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wpoa / open-access-media-importer

A tool for harvesting media files from Open Access articles for upload into Wikimedia Commons
http://commons.wikimedia.org/wiki/User:Open_Access_Media_Importer_Bot
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wikitools.api.APIError: (u'srsearch-text-disabled', u'text search is disabled') #15

Closed Daniel-Mietchen closed 12 years ago

Daniel-Mietchen commented 12 years ago

Traceback (most recent call last): File "./oa-put", line 90, in if is_uploaded(material): File "./oa-put", line 68, in is_uploaded result = request.query() File "/home/daniel/open-access-media-importer/wikitools/api.py", line 143, in query raise APIError(data['error']['code'], data['error']['info'])

wikitools.api.APIError: (u'srsearch-text-disabled', u'text search is disabled')

Affected DOIs: 10.1371/journal.pcbi.1002392 10.1371/journal.pone.0002525 10.1371/journal.pbio.1000596

Daniel-Mietchen commented 12 years ago

Just reran those three DOIs, and they went through smoothly.

erlehmann commented 12 years ago

Then it is an issue on the mediawiki side, I presume?

Daniel-Mietchen commented 12 years ago

I think so too, though it may be prompted by our side being active way above average - the error typically occurs after some files from the same article have been uploaded fine.

Daniel-Mietchen commented 12 years ago

Rerunning did not work for the last few files from 10.1371/journal.pone.0008793 and 10.1371/journal.pone.0010848.

Daniel-Mietchen commented 12 years ago

For those cases in which rerunning does work, it would be good if the bot could do that immediately until the error disappears (may take several times, increasing with the number of relevant files in article), or at least thrice per file.

Daniel-Mietchen commented 12 years ago

The problem still affects hundreds of articles, so promoting to "Do it now".

erlehmann commented 12 years ago

Only problem, I cannot reproduce it. So what should I do now, wait 10 seconds and re-run the query on failure?

Daniel-Mietchen commented 12 years ago

Yep, that would be a solution. Perhaps good to set an upper limit of three repeats per file, i.e. if there are 4 relevant files in that article, there should be a maximum of 12 repeats overall. That should get us about 95% of these cases.

Problem: as long as duplication does not work properly (failure rate is about 50%; see also https://github.com/erlehmann/open-access-media-importer/issues/35 ), this fix can lengthen future scans quite a bit.

Perhaps this could be a command line switch?

Daniel-Mietchen commented 12 years ago

In terms of reproducibility, why not just save the logs of ongoing operations for a while?

A few examples from the last minutes are pasted in below - note that all videos except the very first ( http://commons.wikimedia.org/wiki/File:Coincidence-Detection-of-Place-and-Temporal-Context-in-a-Network-Model-of-Spiking-Hippocampal-pcbi.0030234.sv001.ogv ) and the very last ( http://commons.wikimedia.org/wiki/File:A-Model-for-Integrating-Elementary-Neural-Functions-into-Delayed-Response-Behavior-pcbi.0020025.sv002.ogv ) one were already up on Commons, uploaded by the bot itself. Yet it pretended most of the time to upload them again, with no visible effect other than time passing by. 13 min passed between the two uploads: http://commons.wikimedia.org/w/index.php?title=Special:Contributions/Open_Access_Media_Importer_Bot&offset=20121122015912&target=Open+Access+Media+Importer+Bot&limit=2 .

Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=2134961”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Coincidence Detection of Place and Temporal Context in a Network Model of Spiking Hippocampal Neurons”: 1 × video/quicktime

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134961/bin/pcbi.0030234.sv001.mov. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030234.sv001.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 2077899 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=2077899”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites”: 4 × video/quicktime

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077899/bin/pcbi.0030212.sv001.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077899/bin/pcbi.0030212.sv002.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077899/bin/pcbi.0030212.sv003.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077899/bin/pcbi.0030212.sv004.mov. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030212.sv001.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Traceback (most recent call last): File "./oa-put", line 90, in if is_uploaded(material): File "./oa-put", line 68, in is_uploaded result = request.query() File "/home/daniel/open-access-media-importer/wikitools/api.py", line 143, in query raise APIError(data['error']['code'], data['error']['info']) wikitools.api.APIError: (u'srsearch-text-disabled', u'text search is disabled') Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 2041977 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=2041977”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “A Stochastic View of Spliceosome Assembly and Recycling in the Nucleus ”: 4 × image/tiff 2 × video/x-msvideo

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2041977/bin/pcbi.0030201.sv001.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2041977/bin/pcbi.0030201.sv002.avi. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030201.sv001.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030201.sv002.avi.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1963494 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1963494”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm”: 1 × application/x-zip-compressed 1 × video/x-msvideo

Checking MIME types … /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) DOI 10.1371/journal.pcbi.0030169, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1963494/bin/pcbi.0030169.sd001.zip, source claimed application/x-zip-compressed but is application/zip. 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1963494/bin/pcbi.0030169.sv001.avi. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030169.sv001.avi.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1914373 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1914373”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning”: 2 × video/mpeg

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914373/bin/pcbi.0030134.sv001.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914373/bin/pcbi.0030134.sv002.mpg. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030134.sv001.mpg.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030134.sv002.mpg.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1857812 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1857812”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model”: 4 × video/quicktime 1 × application/msword 1 × application/x-zip-compressed 1 × application/pdf 1 × image/tiff

Checking MIME types … /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) DOI 10.1371/journal.pcbi.0030076, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857812/bin/pcbi.0030076.sd001.tar, source claimed application/x-zip-compressed but is application/x-tar. 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857812/bin/pcbi.0030076.sv001.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857812/bin/pcbi.0030076.sv002.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857812/bin/pcbi.0030076.sv003.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857812/bin/pcbi.0030076.sv004.mov. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030076.sv001.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030076.sv002.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030076.sv003.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030076.sv004.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1851983 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1851983”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus”: 3 × video/x-msvideo 7 × application/pdf

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851983/bin/pcbi.0030068.sv001.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851983/bin/pcbi.0030068.sv002.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851983/bin/pcbi.0030068.sv003.avi. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030068.sv001.avi.ogv”, already exists at http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030068.sv002.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030068.sv003.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1828701 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1828701”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “A Mathematical Model for Neutrophil Gradient Sensing and Polarization”: 2 × video/mpeg 1 × image/jpeg

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1828701/bin/pcbi.0030036.sv001.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1828701/bin/pcbi.0030036.sv002.mpg. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030036.sv001.mpg.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030036.sv002.mpg.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1797823 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1797823”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Repressor Dimerization in the Zebrafish Somitogenesis Clock”: 7 × video/quicktime

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797823/bin/pcbi.0030032.sv001.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797823/bin/pcbi.0030032.sv002.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797823/bin/pcbi.0030032.sv003.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797823/bin/pcbi.0030032.sv004.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797823/bin/pcbi.0030032.sv005.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797823/bin/pcbi.0030032.sv006.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797823/bin/pcbi.0030032.sv007.mov. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030032.sv001.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030032.sv002.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030032.sv003.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030032.sv004.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030032.sv005.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030032.sv006.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030032.sv007.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1797822 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1797822”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Unsupervised Learning of Visual Features through Spike Timing Dependent Plasticity”: 3 × video/quicktime

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797822/bin/pcbi.0030031.sv001.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797822/bin/pcbi.0030031.sv002.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797822/bin/pcbi.0030031.sv003.mov. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030031.sv001.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030031.sv002.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030031.sv003.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1782042 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1782042”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Emergent Dynamics of Thymocyte Development and Lineage Determination”: 2 × video/quicktime 2 × video/x-msvideo 1 × application/pdf

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782042/bin/pcbi.0030013.sv001.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782042/bin/pcbi.0030013.sv002.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782042/bin/pcbi.0030013.sv003.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782042/bin/pcbi.0030013.sv004.avi. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030013.sv001.avi.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0030013.sv004.avi.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1664702 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1664702”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Computational Inference of Neural Information Flow Networks”: 4 × application/postscript 1 × image/png 1 × application/vnd.ms-powerpoint 3 × application/pdf 4 × application/msword

Checking MIME types … /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value.############################################### | param.append(processorskey) DOI 10.1371/journal.pcbi.0020161, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664702/bin/pcbi.0020161.st003.doc, source claimed application/msword but is Composite Document File V2 Document, corrupt: Can't expand summary_info. 100% |##########################################################################################################################################################################################################| Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1513273 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1513273”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method”: 1 × application/vnd.ms-excel 27 × application/pdf 7 × video/quicktime

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513273/bin/pcbi.0020082.sv001.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513273/bin/pcbi.0020082.sv002.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513273/bin/pcbi.0020082.sv003.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513273/bin/pcbi.0020082.sv004.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513273/bin/pcbi.0020082.sv005.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513273/bin/pcbi.0020082.sv006.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513273/bin/pcbi.0020082.sv007.mov. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020082.sv001.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020082.sv002.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020082.sv003.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020082.sv004.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020082.sv005.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020082.sv006.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020082.sv007.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1484588 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1484588”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Noise-Induced Min Phenotypes in E. coli”: 9 × video/quicktime 9 × text/xml 2 × application/pdf

Checking MIME types … /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd001.xml, source claimed text/xml but is application/xml. DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd002.xml, source claimed text/xml but is application/xml. | DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd003.xml, source claimed text/xml but is application/xml. | DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd004.xml, source claimed text/xml but is application/xml. | DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd005.xml, source claimed text/xml but is application/xml. | DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd006.xml, source claimed text/xml but is application/xml. | DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd007.xml, source claimed text/xml but is application/xml. | DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd008.xml, source claimed text/xml but is application/xml. | DOI 10.1371/journal.pcbi.0020080, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sd009.xml, source claimed text/xml but is application/xml. | 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv001.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv002.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv003.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv004.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv005.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv006.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv007.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv008.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484588/bin/pcbi.0020080.sv009.mov. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv001.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv002.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv003.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv004.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv005.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv006.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv007.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv008.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020080.sv009.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1475715 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1475715”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Moving Forward Moving Backward: Directional Sorting of Chemotactic Cells due to Size and Adhesion Differences”: 8 × video/mpeg

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475715/bin/pcbi.0020056.sv001.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475715/bin/pcbi.0020056.sv002.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475715/bin/pcbi.0020056.sv003.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475715/bin/pcbi.0020056.sv004.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475715/bin/pcbi.0020056.sv005.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475715/bin/pcbi.0020056.sv006.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475715/bin/pcbi.0020056.sv007.mpg. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475715/bin/pcbi.0020056.sv008.mpg. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020056.sv001.mpg.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020056.sv002.mpg.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020056.sv003.mpg.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020056.sv004.mpg.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020056.sv005.mpg.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020056.sv006.mpg.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Traceback (most recent call last): File "./oa-put", line 90, in if is_uploaded(material): File "./oa-put", line 68, in is_uploaded result = request.query() File "/home/daniel/open-access-media-importer/wikitools/api.py", line 143, in query raise APIError(data['error']['code'], data['error']['info']) wikitools.api.APIError: (u'srsearch-text-disabled', u'text search is disabled') Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 1428791 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1428791”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “A Model for Integrating Elementary Neural Functions into Delayed-Response Behavior”: 2 × video/quicktime

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1428791/bin/pcbi.0020025.sv001.mov. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1428791/bin/pcbi.0020025.sv002.mov. Skipping “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020025.sv001.mov.ogv”, already exists at http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pcbi.0020025.sv002.mov.ogv” uploaded to http://commons.wikimedia.org/w/api.php.

Daniel-Mietchen commented 12 years ago

Another example - the edits relevant to 10.1371/journal.pone.0006155 in http://commons.wikimedia.org/w/index.php?title=Special:Contributions/Open_Access_Media_Importer_Bot&offset=20121121224442&limit=10&target=Open+Access+Media+Importer+Bot .

I had to rerun that twice in order to get all files up, and the bot thought it uploaded files when they were already there, uploaded in the previous run.

First run:

Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 2705188 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=2705188”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Cellular Contractility Requires Ubiquitin Mediated Proteolysis”: 1 × image/tiff 10 × video/x-msvideo

Checking MIME types … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s002.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s003.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s004.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s005.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s006.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s007.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s008.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s009.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s010.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s011.avi, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s002.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s002.avi.ogv” … 25% |################################################### done.|################################################################################################################################################################################################## | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s003.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s003.avi.ogv” … 7% |############## done.|######################################################################################################################################################################################################## | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s004.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s004.avi.ogv” … 15% |############################### done.|################################################################################################################################################################################################ | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s005.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s005.avi.ogv” … 4% |######## done.|###################################################################################################################################################################################################### | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s006.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s006.avi.ogv” … 2% |##### done.|###################################################################################################################################################################################################### | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s007.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s007.avi.ogv” … 5% |########## done.|#################################################################################################################################################################################################### | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s008.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s008.avi.ogv” … 2% |#### done.|######################################################################################################################################################################################################### | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s009.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s009.avi.ogv” … 2% |##### done.|######################################################################################################################################################################################################## | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s010.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s010.avi.ogv” … 2% |#### done.|######################################################################################################################################################################################################### | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_doi/pone.0006155.s011.avi”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s011.avi.ogv” … 5% |########### done.|##################################################################################################################################################################################################### | “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s002.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s003.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s004.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Traceback (most recent call last): File "./oa-put", line 90, in if is_uploaded(material): File "./oa-put", line 68, in is_uploaded result = request.query() File "/home/daniel/open-access-media-importer/wikitools/api.py", line 143, in query raise APIError(data['error']['code'], data['error']['info']) wikitools.api.APIError: (u'srsearch-text-disabled', u'text search is disabled')

Rerun:

daniel@oami-host:~/open-access-media-importer$ echo 10.1371/journal.pone.0006155 | ./oami_pmc_doi_import Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 2705188 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=2705188”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Cellular Contractility Requires Ubiquitin Mediated Proteolysis”: 1 × image/tiff 10 × video/x-msvideo

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s002.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s003.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s004.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s005.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s006.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s007.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s008.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s009.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s010.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s011.avi. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s002.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s003.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s004.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s005.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s006.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s007.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. Traceback (most recent call last): File "./oa-put", line 90, in if is_uploaded(material): File "./oa-put", line 68, in is_uploaded result = request.query() File "/home/daniel/open-access-media-importer/wikitools/api.py", line 143, in query raise APIError(data['error']['code'], data['error']['info']) wikitools.api.APIError: (u'srsearch-text-disabled', u'text search is disabled') daniel@oami-host:~/open-access-media-importer$ echo 10.1371/journal.pone.0006155 | ./oami_pmc_doi_import Removing “/home/daniel/.local/share/open-access-media-importer/pmc_doi.sqlite” … done. Input DOIs, delimited by whitespace: Getting PubMed Central IDs for given DOIs … found: 2705188 Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=2705188”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_doi” … 100% |##########################################################################################################################################################################################################| /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Cellular Contractility Requires Ubiquitin Mediated Proteolysis”: 1 × image/tiff 10 × video/x-msvideo

Checking MIME types … 100% |##########################################################################################################################################################################################################| Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s002.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s003.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s004.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s005.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s006.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s007.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s008.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s009.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s010.avi. Skipping download of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705188/bin/pone.0006155.s011.avi. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s002.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s003.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s004.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s005.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s006.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s007.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s008.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s009.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s010.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php. “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_doi/pone.0006155.s011.avi.ogv” uploaded to http://commons.wikimedia.org/w/api.php.

erlehmann commented 12 years ago

Possibly related bug: https://bugzilla.wikimedia.org/show_bug.cgi?id=34553

erlehmann commented 12 years ago

Possibly fixed by cde1407ee28f1537f3c9886c8caa8df7b6d740d. Feedback?

Daniel-Mietchen commented 12 years ago

yep: Traceback (most recent call last): File "./oa-get", line 132, in if mediawiki.is_uploaded(material): File "/home/daniel/open-access-media-importer/helpers/mediawiki.py", line 28, in is_uploaded result = _query(request) File "/home/daniel/open-access-media-importer/helpers/mediawiki.py", line 11, in _query stderr.write('Mediawiki API request failed, retrying.\n') NameError: global name 'stderr' is not defined

http://www.google.com/profiles/daniel.mietchen

On Thu, Nov 22, 2012 at 6:50 PM, Nils Dagsson Moskopp < notifications@github.com> wrote:

Possibly fixed by cde1407https://github.com/erlehmann/open-access-media-importer/commit/cde1407ee28f1537f3c9886c8caa8df7b6d740d. Any more reports?

— Reply to this email directly or view it on GitHubhttps://github.com/erlehmann/open-access-media-importer/issues/15#issuecomment-10641416.

erlehmann commented 12 years ago

My fault. Try again.

erlehmann commented 12 years ago

Possibly fixed by 104dfc2fa4a19192059336af25fdaecf816f938e.

erlehmann commented 12 years ago

Fix confirmed.