import from jabref-generated bib file does not import file links/attachments

nilsbecker commented 4 years ago

Report ID:

unavailable: i restarted zotero with debug logging, reproduced the error but the continue button on the better bibtex debug report screen is not clickable.

Full Bib(La)TeX item you are trying to import:

% Encoding: UTF-8

@Article{acar05,
  author    = {Acar, Murat and Becskei, Attila and van Oudenaarden, Alexander},
  title     = {Enhancement of cellular memory by reducing stochastic transitions},
  year      = {2005},
  language  = {en},
  volume    = {435},
  number    = {7039},
  month     = may,
  pages     = {228--232},
  issn      = {0028-0836},
  doi       = {10.1038/nature03524},
  url       = {http://www.nature.com/nature/journal/v435/n7039/abs/nature03524.html},
  urldate   = {2013-09-30},
  abstract  = {On induction of cell differentiation, distinct cell phenotypes are encoded by complex genetic networks. These networks can prevent the reversion of established phenotypes even in the presence of significant fluctuations. Here we explore the key parameters that determine the stability of cellular memory by using the yeast galactose-signalling network as a model system. This network contains multiple nested feedback loops. Of the two positive feedback loops, only the loop mediated by the cytoplasmic signal transducer Gal3p is able to generate two stable expression states with a persistent memory of previous galactose consumption states. The parallel loop mediated by the galactose transporter Gal2p only increases the expression difference between the two states. A negative feedback through the inhibitor Gal80p reduces the strength of the core positive feedback. Despite this, a constitutive increase in the Gal80p concentration tunes the system from having destabilized memory to having persistent memory. A model reveals that fluctuations are trapped more efficiently at higher Gal80p concentrations. Indeed, the rate at which single cells randomly switch back and forth between expression states was reduced. These observations provide a quantitative understanding of the stability and reversibility of cellular differentiation states.},
  copyright = {� 2005 Nature Publishing Group},
  file      = {Acar et al_2005_Enhancement of cellular memory by reducing stochastic transitions.pdf:acar05.pdf:PDF;:nature03524-s1.pdf:PDF},
  groups    = {Gal induction},
  journal   = {Nature},
  keywords  = {astronomy, astrophysics, biochemistry, bioinformatics, biology, biotechnology, cancer, cell cycle, cell signalling, climate change, computational biology, development, developmental biology, {DNA}, drug discovery, earth science, ecology, environmental science, evolution, evolutionary biology, functional genomics, genetics, genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, Nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, physics, proteomics, quantum physics, {RNA}, science, science news, science policy, Signal Transduction, structural biology, Systems Biology, transcriptomics},
  owner     = {nbecker},
  timestamp = {2013.09.30},
}

@Article{acar08v,
  author      = {Acar, Murat and Mettetal, Jerome T. and {van Oudenaarden}, Alexander},
  title       = {Stochastic switching as a survival strategy in fluctuating environments.},
  journal     = {Nat Genet},
  year        = {2008},
  volume      = {40},
  number      = {4},
  pages       = {471--475},
  month       = apr,
  abstract    = {A classic problem in population and evolutionary biology is to understand how a population optimizes its fitness in fluctuating environments. A population might enhance its fitness by allowing individual cells to stochastically transition among multiple phenotypes, thus ensuring that some cells are always prepared for an unforeseen environmental fluctuation. Here we experimentally explore how switching affects population growth by using the galactose utilization network of Saccharomyces cerevisiae. We engineered a strain that randomly transitions between two phenotypes as a result of stochastic gene expression. Each phenotype was designed to confer a growth advantage over the other phenotype in a certain environment. When we compared the growth of two populations with different switching rates, we found that fast-switching populations outgrow slow switchers when the environment fluctuates rapidly, whereas slow-switching phenotypes outgrow fast switchers when the environment changes rarely. These results suggest that cells may tune inter-phenotype switching rates to the frequency of environmental changes.},
  doi         = {10.1038/ng.110},
  file        = {:acar08v.pdf:PDF},
  groups      = {switch, Gal induction},
  institution = {Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. avano@mit.edu},
  keywords    = {Adaptation, Biological; Bacterial Proteins, metabolism; Cell Survival, physiology; Environment; Fluorouracil, metabolism; Fungal Proteins, metabolism; Galactokinase, genetics; Galactose, metabolism; Luminescent Proteins, metabolism; Models, Biological; Orotic Acid, analogs /&/ derivatives/metabolism; Phenotype; Promoter Regions, Genetic, genetics; Saccharomyces cerevisiae Proteins, genetics; Saccharomyces cerevisiae, genetics/growth /&/ development/metabolism; Stochastic Processes; Time Factors; Uracil, metabolism},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {nbecker},
  pii         = {ng.110},
  pmid        = {18362885},
  timestamp   = {2012.02.06},
}

@Article{adib07,
  author     = {Adib, Artur B.},
  title      = {Stochastic Actions for Diffusive Dynamics: Reweighting, Sampling, and Minimization†},
  journal    = {J. Phys. Chem. B},
  year       = {2007},
  volume     = {112},
  number     = {19},
  pages      = {5910--5916},
  issn       = {1520-6106},
  abstract   = {In numerical studies of diffusive dynamics, two different action functionals are often used to specify the probability distribution of trajectories, one of which requires the evaluation of the second derivative of the potential in addition to the force. Here it is argued that both actions are equivalent prescriptions for the purposes of reweighting and sampling trajectories, whereas the most probable path is more generally given by the global minimum of the action involving the second derivative term. The answer to this apparent paradox lies in the nondifferentiable character of Brownian paths, as well as in the ?entropy? associated with a given trajectory. In numerical studies of diffusive dynamics, two different action functionals are often used to specify the probability distribution of trajectories, one of which requires the evaluation of the second derivative of the potential in addition to the force. Here it is argued that both actions are equivalent prescriptions for the purposes of reweighting and sampling trajectories, whereas the most probable path is more generally given by the global minimum of the action involving the second derivative term. The answer to this apparent paradox lies in the nondifferentiable character of Brownian paths, as well as in the ?entropy? associated with a given trajectory.},
  doi        = {10.1021/jp0751458},
  file       = {ACS Full Text PDF:adib07.pdf:PDF},
  groups     = {importance sampling (mathematical)},
  shorttitle = {Stochastic Actions for Diffusive Dynamics},
  timestamp  = {2012.05.29},
}

@Article{adland03,
  author        = {Adland, H. M. and Mikkelsen, A.},
  title         = {Rotational diffusion of two-segmented macromolecules with a ball-socket joint: {A} kinetic theory approach},
  journal       = {Journal of Chemical Physics},
  year          = {2003},
  volume        = {118},
  number        = {7},
  pages         = {3376--3391},
  date-modified = {2008-04-23 18:42:31 +0200},
}

@Article{agarwal72,
  Title                    = {Fluctuation-dissipation theorems for systems in non-thermal equilibrium and applications},
  Author                   = {Agarwal, G. S.},
  Journal                  = {Zeitschrift f\"ur Physik},
  Year                     = {1972},
  Month                    = feb,
  Pages                    = {25--38},
  Volume                   = {252},
  Doi                      = {10.1007/BF01391621},
  ISSN                     = {1434-6001, {1434-601X}},
  Url                      = {http://www.springerlink.com/content/k8340606560143k8/}
}

@Article{aggarwal88,
  author        = {Aggarwal, A.K. and Rodgers, D.W. and Drottar, M. and Ptashne, M. and Harrison, S.C.},
  title         = {Recognition of a {DNA} operator by the repressor of phage 434: a view at high resolution.},
  journal       = {Science},
  year          = {1988},
  volume        = {242},
  number        = {4880},
  pages         = {899--907},
  abstract      = {The repressors of temperate bacteriophages such as 434 and lambda control transcription by binding to a set of DNA operator sites. The different affinity of repressor for each of these sites ensures efficient regulation. High-resolution x-ray crystallography was used to study the DNA-binding domain of phage 434 repressor in complex with a synthetic DNA operator. The structure shows recognition of the operator by direct interactions with base pairs in the major groove, combined with the sequence-dependent ability of DNA to adopt the required conformation on binding repressor. In particular, a network of three-centered bifurcated hydrogen bonds among base pairs in the operator helps explain why 434 repressor prefers certain sites over others. These bonds, which stabilize the conformation of the bound DNA, can form only with certain sequences.},
  date-modified = {2008-04-23 18:42:25 +0200},
  file          = {aggarwal88.pdf:aggarwal88.pdf:PDF},
  keywords      = {Base Composition ; Base Sequence ; Binding Sites ;1Comparative Study ; DNA/*metabolism ; *DNA-Binding1Proteins ; Hydrogen Bonding ; Molecular Structure ;1Nucleic Acid Conformation ; *Operator Regions1(Genetics) ; Protein Binding ; Protein Conformation ;1Repressor Proteins/*metabolism ; Research Support,1Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ;1Software ; Transcription Factors/*metabolism ; Viral1Proteins/*metabolism ; X-Ray Diffraction},
  url           = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=3187531},
}

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Expected behavior:

import of the .bib file into a new group in my zotero library, including the file links as either attachments or as links, according to the selected preference.

Actual behavior:

no files are attached or linked at all.

Remarks:

i tried setting the linked attachment base directory to the folder containing all the pdfs, to no avail. in any case i would have expected some kind of error message stating that files are not found, if the bibtex link location does not resolve properly on import?

label-gun[bot] commented 4 years ago

It looks like you did not upload an debug report. The debug report is important; it gives @retorquere your current BBT settings and a copy of the problematic reference as a test case so he can best replicate your problem. Without it, @retorquere is effectively blind. Debug reports are useful for both bug analysis and enhancement requests; in the case of export enhancements, I need the copy of the references you have in mind.

If your issue relates to how BBT behaves around a specific reference(s), such as citekey generation or export, select at least one of the problematic reference(s), right-click it, and submit an BBT debug report from that popup menu. If the problem is with export, please do include a sample of what you see exported, and what you expected to see exported for these references.
If the issue does not relate to references and is of a more general nature, generate an debug report by restarting Zotero with debugging enabled (Help -> Debug Output Logging -> Restart with logging enabled), reproducing your problem, and selecting "Send Better BibTeX debug report..." from the help menu.

Once done, you will see a debug ID in red. Please post that debug id in the issue here.

Thank you!

nilsbecker commented 4 years ago

Report ID:

7629VSGR-euc

(now, on the second try, sending the report worked?!)