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, 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 cli(query: str, git: bool, sort_field: Optional[str], doc_folder: str,
sort_reverse: bool) -> None:
"""Rename entry"""
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:rename')
if not documents:
logger.warning(papis.strings.no_documents_retrieved_message)
docs = papis.pick.pick_doc(documents)
if not docs:
return
document = docs[0]
new_name = papis.tui.utils.prompt(
"Enter new folder name:\n"
">",
default=document.get_main_folder_name() or '')
run(document, new_name, git=git)
def add(self,
doc_manager=None,
document=None,
folder_name=None,
key=None,
value=None,
doc=False,
file=False,
file_name=None):
if doc_manager is not None:
document = doc_manager.get_document()
folder_name = document.get_main_folder_name()
folder_path = self.get_folder_path(folder_name)
if file or doc:
self.add_file(folder_name,
file_path=value,
file_name=file_name,
doc=doc,
file=file)
if file:
document.set_key(key, file_name, append=True)
document.save()
self.update(document)
elif doc:
document = papis.document.Document(folder_path, document)
document.save(data=document)
self._database.add(document)
return document
def move_files_to_shared_library(self, document, validation=False):
folder_name = document.get_main_folder_name()
for library in self._library:
folder_path = self.get_folder_path(folder_name,
library=library.get_path())
files = []
if os.path.exists(folder_path):
files = [
f for f in os.listdir(folder_path)
if os.path.isfile(os.path.join(folder_path, f))
]
extension, include = self.get_extension_to_ignore(library)
for f in files:
if not self.is_extension_in_library(f, extension, include):
if validation:
return False
self.add_file(folder_name,
file_path=os.path.join(folder_path, f),
file=True,
file_name=os.path.basename(f))
os.unlink(os.path.join(folder_path, f))
if validation:
return True
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, 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 cli(query: str, git: bool, sort_field: Optional[str], doc_folder: str,
sort_reverse: bool) -> None:
"""Move a document into some other path"""
# Leave this imports here for performance
import prompt_toolkit
import prompt_toolkit.completion
logger = logging.getLogger('cli:mv')
if doc_folder:
documents = [papis.document.from_folder(doc_folder)]
else:
documents = papis.database.get().query(query)
if not documents:
logger.warning(papis.strings.no_documents_retrieved_message)
return
if sort_field:
documents = papis.document.sort(documents, sort_field, sort_reverse)
docs = papis.pick.pick_doc(documents)
if not docs:
return
document = docs[0]
lib_dir = os.path.expanduser(papis.config.get_lib_dirs()[0])
completer = prompt_toolkit.completion.PathCompleter(
only_directories=True, get_paths=lambda: [lib_dir])
try:
new_folder = os.path.join(
lib_dir,
prompt_toolkit.prompt(
message=("Enter directory : (Tab completion enabled)\n"
"Current directory: ({dir})\n".format(
dir=document.get_main_folder_name()) + "> "),
completer=completer,
complete_while_typing=True))
except Exception as e:
logger.error(e)
return
logger.info(new_folder)
if not os.path.exists(new_folder):
logger.info("Creating path %s" % new_folder)
os.makedirs(new_folder, mode=papis.config.getint('dir-umask') or 0o666)
run(document, new_folder, git=git)
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"]
)
