def run(document, data=dict(), interactive=False, force=False):
# 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, force, interactive)
document.save()
papis.database.get().update(document)
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 update_doc_from_data_interactively(
document: Union[papis.document.Document, Dict[str, Any]],
data: Dict[str, Any], data_name: str) -> None:
import papis.tui.widgets.diff
docdata = copy.copy(document)
# do not compare some entries
docdata.pop('files', None)
docdata.pop('tags', None)
document.update(papis.tui.widgets.diff.diffdict(
docdata,
data,
namea=papis.document.describe(document),
nameb=data_name))
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,
data=dict(),
interactive=False,
force=False,
from_yaml=False,
from_bibtex=False,
from_url=False,
from_doi=False,
args=False):
logger = logging.getLogger('update:run')
if from_yaml:
import yaml
data.update(yaml.load(open(from_yaml)))
elif from_bibtex:
try:
bib_data = papis.bibtex.bibtex_to_dict(from_bibtex)
data.update(bib_data[0])
except Exception:
pass
elif from_url:
try:
url_data = papis.downloaders.utils.get(from_url)
data.update(url_data["data"])
except Exception:
pass
elif from_doi:
logger.debug("Try using doi %s" % from_doi)
data.update(papis.utils.doi_to_data(from_doi))
# 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, force, interactive)
document.save()
papis.database.get().update(document)
def run(document=papis.document.Document(),
file_list=[],
importer_list=(),
file_format=None,
folder_format=None,
ref_format=None,
confirm_flag=True,
edit_flag=True,
suffix_flag=True):
log_prefix = "add:{0}".format("document")
logger = logging.getLogger(log_prefix)
if file_format is None and user._add_file_name:
file_format = user._add_file_name
if folder_format is None and user._add_folder_name:
folder_format = user._add_folder_name
if ref_format is None and user._add_ref_name:
ref_format = user._add_ref_name
file_list = papis.utils._get_list(file_list)
ctx = get_data_from_importer(importer_list)
for key in ctx.data.keys():
document.set_key(key, ctx.data[key], append=True)
if papis.utils._validate_list(ctx.files):
file_list.append(ctx.files[0])
if not document.keys():
logger.error(log.no_data_retrieved) # @log
return 1
if confirm_flag:
data = papis.document.from_input(
document, "The following document will be added to your library")
if not data:
return 1
else:
document.update(data)
folder_name, document = papis.support.identifier.get_identifier(
data=document,
file_list=file_list,
folder_format=folder_format,
file_format=file_format,
ref_format=ref_format,
suffix=suffix_flag)
lib_mgr = papis.libmanager.get_lib_manager(logger=logger)
document = lib_mgr.add(document=document,
folder_name=folder_name,
value=file_list,
doc=True,
file_name=document[user._files_name])
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_editor),
fun_mark=None,
pick=False)
run(doc_mgr, open_task=task._task_editor, verbose=False)
return document
def run(document, data=dict()):
# 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)
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
