7 files changed, 78 insertions, 0 deletions
diff --git a/fatcat_scholar/identifiers.py b/fatcat_scholar/identifiers.py
index 2ea09c7..34e9ebb 100644
--- a/fatcat_scholar/identifiers.py
+++ b/fatcat_scholar/identifiers.py
@@ -57,6 +57,10 @@ def clean_doi(raw: Optional[str]) -> Optional[str]:
 
 
 def test_clean_doi() -> None:
+    assert clean_doi(None) == None
+    assert clean_doi("") == None
+    assert clean_doi("asdf") == None
+    assert clean_doi("10.123") == None
     assert clean_doi("10.1234/asdf ") == "10.1234/asdf"
     assert clean_doi("10.1037//0002-9432.72.1.50") == "10.1037/0002-9432.72.1.50"
     assert clean_doi("10.1037/0002-9432.72.1.50") == "10.1037/0002-9432.72.1.50"
@@ -86,5 +90,6 @@ def clean_pmcid(raw: Optional[str]) -> Optional[str]:
 def test_clean_pmcid() -> None:
     assert clean_pmcid("10.1234/asdf ") == None
     assert clean_pmcid("") == None
+    assert clean_pmcid("1 2") == None
     assert clean_pmcid(None) == None
     assert clean_pmcid("PMC123") == "PMC123"
diff --git a/settings.toml b/settings.toml
index aeb8a02..a4434a5 100644
--- a/settings.toml
+++ b/settings.toml
@@ -22,6 +22,7 @@ ONION_DOMAIN = "scholar-qa.archivev3qli37bju4rlh27glh24lljyezwxf4pokmrdbpefjlcrp
 [test]
 SCHOLAR_ENV = "test"
 FATCAT_API_HOST = "http://localhost:9411/v0"
+SCHOLAR_ISSUEDB_PATH = ":memory:"
 
 [development]
 SCHOLAR_ENV = "dev"
diff --git a/tests/files/release_hsmo6p4smrganpb3fndaj2lon4_sans.json b/tests/files/release_hsmo6p4smrganpb3fndaj2lon4_sans.json
new file mode 100644
index 0000000..e2145b8
--- /dev/null
+++ b/tests/files/release_hsmo6p4smrganpb3fndaj2lon4_sans.json
@@ -0,0 +1 @@
+{"abstracts":[],"refs":[{"index":7,"extra":{"authors":["Björk"],"doi":"10.1016/j.joi.2016.08.002","volume":"10"},"key":"10.7717/peerj.4375/ref-8","year":2016,"container_name":"Journal of Informetrics","title":"Hybrid open access—a longitudinal study","locator":"919"}],"contribs":[{"index":0,"raw_name":"Heather Piwowar","role":"author","raw_affiliation":"Impactstory, Sanford, NC, USA","extra":{"seq":"first"}}],"license_slug":"CC-BY","language":"en","publisher":"PeerJ","pages":"e4375","ext_ids":{"doi":"10.7717/peerj.4375","wikidata_qid":"Q49873702","pmid":"29456894","pmcid":"PMC5815332"},"release_year":2018,"release_date":"2018-02-13","release_stage":"published","release_type":"article-journal","container_id":"eyfkjqp7sva5bbnwatk5zazi7q","webcaptures":[],"filesets":[],"files":[{"release_ids":["bsamgk5hsngejamqdd2naz6fsu","hsmo6p4smrganpb3fndaj2lon4","xqk6bvvwcfgu3ftjjk7jqyhnqa"],"mimetype":"application/pdf","urls":[{"url":"https://web.archive.org/web/20180724215659/https://peerj.com/articles/4375.pdf","rel":"webarchive"},{"url":"https://peerj.com/articles/4375.pdf","rel":"web"}],"sha1":"bca1531b0562c6d72e0c283c1ccb97eb5cb02117","size":2433346,"revision":"2aed7279-0dd2-474e-b66d-5c6882709658","ident":"f76kdq5bxbftnknlyvtmnjtdnq","state":"active"}],"container":{"wikidata_qid":"Q2000010","issnl":"2167-8359","publisher":"PeerJ","name":"PeerJ","extra":{"abbrev":"PeerJ","country":"us","default_license":"CC-BY","doaj":{"archive":["LOCKSS","CLOCKSS","Portico","PMC/Europe PMC/PMC Canada"],"as_of":"2019-07-31","country":"us","crawl-permission":true,"default_license":"CC-BY","issne":"2167-8359","mimetypes":null,"publisher":"PeerJ Inc","seal":true},"issne":"2167-8359","issnp":"2167-8359","kbart":{"clockss":{"year_spans":[[2014,2015]]},"lockss":{"year_spans":[[2013,2013],[2016,2017]]},"portico":{"year_spans":[[2013,2019]]}},"languages":["en"],"road":{"as_of":"2018-01-24"},"sherpa_romeo":{"color":"green"},"urls":["http://www.peerj.com/","http://bibpurl.oclc.org/web/53853"]},"revision":"9c613fec-4801-4ed6-b75f-963846b6ab0f","ident":"eyfkjqp7sva5bbnwatk5zazi7q","state":"active"},"work_id":"fyvohvh7ufcwjcluvjivszmkiq","title":"The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles","state":"active","ident":"hsmo6p4smrganpb3fndaj2lon4","revision":"de98deaf-4720-430a-8a97-1ff244cb602f","extra":{"crossref":{"alternative-id":["10.7717/peerj.4375"],"archive":["CLOCKSS","LOCKSS","Portico"],"license":[{"URL":"http://creativecommons.org/licenses/by/4.0/","content-version":"unspecified","delay-in-days":0,"start":"2018-02-13T00:00:00Z"}],"type":"journal-article"}}}
diff --git a/tests/files/sim_page_bundle.json b/tests/files/sim_page_bundle.json
new file mode 100644
index 0000000..6a6e343
--- /dev/null
+++ b/tests/files/sim_page_bundle.json
@@ -0,0 +1 @@
+{"doc_type":"sim_page","releases":[],"sim_fulltext":{"issue_item":"sim_russian-journal-of-general-chemistry_1955-12_25_13","issue_item_metadata":{"created":1603420766,"d1":"ia903209.us.archive.org","d2":"ia803209.us.archive.org","dir":"/29/items/sim_russian-journal-of-general-chemistry_1955-12_25_13","files_count":22,"item_last_updated":1602343145,"item_size":207482064,"metadata":{"access-restricted-item":"true","adaptive_ocr":"true","addeddate":"2020-03-18 21:07:49","auditor":"Evangilyn","boxid":"IA1534521","canister":"IA1534521-02","collection":["pub_russian-journal-of-general-chemistry","inlibrary","printdisabled","sim_microfilm","periodicals"],"contrast_max":"232","contrast_min":"1","contributor":"Internet Archive","copies":"3","date":"1955-12","derive_version":"0.0.10","description":"Journal of General Chemistry of the USSR 1955-12: <a href=\"https://archive.org/search.php?query=sim_pubid%3A10835%20AND%20volume%3A25\" rel=\"nofollow\">Volume 25</a>, Issue 13.<br />Digitized from 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COPY AVAILABLE\nTHE\nJOURNAL OF GENERAL CHEMISTRY OF THE U.S.S.R.\nVolume 25, Number 13 December, 1955\nEditoria 1 Board\nA.E. Arbuzov, S.N. Danilov (Editor in Chief). N.A. Domnin (Assoc. Editor), E.D. Kaverzneva, M.A. Klochko, K.P. Mishchenko, B.V. Ptitsyn, S.A. Shchukarev, E.D. Venus-Dani lova, Yu.K. Yuryev,\nA.I. Zakharova (Corresp. Sec'y)\n(A Publication of the Academy of Sciences of the U.S.S.R.)\nIN ENGUSH TRANSLATION\nCopyright, 1956\nCONSULTANTS BUREAU, INC. 227 West 17th Street Nev/ York 11, N.Y,\nPrinted in the United States\nAnnual subscription Single issue\n$ 175.00 30.00\nNote: The sale of photostatic copies of any portion of this copyright translation is expressly prohibited by the copyright owners. A complete copy of any paper in this issue may be purchased from the publisher for $ 7.50."}],"pages":"None","pub_item_metadata":{"created":1603420767,"d1":"ia601901.us.archive.org","d2":"ia801901.us.archive.org","dir":"/26/items/pub_russian-journal-of-general-chemistry","files_count":8,"is_collection":true,"item_last_updated":1602558568,"item_size":262932,"metadata":{"addeddate":"2020-03-18 16:15:39","collection":["sim_microfilm","periodicals","texts"],"contributor":"Internet Archive","copyright-renewal-date":"none","country":"Netherlands","coverage":"NL","date":"1949-1991","description":"Russian Journal of General Chemistry is a peer-reviewed scholarly journal published in Netherlands focused on Mathematical & Physical Sciences. This collection contains microfilm published between 1949 and 1991. 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documents</ref>\n\t\t\t\t</application>\n\t\t\t</appInfo>\n\t\t</encodingDesc>\n\t\t<fileDesc>\n\t\t\t<titleStmt>\n\t\t\t\t<title level=\"a\" type=\"main\">Patient-ventilator asynchrony during conventional mechanical ventilation in children</title>\n\t\t\t</titleStmt>\n\t\t\t<publicationStmt>\n\t\t\t\t<publisher/>\n\t\t\t\t<availability status=\"unknown\"><licence/></availability>\n\t\t\t\t<date type=\"published\" when=\"2017\">2017</date>\n\t\t\t</publicationStmt>\n\t\t\t<sourceDesc>\n\t\t\t\t<biblStruct>\n\t\t\t\t\t<analytic>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Guillaume</forename><surname>Mortamet</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Alexandrine</forename><surname>Larouche</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Laurence</forename><surname>Ducharme-Crevier</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Olivier</forename><surname>Fléchelles</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Gabrielle</forename><surname>Constantin</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Sandrine</forename><surname>Essouri</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Amélie-Ann</forename><surname>Pellerin-Leblanc</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Jennifer</forename><surname>Beck</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Christer</forename><surname>Sinderby</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Philippe</forename><surname>Jouvet</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<author>\n\t\t\t\t\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">Guillaume</forename><surname>Emeriaud</surname></persName>\n\t\t\t\t\t\t</author>\n\t\t\t\t\t\t<title level=\"a\" type=\"main\">Patient-ventilator asynchrony during conventional mechanical ventilation in children</title>\n\t\t\t\t\t</analytic>\n\t\t\t\t\t<monogr>\n\t\t\t\t\t\t<title level=\"j\" type=\"main\">Intensive Care</title>\n\t\t\t\t\t\t<imprint>\n\t\t\t\t\t\t\t<biblScope unit=\"volume\">7</biblScope>\n\t\t\t\t\t\t\t<biblScope unit=\"page\">122</biblScope>\n\t\t\t\t\t\t\t<date type=\"published\" when=\"2017\">2017</date>\n\t\t\t\t\t\t</imprint>\n\t\t\t\t\t</monogr>\n\t\t\t\t\t<idno type=\"DOI\">10.1186/s13613-017-0344-8</idno>\n\t\t\t\t\t<idno type=\"PMID\">29264742</idno>\n\t\t\t\t\t<idno type=\"PMCID\">PMC5738329</idno>\n\t\t\t\t\t<idno type=\"fatcat\">release_lfrzpycwgnaddg6eyaa6vgqh54</idno>\n\t\t\t\t\t<idno type=\"wikidata\">Q47116297</idno>\n\t\t\t\t\t<note>RESEARCH</note>\n\t\t\t\t</biblStruct>\n\t\t\t</sourceDesc>\n\t\t</fileDesc>\n\t\t<profileDesc>\n\t\t\t<textClass>\n\t\t\t\t<keywords>\n\t\t\t\t\t<term>Diaphragm function</term>\n\t\t\t\t\t<term>Mechanical ventilation</term>\n\t\t\t\t\t<term>Patient-ventilator asynchrony</term>\n\t\t\t\t\t<term>Patient-ventilator interaction</term>\n\t\t\t\t\t<term>Pediatric intensive care unit</term>\n\t\t\t\t\t<term>Pediatrics</term>\n\t\t\t\t</keywords>\n\t\t\t</textClass>\n\t\t\t<abstract>\n<div xmlns=\"http://www.tei-c.org/ns/1.0\"><p>Background: We aimed (1) to describe the characteristics of patient-ventilator asynchrony in a population of critically ill children, (2) to describe the risk factors associated with patient-ventilator asynchrony, and (3) to evaluate the association between patient-ventilator asynchrony and ventilator-free days at day 28.</p></div>\n<div xmlns=\"http://www.tei-c.org/ns/1.0\"><head>Methods:</head><p>In this single-center prospective study, consecutive children admitted to the PICU and mechanically ventilated for at least 24 h were included. Patient-ventilator asynchrony was analyzed by comparing the ventilator pressure curve and the electrical activity of the diaphragm (Edi) signal with (1) a manual analysis and (2) using a standardized fully automated method.</p><p>Results: Fifty-two patients (median age 6 months) were included in the analysis. Eighteen patients had a very low ventilatory drive (i.e., peak Edi &lt; 2 µV on average), which prevented the calculation of patient-ventilator asynchrony. Children spent 27% (interquartile 22-39%) of the time in conflict with the ventilator. Cycling-off errors and trigger delays contributed to most of this asynchronous time. The automatic algorithm provided a NeuroSync index of 45%, confirming the high prevalence of asynchrony. No association between the severity of asynchrony and ventilator-free days at day 28 or any other clinical secondary outcomes was observed, but the proportion of children with good synchrony was very low.</p><p>Conclusion: Patient-ventilator interaction is poor in children supported by conventional ventilation, with a high frequency of depressed ventilatory drive and a large proportion of time spent in asynchrony. The clinical benefit of strategies to improve patient-ventilator interactions should be evaluated in pediatric critical care. which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.</p></div>\n\t\t\t</abstract>\n\t\t</profileDesc>\n\t</teiHeader>\n\t<text xml:lang=\"en\">\n\t\t<body>\n<div xmlns=\"http://www.tei-c.org/ns/1.0\"><head>Results</head></div>\n<div xmlns=\"http://www.tei-c.org/ns/1.0\"><head>Outcome</head><p>We did not observe any association between the level of asynchrony and neither ventilator-free days at day 28, nor the secondary outcomes <ref type=\"table\" target=\"#tab_2\">(Table 2</ref>). This holds true with the manual classification as severe PVA or not <ref type=\"table\" target=\"#tab_2\">(Table 2)</ref>, as well as with the automated NeuroSync index (correlation with ventilation duration: R 2 = 0.12; p = 0.58). None of the patient characteristics were associated with the duration of mechanical ventilation.</p></div>\n<div xmlns=\"http://www.tei-c.org/ns/1.0\"><head>Conclusion</head><p>Patient-ventilator interaction is poor in critically ill children supported by conventional ventilation. The study did not permit to ascertain if these poor interactions have important clinical consequence. But the magnitude of PVA and the prevalence of low ventilatory drive warrant further studies to assess whether strategies to optimize patient-ventilator interactions can improve the outcome of PICU patients. <ref type=\"figure\">Fig. 4</ref> Relationship between the asynchrony results obtained using the two methods: the automatic NeuroSync index and the percentage of time spent in asynchrony derived from the manual breath-bybreath analysis</p></div><figure xmlns=\"http://www.tei-c.org/ns/1.0\" xml:id=\"fig_0\"><head>Fig. 1</head><label>1</label><figDesc>Study flowchart (*patients could be excluded for two reasons)</figDesc></figure>\n<figure xmlns=\"http://www.tei-c.org/ns/1.0\" xml:id=\"fig_1\"><head></head><label></label><figDesc>1 Characteristics of population (n = 52) Data are expressed as median (interquartile range) or n (%) Edi electrical activity of the diaphragm, MV mechanical ventilation, PICU pediatric intensive care unit, PEEP positive end-expiratory pressure *Significant difference between the two groups (</figDesc></figure>\n<figure xmlns=\"http://www.tei-c.org/ns/1.0\" xml:id=\"fig_2\"><head>Fig. 2</head><label>2</label><figDesc>Contribution of the different types of asynchrony in the total time spent in conflict with the ventilator</figDesc></figure>\n<figure xmlns=\"http://www.tei-c.org/ns/1.0\" xml:id=\"fig_3\"><head>Fig. 3</head><label>3</label><figDesc>Evolution of inspiratory Edi (panel a) and of the time spent in asynchrony (panel b) from inclusion time (time 1) to pre-extubation period (time 2)</figDesc></figure>\n<figure xmlns=\"http://www.tei-c.org/ns/1.0\" type=\"table\" xml:id=\"tab_0\" validated=\"false\"><head>Table</head><label></label><figDesc></figDesc><table></table></figure>\n<figure xmlns=\"http://www.tei-c.org/ns/1.0\" type=\"table\" xml:id=\"tab_2\" validated=\"true\"><head>Table 2</head><label>2</label><figDesc>Characteristics of patients depending on the level of asynchrony (in patients with Edi &gt; 2 µV, n = 34)</figDesc><table>\n</table></figure>\n<figure xmlns=\"http://www.tei-c.org/ns/1.0\" type=\"table\" xml:id=\"tab_3\" validated=\"true\"><head>Table 2 continued</head><label>2</label><figDesc>% time spent in asynchrony &lt; 39% (n = 25) % time spent in asynchrony &gt; 39% (n = 9) p value</figDesc><table>\n\n</table></figure>\n\t\t</body>\n\t\t<back>\n\n\t\t\t<div type=\"acknowledgement\">\n<div xmlns=\"http://www.tei-c.org/ns/1.0\"><head>Acknowledgements</head><p>The authors are indebted to the patients and their families for their willingness to participate in our study. We thank Mariana Dumitrascu, Laurence Bertout, and Noémie Loron for their help in the screening and enrollment process, Lucy Clayton for the study management support, the respiratory therapists for their logistic help, the PICU fellows, attending healthcare providers, and PICU nurses for their collaboration, and Norman Comtois for his invaluable support regarding signal recording and analysis. This work was performed in CHU Sainte-Justine, Pediatric Intensive Care Unit, Montreal, Quebec, Canada.</p></div>\n\t\t\t</div>\n\n\t\t\t<div type=\"annex\">\n<div xmlns=\"http://www.tei-c.org/ns/1.0\"><head>Abbreviations</head><p>Edi: electrical activity of the diaphragm; ETT: endotracheal tube; NAVA: neurally adjusted ventilatory assist; PICU: pediatric intensive care unit; PSV: pressure support ventilation; PVA: patient-ventilator asynchrony.</p><p>Authors' contributions AL, GE, OF, SE, and PJ designed the study. GM, AL, GC, AAPL, OF, JB, CS, and GE performed the analysis and carried out the chart review and data collection. GM, JB, CS, PJ, and GE wrote the manuscript, which was reviewed, edited, and approved by all authors. As the corresponding author, GE has full access to all the data in the study and has final responsibility for the decision to submit for publication. All authors read and approved the final manuscript. <ref type=\"bibr\" target=\"#b0\">1</ref> Pediatric Intensive Care Unit, CHU Sainte-Justine, 3175 Côte Sainte-Catherine,</p></div>\n<div xmlns=\"http://www.tei-c.org/ns/1.0\"><head>Publisher's Note</head><p>Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. </p></div>\t\t\t</div>\n\t\t\t<div type=\"references\">\n\n\t\t\t\t<listBibl>\n\n<biblStruct xml:id=\"b0\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">Risk factors associated with increased length of mechanical ventilation in children</title>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">V</forename><surname>Payen</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">P</forename><surname>Jouvet</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">J</forename><surname>Lacroix</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">T</forename><surname>Ducruet</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">F</forename><surname>Gauvin</surname></persName>\n\t\t</author>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Pediatr Crit Care Med</title>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">13</biblScope>\n\t\t\t<biblScope unit=\"issue\">2</biblScope>\n\t\t\t<biblScope unit=\"page\" from=\"152\" to=\"159\" />\n\t\t\t<date type=\"published\" when=\"2012\" />\n\t\t</imprint>\n\t</monogr>\n\t<note type=\"raw_reference\">Payen V, Jouvet P, Lacroix J, Ducruet T, Gauvin F. Risk factors associated with increased length of mechanical ventilation in children. Pediatr Crit Care Med. 2012;13(2):152-7.</note>\n</biblStruct>\n\n<biblStruct xml:id=\"b1\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">Ventilator-induced diaphragmatic dysfunction: what have we learned?</title>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">B</forename><forename type=\"middle\">J</forename><surname>Petrof</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">S</forename><forename type=\"middle\">N</forename><surname>Hussain</surname></persName>\n\t\t</author>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Curr Opin Crit Care</title>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">22</biblScope>\n\t\t\t<biblScope unit=\"issue\">1</biblScope>\n\t\t\t<biblScope unit=\"page\" from=\"67\" to=\"72\" />\n\t\t\t<date type=\"published\" when=\"2016\" />\n\t\t</imprint>\n\t</monogr>\n\t<note type=\"raw_reference\">Petrof BJ, Hussain SN. Ventilator-induced diaphragmatic dysfunction: what have we learned? Curr Opin Crit Care. 2016;22(1):67-72.</note>\n</biblStruct>\n\n<biblStruct xml:id=\"b2\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">Patient-ventilator interaction during neurally adjusted ventilatory assist in low birth weight infants</title>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">J</forename><surname>Beck</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">M</forename><surname>Reilly</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">G</forename><surname>Grasselli</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">L</forename><surname>Mirabella</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">A</forename><forename type=\"middle\">S</forename><surname>Slutsky</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">M</forename><forename type=\"middle\">S</forename><surname>Dunn</surname></persName>\n\t\t</author>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Pediatr Res</title>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">65</biblScope>\n\t\t\t<biblScope unit=\"issue\">6</biblScope>\n\t\t\t<biblScope unit=\"page\" from=\"663\" to=\"671\" />\n\t\t\t<date type=\"published\" when=\"2009\" />\n\t\t</imprint>\n\t</monogr>\n\t<note type=\"raw_reference\">Beck J, Reilly M, Grasselli G, Mirabella L, Slutsky AS, Dunn MS, et al. Patient-ventilator interaction during neurally adjusted ventilatory assist in low birth weight infants. Pediatr Res. 2009;65(6):663-8.</note>\n</biblStruct>\n\n<biblStruct xml:id=\"b37\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">Neurally adjusted ventilatory assist as an alternative to pressure support ventilation in adults: a French multicentre randomized trial</title>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">A</forename><surname>Demoule</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">M</forename><surname>Clavel</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">C</forename><surname>Rolland-Debord</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">S</forename><surname>Perbet</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">N</forename><surname>Terzi</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName xmlns=\"http://www.tei-c.org/ns/1.0\"><forename type=\"first\">A</forename><surname>Kouatchet</surname></persName>\n\t\t</author>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Intensive Care Med</title>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">42</biblScope>\n\t\t\t<biblScope unit=\"issue\">11</biblScope>\n\t\t\t<biblScope unit=\"page\" from=\"1723\" to=\"1755\" />\n\t\t\t<date type=\"published\" when=\"2016\" />\n\t\t</imprint>\n\t</monogr>\n\t<note type=\"raw_reference\">Demoule A, Clavel M, Rolland-Debord C, Perbet S, Terzi N, Kouatchet A, et al. Neurally adjusted ventilatory assist as an alternative to pressure sup- port ventilation in adults: a French multicentre randomized trial. Intensive Care Med. 2016;42(11):1723-32.</note>\n</biblStruct>\n\n\t\t\t\t</listBibl>\n\t\t\t</div>\n\t\t</back>\n\t</text>\n</TEI>\n\n","release_ident":"lfrzpycwgnaddg6eyaa6vgqh54","file_ident":"p7oo4tpegjcuvklk4u52lava64"},"pdf_meta":{"pdf_meta":{"sha1hex":"7d8cced606bae983c5119755056d210ef0dc4679","updated":"2020-06-28T20:30:01.34188+00:00","status":"success","has_page0_thumbnail":true,"page_count":11,"word_count":7060,"page0_height":790.866,"page0_width":595.276,"permanent_id":"d5ee663f27b58ed6561515bd672e6a08","pdf_created":"2017-12-19T13:39:20+00:00","pdf_version":"1.6","metadata":{"doi":"10.1186/s13613-017-0344-8","title":"Patientventilator asynchrony during conventional mechanical ventilation in children","author":"Guillaume Mortamet ","creator":"Springer","subject":"Annals of Intensive Care, https://doi.org/10.1186/s13613-017-0344-8","producer":"Acrobat Distiller 10.1.8 (Windows); modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (AGPL-version)"}},"release_ident":"lfrzpycwgnaddg6eyaa6vgqh54","file_ident":"p7oo4tpegjcuvklk4u52lava64"}}
diff --git a/tests/test_transform.py b/tests/test_transform.py
index e073591..927c13b 100644
--- a/tests/test_transform.py
+++ b/tests/test_transform.py
@@ -2,6 +2,7 @@ from fatcat_openapi_client import ReleaseEntity
 
 from fatcat_scholar.schema import *
 from fatcat_scholar.api_entities import *
+from fatcat_scholar.transform import *
 
 
 def test_es_release_from_release() -> None:
@@ -31,3 +32,45 @@ def test_es_biblio_from_release() -> None:
         == d["release_ident"]
         == "hsmo6p4smrganpb3fndaj2lon4"
     )
+
+
+def test_run_refs() -> None:
+
+    with open("tests/files/work_iarm6swodra2bcrzhxrfaah7py_bundle.json", "r") as f:
+        run_refs(f.readlines())
+
+
+def test_run_transform() -> None:
+
+    with open("tests/files/work_iarm6swodra2bcrzhxrfaah7py_bundle.json", "r") as f:
+        run_transform(f.readlines())
+
+    with open("tests/files/sim_page_bundle.json", "r") as f:
+        run_transform(f.readlines())
+
+
+def test_biblio_metadata_hacks() -> None:
+    biblio = ScholarBiblio(
+        title="some example paper",
+        contrib_names=["able seaperson"],
+        release_year=2000,
+        volume="10",
+        issue="5",
+        publisher="some university",
+        issns=[],
+        affiliations=[],
+    )
+    out = biblio_metadata_hacks(biblio)
+
+    biblio.release_year = 2030
+    out = biblio_metadata_hacks(biblio)
+    assert out.release_year == None
+
+    biblio.doi_prefix = "10.1101"
+    biblio.container_name = None
+    biblio.release_stage = None
+    biblio.release_type = "post"
+    out = biblio_metadata_hacks(biblio)
+    assert out.container_name
+    assert out.release_stage == "submitted"
+    assert out.release_type == "article"
diff --git a/tests/test_work_pipeline.py b/tests/test_work_pipeline.py
new file mode 100644
index 0000000..439a186
--- /dev/null
+++ b/tests/test_work_pipeline.py
@@ -0,0 +1,26 @@
+from fatcat_scholar.issue_db import IssueDB
+from fatcat_scholar.sandcrawler import (
+    SandcrawlerPostgrestClient,
+    SandcrawlerMinioClient,
+)
+from fatcat_scholar.work_pipeline import *
+from fatcat_scholar.config import settings
+
+
+def test_run_transform() -> None:
+
+    issue_db = IssueDB(settings.SCHOLAR_ISSUEDB_PATH)
+    issue_db.init_db()
+
+    wp = WorkPipeline(
+        issue_db=issue_db,
+        sandcrawler_db_client=SandcrawlerPostgrestClient(
+            api_url=settings.SANDCRAWLER_DB_API
+        ),
+        sandcrawler_s3_client=SandcrawlerMinioClient(
+            host_url=settings.SANDCRAWLER_S3_API
+        ),
+    )
+
+    with open("tests/files/release_hsmo6p4smrganpb3fndaj2lon4_sans.json", "r") as f:
+        wp.run_releases(f.readlines())