the bibtex file.')
for bib_element in bib_data:
doc = papis.document.Document(data=bib_element)
located_doc = papis.utils.locate_document(doc, documents)
if located_doc is None:
self.logger.error(
"The following information could not be located")
self.logger.error('\n' + doc.dump())
else:
located_doc.update(bib_element, self.args.force,
self.args.interactive)
located_doc.save()
return 0
data.update(bib_data[0])
if self.args.from_yaml:
import yaml
data.update(yaml.load(open(self.args.from_yaml)))
# For the coming parts we need to pick a document
document = self.pick(documents)
if not document: return 0
if self.args.auto:
if 'doi' in document.keys() and not self.args.from_doi:
self.args.from_doi = document['doi']
if 'title' in document.keys() and not self.args.from_isbnplus:
self.args.from_isbnplus = document['title']
if self.args.from_isbnplus:
import papis.isbn
doc = self.pick([
papis.document.Document(data=d)
for d in papis.isbn.get_data(query=self.args.from_isbnplus)
])
if doc:
data.update(doc.to_dict())
if self.args.from_url:
url_data = papis.downloaders.utils.get(self.args.from_url)
data.update(url_data["data"])
document_paths = url_data["documents_paths"]
if not len(document_paths) == 0:
document_path = document_paths[0]
old_doc = self.pick(document["files"])
if papis.utils.confirm("Really replace document %s?" %
old_doc):
new_path = os.path.join(document.get_main_folder(),
old_doc)
self.logger.debug("Moving %s to %s" %
(document_path, new_path))
shutil.move(document_path, new_path)
if self.args.from_doi:
self.logger.debug("Try using doi %s" % self.args.from_doi)
data.update(papis.utils.doi_to_data(self.args.from_doi))
document.update(data, self.args.force, self.args.interactive)
document.save()
def main(self):
if papis.config.in_mode("contact"):
self.init_contact_mode()
lib_dir = os.path.expanduser(papis.config.get('dir'))
data = dict()
# The folder name of the new document that will be created
out_folder_name = None
# The real paths of the documents to be added
in_documents_paths = self.args.document
# The basenames of the documents to be added
in_documents_names = []
# The folder name of the temporary document to be created
temp_dir = tempfile.mkdtemp("-"+self.args.lib)
if self.args.from_lib:
doc = self.pick(
papis.api.get_documents_in_lib(self.get_args().from_lib)
)
if doc:
self.args.from_folder = doc.get_main_folder()
if self.args.from_folder:
original_document = papis.document.Document(self.args.from_folder)
self.args.from_yaml = original_document.get_info_file()
in_documents_paths = original_document.get_files()
if self.args.from_url:
url_data = papis.downloaders.utils.get(self.args.from_url)
data.update(url_data["data"])
in_documents_paths.extend(url_data["documents_paths"])
# If no data was retrieved and doi was found, try to get
# information with the document's doi
if not data and url_data["doi"] is not None and\
not self.args.from_doi:
self.logger.warning(
"I could not get any data from %s" % self.args.from_url
)
self.args.from_doi = url_data["doi"]
if self.args.from_bibtex:
bib_data = papis.bibtex.bibtex_to_dict(self.args.from_bibtex)
if len(bib_data) > 1:
self.logger.warning(
'Your bibtex file contains more than one entry,'
' I will be taking the first entry'
)
data.update(bib_data[0])
if self.args.from_pmid:
self.logger.debug(
"I'll try using PMID %s via HubMed" % self.args.from_pmid
)
hubmed_url = "http://pubmed.macropus.org/articles/"\
"?format=text%%2Fbibtex&id=%s" % self.args.from_pmid
bibtex_data = papis.downloaders.utils.get_downloader(
hubmed_url,
"get"
).get_document_data().decode("utf-8")
bibtex_data = papis.bibtex.bibtex_to_dict(bibtex_data)
if len(bibtex_data):
data.update(bibtex_data[0])
if "doi" in data and not self.args.from_doi:
self.args.from_doi = data["doi"]
else:
self.logger.error(
"PMID %s not found or invalid" % self.args.from_pmid
)
if self.args.from_doi:
self.logger.debug("I'll try using doi %s" % self.args.from_doi)
data.update(papis.utils.doi_to_data(self.args.from_doi))
if len(self.get_args().document) == 0 and \
papis.config.get('doc-url-key-name') in data.keys():
doc_url = data[papis.config.get('doc-url-key-name')]
self.logger.info(
'I am trying to download the document from %s' % doc_url
)
down = papis.downloaders.utils.get_downloader(
doc_url,
'get'
)
file_name = tempfile.mktemp()
with open(file_name, 'wb+') as fd:
fd.write(down.get_document_data())
self.logger.info('Opening the file')
papis.api.open_file(file_name)
if papis.utils.confirm('Do you want to use this file?'):
self.args.document.append(file_name)
if self.args.from_yaml:
self.logger.debug("Yaml input file = %s" % self.args.from_yaml)
data.update(papis.utils.yaml_to_data(self.args.from_yaml))
if self.args.from_vcf:
data.update(papis.utils.vcf_to_data(self.args.from_vcf))
in_documents_names = [
papis.utils.clean_document_name(doc_path)
for doc_path in in_documents_paths
]
# Decide if we are adding the documents to an already existing document
# or it is a new document
if self.args.to:
self.logger.debug(
"Searching for the document where to add the files"
)
documents = papis.api.get_documents_in_dir(
lib_dir,
self.args.to
)
document = self.pick(documents)
if not document: return 0
document.update(
data,
interactive=self.args.interactive
)
document.save()
data = document.to_dict()
in_documents_paths = document.get_files() + in_documents_paths
data["files"] = [os.path.basename(f) for f in in_documents_paths]
# set out folder name the folder of the found document
out_folder_name = document.get_main_folder_name()
out_folder_path = document.get_main_folder()
else:
document = papis.document.Document(temp_dir)
if not papis.config.in_mode("contact"):
if len(in_documents_paths) == 0:
if not self.get_args().no_document:
self.logger.error("No documents to be added")
return 1
else:
in_documents_paths = [document.get_info_file()]
# We need the names to add them in the file field
# in the info file
in_documents_names = [papis.utils.get_info_file_name()]
# Save document to create the info file
document.update(
data, force=True, interactive=self.args.interactive
)
document.save()
data["title"] = self.args.title or self.get_default_title(
data,
in_documents_paths[0]
)
data["author"] = self.args.author or self.get_default_author(
data,
in_documents_paths[0]
)
self.logger.debug("Author = % s" % data["author"])
self.logger.debug("Title = % s" % data["title"])
if not self.args.name:
self.logger.debug("Getting an automatic name")
out_folder_name = self.get_hash_folder(
data,
in_documents_paths[0]
)
else:
temp_doc = papis.document.Document(data=data)
out_folder_name = papis.utils.format_doc(
self.args.name,
temp_doc
)
out_folder_name = papis.utils.clean_document_name(
out_folder_name
)
del temp_doc
if len(out_folder_name) == 0:
self.logger.error('The output folder name is empty')
return 1
data["files"] = in_documents_names
out_folder_path = os.path.join(
lib_dir, self.args.dir, out_folder_name
)
self.logger.debug("Folder name = % s" % out_folder_name)
self.logger.debug("Folder path = % s" % out_folder_path)
self.logger.debug("File(s) = % s" % in_documents_paths)
# Create folders if they do not exists.
if not os.path.isdir(temp_dir):
self.logger.debug("Creating directory '%s'" % temp_dir)
os.makedirs(temp_dir, mode=papis.config.getint('dir-umask'))
# Check if the user wants to edit before submitting the doc
# to the library
if self.args.edit:
document.update(
data, force=True, interactive=self.args.interactive
)
document.save()
self.logger.debug("Editing file before adding it")
papis.api.edit_file(document.get_info_file())
self.logger.debug("Loading the changes made by editing")
document.load()
data = document.to_dict()
# First prepare everything in the temporary directory
for i in range(min(len(in_documents_paths), len(data["files"]))):
in_doc_name = data["files"][i]
in_file_path = in_documents_paths[i]
assert(os.path.exists(in_file_path))
endDocumentPath = os.path.join(
document.get_main_folder(),
in_doc_name
)
if os.path.exists(endDocumentPath):
self.logger.debug(
"%s already exists, ignoring..." % endDocumentPath
)
continue
if not self.args.no_document:
self.logger.debug(
"[CP] '%s' to '%s'" %
(in_file_path, endDocumentPath)
)
shutil.copy(in_file_path, endDocumentPath)
# Duplication checking
self.logger.debug("Check if the added document is already existing")
found_document = papis.utils.locate_document(
document, papis.api.get_documents_in_lib(papis.api.get_lib())
)
if found_document is not None:
self.logger.warning("DUPLICATION WARNING")
self.logger.warning(
"This document seems to be already in your libray: \n\n" +
found_document.dump()
)
self.logger.warning(
"Use the update command if you just want to update the info."
)
self.args.confirm = True
document.update(data, force=True)
if self.get_args().open:
for d_path in in_documents_paths:
papis.api.open_file(d_path)
if self.args.confirm:
if not papis.utils.confirm('Really add?'):
return 0
document.save()
if self.args.to:
return 0
self.logger.debug(
"[MV] '%s' to '%s'" %
(document.get_main_folder(), out_folder_path)
)
shutil.move(document.get_main_folder(), out_folder_path)
# Let us chmod it because it might come from a temp folder
# and temp folders are per default 0o600
os.chmod(out_folder_path, papis.config.getint('dir-umask'))
papis.api.clear_lib_cache()
if self.args.commit and papis.utils.lib_is_git_repo(self.args.lib):
subprocess.call(["git", "-C", out_folder_path, "add", "."])
subprocess.call(
["git", "-C", out_folder_path, "commit", "-m", "Add document"]
)
def run(paths,
data=dict(),
name=None,
file_name=None,
subfolder=None,
interactive=False,
from_bibtex=None,
from_yaml=None,
from_folder=None,
from_url=None,
from_doi=None,
from_pmid=None,
confirm=False,
open_file=False,
edit=False,
commit=False,
no_document=False):
"""
:param paths: Paths to the documents to be added
:type paths: []
:param data: Data for the document to be added.
If more data is to be retrieved from other sources, the data dictionary
will be updated from these sources.
:type data: dict
:param name: Name of the folder where the document will be stored
:type name: str
:param file_name: File name of the document's files to be stored.
:type file_name: str
:param subfolder: Folder within the library where the document's folder
should be stored.
:type subfolder: str
:param interactive: Wether or not interactive functionality of this command
should be activated.
:type interactive: bool
:param from_bibtex: Filepath where to find a file containing bibtex info.
:type from_bibtex: str
:param from_yaml: Filepath where to find a file containing yaml info.
:type from_yaml: str
:param from_folder: Filepath where to find a papis document (folder +
info file) to be added to the library.
:type from_folder: str
:param from_url: Url to try to download information and files from.
:type from_url: str
:param from_url: doi number to try to download information from.
:type from_url: str
:param from_url: pmid number to try to download information from.
:type from_url: str
:param confirm: Wether or not to ask user for confirmation before adding.
:type confirm: bool
:param open_file: Wether or not to ask user for opening file before adding.
:type open_file: bool
:param edit: Wether or not to ask user for editing the infor file
before adding.
:type edit: bool
:param commit: Wether or not to ask user for committing before adding,
in the case of course that the library is a git repository.
:type commit: bool
:param no_document: Wether or not the document has no files attached.
:type no_document: bool
"""
logger = logging.getLogger('add:run')
# The folder name of the new document that will be created
out_folder_name = None
# The real paths of the documents to be added
in_documents_paths = paths
# The basenames of the documents to be added
in_documents_names = []
# The folder name of the temporary document to be created
temp_dir = tempfile.mkdtemp()
if from_folder:
original_document = papis.document.Document(from_folder)
from_yaml = original_document.get_info_file()
in_documents_paths = original_document.get_files()
if from_url:
url_data = papis.downloaders.utils.get(from_url)
data.update(url_data["data"])
in_documents_paths.extend(url_data["documents_paths"])
# If no data was retrieved and doi was found, try to get
# information with the document's doi
if not data and url_data["doi"] is not None and\
not from_doi:
logger.warning("I could not get any data from %s" % from_url)
from_doi = url_data["doi"]
if from_bibtex:
bib_data = papis.bibtex.bibtex_to_dict(from_bibtex)
if len(bib_data) > 1:
logger.warning('Your bibtex file contains more than one entry,'
' I will be taking the first entry')
data.update(bib_data[0])
if from_pmid:
logger.debug("I'll try using PMID %s via HubMed" % from_pmid)
hubmed_url = "http://pubmed.macropus.org/articles/"\
"?format=text%%2Fbibtex&id=%s" % from_pmid
bibtex_data = papis.downloaders.utils.get_downloader(
hubmed_url, "get").get_document_data().decode("utf-8")
bibtex_data = papis.bibtex.bibtex_to_dict(bibtex_data)
if len(bibtex_data):
data.update(bibtex_data[0])
if "doi" in data and not from_doi:
from_doi = data["doi"]
else:
logger.error("PMID %s not found or invalid" % from_pmid)
if from_doi:
logger.debug("I'll try using doi %s" % from_doi)
data.update(papis.utils.doi_to_data(from_doi))
if len(paths) == 0 and \
papis.config.get('doc-url-key-name') in data.keys():
doc_url = data[papis.config.get('doc-url-key-name')]
logger.info('I am trying to download the document from %s' %
doc_url)
down = papis.downloaders.utils.get_downloader(doc_url, 'get')
file_name = tempfile.mktemp()
with open(file_name, 'wb+') as fd:
fd.write(down.get_document_data())
logger.info('Opening the file')
papis.api.open_file(file_name)
if papis.utils.confirm('Do you want to use this file?'):
paths.append(file_name)
if from_yaml:
logger.debug("Yaml input file = %s" % from_yaml)
data.update(papis.utils.yaml_to_data(from_yaml))
for p in in_documents_paths:
if not os.path.exists(p):
raise IOError('Document %s not found' % p)
in_documents_names = [
papis.utils.clean_document_name(doc_path)
for doc_path in in_documents_paths
]
document = papis.document.Document(temp_dir)
if len(in_documents_paths) == 0:
if not no_document:
logger.error("No documents to be added")
return status.file_not_found
else:
in_documents_paths = [document.get_info_file()]
# We need the names to add them in the file field
# in the info file
in_documents_names = [papis.utils.get_info_file_name()]
# Save document to create the info file
document.update(data, force=True, interactive=interactive)
document.save()
if not name:
logger.debug("Getting an automatic name")
if not os.path.isfile(in_documents_paths[0]):
return status.file_not_found
out_folder_name = get_hash_folder(data, in_documents_paths[0])
else:
temp_doc = papis.document.Document(data=data)
out_folder_name = papis.utils.format_doc(name, temp_doc)
out_folder_name = papis.utils.clean_document_name(out_folder_name)
del temp_doc
if len(out_folder_name) == 0:
logger.error('The output folder name is empty')
return status.file_not_found
data["files"] = in_documents_names
out_folder_path = os.path.expanduser(
os.path.join(papis.config.get('dir'), subfolder or '',
out_folder_name))
logger.debug("Folder name = % s" % out_folder_name)
logger.debug("Folder path = % s" % out_folder_path)
logger.debug("File(s) = % s" % in_documents_paths)
# First prepare everything in the temporary directory
g = papis.utils.create_identifier(ascii_lowercase)
string_append = ''
if file_name is not None: # Use args if set
papis.config.set("file-name", file_name)
new_file_list = []
for i in range(min(len(in_documents_paths), len(data["files"]))):
in_file_path = in_documents_paths[i]
if not os.path.exists(in_file_path):
return status.file_not_found
# Rename the file in the staging area
new_filename = papis.utils.clean_document_name(
get_file_name(data, in_file_path, suffix=string_append))
new_file_list.append(new_filename)
endDocumentPath = os.path.join(document.get_main_folder(),
new_filename)
string_append = next(g)
# Check if the absolute file path is > 255 characters
if len(os.path.abspath(endDocumentPath)) >= 255:
logger.warning('Length of absolute path is > 255 characters. '
'This may cause some issues with some pdf viewers')
if os.path.exists(endDocumentPath):
logger.debug("%s already exists, ignoring..." % endDocumentPath)
continue
if not no_document:
logger.debug("[CP] '%s' to '%s'" % (in_file_path, endDocumentPath))
shutil.copy(in_file_path, endDocumentPath)
data['files'] = new_file_list
# Check if the user wants to edit before submitting the doc
# to the library
if edit:
document.update(data, force=True, interactive=interactive)
document.save()
logger.debug("Editing file before adding it")
papis.api.edit_file(document.get_info_file(), wait=True)
logger.debug("Loading the changes made by editing")
document.load()
data = papis.document.to_dict(document)
# Duplication checking
logger.debug("Check if the added document is already existing")
found_document = papis.utils.locate_document(
document, papis.api.get_documents_in_lib(papis.api.get_lib()))
if found_document is not None:
logger.warning('\n' + papis.document.dump(found_document))
print("\n\n")
logger.warning("DUPLICATION WARNING")
logger.warning(
"The document above seems to be already in your library: \n\n")
logger.warning(
"(Hint) Use the update command if you just want to update"
" the info.")
confirm = True
document.update(data, force=True)
if open_file:
for d_path in in_documents_paths:
papis.api.open_file(d_path)
if confirm:
if not papis.utils.confirm('Really add?'):
return status.success
document.save()
logger.debug("[MV] '%s' to '%s'" %
(document.get_main_folder(), out_folder_path))
papis.document.move(document, out_folder_path)
papis.database.get().add(document)
if commit and papis.utils.lib_is_git_repo(papis.config.get_lib()):
subprocess.call(["git", "-C", out_folder_path, "add", "."])
subprocess.call(
["git", "-C", out_folder_path, "commit", "-m", "Add document"])
return status.success