Don't exit if PMID is missing

[Daniel-Mietchen]

For newly published articles, the PMID may sometimes be missing when PMCID and DOI are already available. This currently causes the script to exit before upload, but I would prefer the upload to take place without PMID, which can always be added later.

Sample log:

Input PMCIDs, delimited by whitespace: Removing “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_pmcid/efetch.fcgi0” … done. Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=3511399”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_pmcid” … 100% |#########################################################################################################################################################################################################| Skipping 12 records … PLOS ONE 2012 Dynamic Volume Changes in Astrocytes Are an Intrinsic Phenomenon Mediated by Bicarbonate Ion Flux /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Dynamic Volume Changes in Astrocytes Are an Intrinsic Phenomenon Mediated by Bicarbonate Ion Flux”: 2 × video/quicktime

Checking MIME types … 100% |#########################################################################################################################################################################################################| Unknown, possibly non-free license: http://www.frontiersin.org/licenseagreement Unknown, possibly non-free license: http://www.frontiersin.org/licenseagreement Unknown, possibly non-free license: http://www.frontiersin.org/licenseagreement Unknown, possibly non-free license: http://creativecommons.org/licenses/by-nc-sa/3.0/ Unknown, possibly non-free license: http://creativecommons.org/licenses/by-nc-sa/3.0/ Unknown, possibly non-free license: http://creativecommons.org/licenses/by-nc-sa/3.0/ Unknown, possibly non-free license: http://creativecommons.org/licenses/by-nc-sa/3.0/ Unknown, possibly non-free license: http://creativecommons.org/licenses/by-nc-sa/3.0/ Unknown, possibly non-free license: http://creativecommons.org/licenses/by-nc-sa/3.0/ Unknown, possibly non-free license: http://creativecommons.org/licenses/by-nc-sa/3.0/ Unknown, possibly non-free license: http://creativecommons.org/licenses/by-nc-sa/3.0/ Unknown, possibly non-free license: Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511399/bin/pone.0051124.s001.mov, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid” … 100% |#########################################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511399/bin/pone.0051124.s002.mov, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid” … 100% |#########################################################################################################################################################################################################| Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid/pone.0051124.s001.mov”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_pmcid/pone.0051124.s001.mov.ogv” … 35% |####################################################################### done.|########################################################################################################################################################################################## | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid/pone.0051124.s002.mov”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_pmcid/pone.0051124.s002.mov.ogv” … 50% |#################################################################################################### done.|############################################################################################################################################################################### | Traceback (most recent call last): File "./oa-put", line 70, in article_pmid = efetch.get_pmid_from_doi(article_doi) File "/home/daniel/open-access-media-importer/helpers/efetch.py", line 33, in get_pmid_from_doi return tree.find('IdList/Id').text AttributeError: 'NoneType' object has no attribute 'text' Input PMCIDs, delimited by whitespace: Removing “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_pmcid/efetch.fcgi0” … done.

[erlehmann]

Fixed by 5e76cfac762bcc599a553c3e259a95e3601754e2.

[Daniel-Mietchen]

Still getting errors on this one: Downloading “http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=3511835”, saving into directory “/home/daniel/.cache/open-access-media-importer/metadata/raw/pmc_pmcid” … 100% |#############################################################################################################################################################################################| Skipping 3 records … Evidence-based Complementary and Alternative Medicine 2012 Bioassay-Guided Isolation and HPLC Determination of Bioactive Compound That Relate to the Antiplatelet Activity (Adhesion, Secretion, and Aggregation) from Solanum lycopersicum /usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py:463: SAWarning: Unicode type received non-unicode bind param value. param.append(processorskey) “Bioassay-Guided Isolation and HPLC Determination of Bioactive Compound That Relate to the Antiplatelet Activity (Adhesion, Secretion, and Aggregation) from Solanum lycopersicum”: 3 × video/x-ms-wmv

Checking MIME types … When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517510/bin/1471-2148-12-81-S1.doc, the following error occured: “HTTP Error 416: Wrong Request”. When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517510/bin/1471-2148-12-81-S2.pdf, the following error occured: “HTTP Error 416: Wrong Request”. When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517510/bin/1471-2148-12-81-S3.pdf, the following error occured: “HTTP Error 416: Wrong Request”. When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517358/bin/1472-6920-12-70-S1.pdf, the following error occured: “HTTP Error 416: Wrong Request”. When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517358/bin/1472-6920-12-70-S2.pdf, the following error occured: “HTTP Error 416: Wrong Request”. When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517534/bin/1745-6215-13-191-S1.pdf, the following error occured: “HTTP Error 416: Wrong Request”. When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511835/bin/147031.f1.wmv, the following error occured: “HTTP Error 416: Wrong Request”. When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511835/bin/147031.f2.wmv, the following error occured: “HTTP Error 416: Wrong Request”. When trying to download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511835/bin/147031.f3.wmv, the following error occured: “HTTP Error 416: Wrong Request”. Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511835/bin/147031.f1.wmv, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid” … 100% |#############################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511835/bin/147031.f2.wmv, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid” … 100% |#############################################################################################################################################################################################| Downloading http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511835/bin/147031.f3.wmv, saving into directory “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid” … 100% |#############################################################################################################################################################################################| Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid/147031.f1.wmv”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_pmcid/147031.f1.wmv.ogv” … 2% |#### done.|############################################################################################################################################################################################ | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid/147031.f2.wmv”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_pmcid/147031.f2.wmv.ogv” … 3% |##### done.|######################################################################################################################################################################################### | Converting “/home/daniel/.cache/open-access-media-importer/media/raw/pmc_pmcid/147031.f3.wmv”, saving into “/home/daniel/.cache/open-access-media-importer/media/refined/pmc_pmcid/147031.f3.wmv.ogv” … 0% | done.|############################################################################################################################################################################################ | Traceback (most recent call last): File "./oa-put", line 86, in categories += efetch.get_categories_from_pmid(article_pmid) File "/home/daniel/open-access-media-importer/helpers/efetch.py", line 47, in get_categories_from_pmid raise TypeError, "Cannot get Categories for PMID %s of type %s." % (pmid, type(pmid)) TypeError: Cannot get Categories for PMID 2012 of type <type 'str'>

[Daniel-Mietchen]

Reopening due to "TypeError: Cannot get Categories for PMID 2012 of type" (see end of log in previous comment).

[erlehmann]

Fixed by 5b4084c0c9e30e8a662b0e456efe77f7c1d4178a.