Removed hyphens from data model keys (#49)

* Fixed issue #48

adsingestp/parsers/base.py

@@ -289,12 +289,12 @@ def format(self, input_dict, format):
             {
                 "name": {
                     "surname": i.get("surname", ""),
-                    "given-name": i.get("given", ""),
-                    "middle-name": i.get("middle", ""),
+                    "given_name": i.get("given", ""),
+                    "middle_name": i.get("middle", ""),
                     "prefix": i.get("prefix", ""),
                     "suffix": i.get("suffix", ""),
                     "pubraw": i.get("nameraw", ""),
-                    # "native-lang": "XXX",
+                    # "native_lang": "XXX",
                     "collab": i.get("collab", ""),
                 },
                 "affiliation": [
@@ -323,12 +323,12 @@ def format(self, input_dict, format):
                 "contrib": {
                     "name": {
                         "surname": i.get("surname", ""),
-                        "given-name": i.get("given", ""),
-                        "middle-name": i.get("middle", ""),
+                        "given_name": i.get("given", ""),
+                        "middle_name": i.get("middle", ""),
                         "prefix": i.get("prefix", ""),
                         "suffix": i.get("suffix", ""),
                         "pubraw": i.get("nameraw", ""),
-                        # "native-lang": "XXX",
+                        # "native_lang": "XXX",
                         "collab": i.get("collab", ""),
                     },
                     "affiliation": [

pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     'nameparser==1.1.1',
     'ordered-set==4.1.0',
     'python-dateutil==2.8.1',
-    'adsingestschema @ git+https://github.com/adsabs/ingest_data_model@v1.0.7#egg=adsingestschema',
+    'adsingestschema @ git+https://github.com/adsabs/ingest_data_model@v1.0.8#egg=adsingestschema',
 ]
 
 

tests/stubdata/output/arxiv_0901_2443.json

@@ -1,13 +1,13 @@
 {"abstract": {"textEnglish": "The $^{112,120}$Sn$(\\gamma,\\gamma')$ reactions have been studied at the S-DALINAC. Electric dipole (E1) strength distributions have been determined including contributions from unresolved strength extracted by a fluctuation analysis. Together with available data on $^{116,124}$Sn, an experimental systematics of the pygmy dipole resonance (PDR) in stable even-mass tin isotopes is established. The PDR centroid excitation energies and summed strengths are in reasonable agreement with quasiparticle-phonon model calculations based on a nonrelativistic description of the mean field but disagree with relativistic quasiparticle random-phase approximation predictions."},
- "authors": [{"name": {"given-name": "B.", "pubraw": "Özel, B.", "surname": "Özel"}},
-   {"name": {"given-name": "J.", "pubraw": "Enders, J.", "surname": "Enders"}},
-   {"name": {"given-name": "H.", "pubraw": "Lenske, H.", "surname": "Lenske"}},
-   {"name": {"given-name": "P.", "pubraw": "von Neumann-Cosel, P.", "surname": "von Neumann-Cosel"}},
-   {"name": {"given-name": "I.", "pubraw": "Poltoratska, I.", "surname": "Poltoratska"}},
-   {"name": {"given-name": "V.", "middle-name": "Yu.", "pubraw": "Ponomarev, V. Yu.", "surname": "Ponomarev"}},
-   {"name": {"given-name": "A.", "pubraw": "Richter, A.", "surname": "Richter"}},
-   {"name": {"given-name": "D.", "pubraw": "Savran, D.", "surname": "Savran"}},
-   {"name": {"given-name": "N.", "pubraw": "Tsoneva, N.", "surname": "Tsoneva"}}],
+ "authors": [{"name": {"given_name": "B.", "pubraw": "Özel, B.", "surname": "Özel"}},
+   {"name": {"given_name": "J.", "pubraw": "Enders, J.", "surname": "Enders"}},
+   {"name": {"given_name": "H.", "pubraw": "Lenske, H.", "surname": "Lenske"}},
+   {"name": {"given_name": "P.", "pubraw": "von Neumann-Cosel, P.", "surname": "von Neumann-Cosel"}},
+   {"name": {"given_name": "I.", "pubraw": "Poltoratska, I.", "surname": "Poltoratska"}},
+   {"name": {"given_name": "V.", "middle_name": "Yu.", "pubraw": "Ponomarev, V. Yu.", "surname": "Ponomarev"}},
+   {"name": {"given_name": "A.", "pubraw": "Richter, A.", "surname": "Richter"}},
+   {"name": {"given_name": "D.", "pubraw": "Savran, D.", "surname": "Savran"}},
+   {"name": {"given_name": "N.", "pubraw": "Tsoneva, N.", "surname": "Tsoneva"}}],
  "comments": [{"commentOrigin": "arxiv", "commentText": "Comment: submitted to Phys. Lett. B"}],
  "keywords": [{"keyString": "Nuclear Experiment", "keySystem": "arxiv"}],
  "persistentIDs": [{"preprint": {"identifier": "0901.2443", "source": "arXiv"}}],

tests/stubdata/output/arxiv_1711_04702.json

@@ -1,9 +1,9 @@
 {"abstract": {"textEnglish": "Background: Gene co-expression network analyses have become a central approach for the systems-level analysis of biological data. Several software packages exist for generating and analyzing such networks, either from correlation scores or the absolute value of a transformed score called weighted topological overlap (wTO). However, since some genes are able to up- or down-regulate other genes, it is important to explicitly consider both positive and negative correlations when constructing a gene co-expression network. Additionally, there has been a growing interest in the systematic comparison of multiple networks to identify deferentially changed links. Typically, such analyses are focused on the comparison of networks or data from two different conditions. Results: Here, we present an R package for calculating the weighted topological overlap (wTO), that explicitly addresses the sign of wTO values. The package includes the calculation of p-values (raw and adjusted) for each pairwise gene score. Our package also allows the calculation of networks from time series, without replicates. Additionally, our R package incorporates a novel method for calculating a consensus network (CN) from two or more networks. To visualize the resulting networks, the R package contains a visualization tool which allows for the direct network manipulation and access of node and link information. When testing the package on a standard laptop computer, we can conduct all calculations for systems of 20,000 genes in under two hours. Conclusion: In this work, we developed an R package that allows the computation of wTO networks, CNs and a visualization tool in the R statistical environment. It is publicly available on CRAN repositories under the GPL-2 Open Source License (https://cran.r-project.org/web/packages/wTO/)."},
- "authors": [{"name": {"given-name": "Deisy", "pubraw": "Gysi, Deisy Morselli", "surname": "Morselli Gysi"}},
-   {"name": {"given-name": "Andre", "pubraw": "Voigt, Andre", "surname": "Voigt"}},
-   {"name": {"given-name": "Tiago", "pubraw": "Fragoso, Tiago de Miranda", "middle-name": "de Miranda", "surname": "Fragoso"}},
-   {"name": {"given-name": "Eivind", "pubraw": "Almaas, Eivind", "surname": "Almaas"}},
-   {"name": {"given-name": "Katja", "pubraw": "Nowick, Katja", "surname": "Nowick"}}],
+ "authors": [{"name": {"given_name": "Deisy", "pubraw": "Gysi, Deisy Morselli", "surname": "Morselli Gysi"}},
+   {"name": {"given_name": "Andre", "pubraw": "Voigt, Andre", "surname": "Voigt"}},
+   {"name": {"given_name": "Tiago", "pubraw": "Fragoso, Tiago de Miranda", "middle_name": "de Miranda", "surname": "Fragoso"}},
+   {"name": {"given_name": "Eivind", "pubraw": "Almaas, Eivind", "surname": "Almaas"}},
+   {"name": {"given_name": "Katja", "pubraw": "Nowick, Katja", "surname": "Nowick"}}],
  "comments": [{"commentOrigin": "arxiv", "commentText": "Comment: 13 pages, 3 Figures"}],
  "keywords": [{"keyString": "Quantitative Biology - Molecular Networks", "keySystem": "arxiv"}],
  "persistentIDs": [{"preprint": {"identifier": "1711.04702", "source": "arXiv"}}],

tests/stubdata/output/arxiv_1711_05739.json

@@ -1,5 +1,5 @@
 {"abstract": {"textEnglish": "We explore the occurrence and detectability of planet-planet occultations (PPOs) in exoplanet systems. These are events during which a planet occults the disk of another planet in the same system, imparting a small photometric signal as its thermal or reflected light is blocked. We focus on the planets in TRAPPIST-1, whose orbital planes we show are aligned to within 0.3 degrees at 90% confidence. We present a photodynamical model for predicting and computing PPOs in TRAPPIST-1 and other systems for various assumptions of the planets' atmospheric states. When marginalizing over the uncertainties on all orbital parameters, we find that the rate of PPOs in TRAPPIST-1 is about 1.4 per day. We investigate the prospects for detection of these events with the James Webb Space Telescope, finding that ~10-20 occultations per year of b and c should be above the noise level at 12-15 microns. Joint modeling of several of these PPOs could lead to a robust detection. Alternatively, observations with the proposed Origins Space Telescope should be able to detect individual PPOs at high signal-to-noise. We show how PPOs can be used to break transit timing variation degeneracies, imposing strong constraints on the eccentricities and masses of the planets, as well as to constrain the longitudes of nodes and thus the complete three-dimensional structure of the system. We further show how modeling of these events can be used to reveal a planet's day/night temperature contrast and construct crude surface maps. We make our photodynamical code available on github."},
- "authors": [{"name": {"given-name": "Rodrigo", "pubraw": "Luger, Rodrigo", "surname": "Luger"}}, {"name": {"given-name": "Jacob", "pubraw": "Lustig-Yaeger, Jacob", "surname": "Lustig-Yaeger"}}, {"name": {"given-name": "Eric", "pubraw": "Agol, Eric", "surname": "Agol"}}],
+ "authors": [{"name": {"given_name": "Rodrigo", "pubraw": "Luger, Rodrigo", "surname": "Luger"}}, {"name": {"given_name": "Jacob", "pubraw": "Lustig-Yaeger, Jacob", "surname": "Lustig-Yaeger"}}, {"name": {"given_name": "Eric", "pubraw": "Agol, Eric", "surname": "Agol"}}],
  "comments": [{"commentOrigin": "arxiv", "commentText": "Comment: 36 pages, 25 figures. Accepted to ApJ. Multi-purpose photodynamical code available at github.com/rodluger/planetplanet"}],
  "keywords": [{"keyString": "Astrophysics - Earth and Planetary Astrophysics", "keySystem": "arxiv"}],
  "persistentIDs": [{"preprint": {"identifier": "1711.05739", "source": "arXiv"}}],

tests/stubdata/output/arxiv_math_0306266.json

@@ -1,5 +1,5 @@
 {"abstract": {"textEnglish": "We study the Lovasz number theta along with two further SDP relaxations theta1, theta1/2 of the independence number and the corresponding relaxations of the chromatic number on random graphs G(n,p). We prove that these relaxations are concentrated about their means Moreover, extending a result of Juhasz, we compute the asymptotic value of the relaxations for essentially the entire range of edge probabilities p. As an application, we give an improved algorithm for approximating the independence number in polynomial expected time, thereby extending a result of Krivelevich and Vu. We also improve on the analysis of an algorithm of Krivelevich for deciding whether G(n,p) is k-colorable."},
- "authors": [{"name": {"given-name": "Amin", "pubraw": "Coja-Oghlan, Amin", "surname": "Coja-Oghlan"}}],
+ "authors": [{"name": {"given_name": "Amin", "pubraw": "Coja-Oghlan, Amin", "surname": "Coja-Oghlan"}}],
  "keywords": [{"keyString": "Mathematics - Combinatorics", "keySystem": "arxiv"},
    {"keyString": "05C80, 05C15", "keySystem": "arxiv"}],
  "persistentIDs": [{"DOI": "10.1017/S0963548305006826", "preprint": {"identifier": "math/0306266", "source": "arXiv"}}],

tests/stubdata/output/crossref_10.1002_1521-3994.json

@@ -1,4 +1,4 @@
-{"authors": [{"name": {"given-name": "E.", "surname": "Schmutzer"}}],
+{"authors": [{"name": {"given_name": "E.", "surname": "Schmutzer"}}],
  "pagination": {"firstPage": "1", "lastPage": "19"},
  "persistentIDs": [{"DOI": "10.1002/1521-3994(199903)320:1<1::AID-ASNA1>3.0.CO;2-8"}],
  "pubDate": {"printDate": "1999-03-00"},

tests/stubdata/output/crossref_10.1103_PhysRevD_64-117303.json

@@ -1,4 +1,4 @@
-{"authors": [{"name": {"given-name": "Ernest", "surname": "Ma"}}, {"name": {"given-name": "G.", "surname": "Rajasekaran"}}],
+{"authors": [{"name": {"given_name": "Ernest", "surname": "Ma"}}, {"name": {"given_name": "G.", "surname": "Rajasekaran"}}],
  "pagination": {"electronicID": "117303"},
  "persistentIDs": [{"DOI": "10.1103/PhysRevD.64.117303"}],
  "pubDate": {"electrDate": "2001-11-08"},

tests/stubdata/output/crossref_10.3847_2041-8213.json

@@ -1,8 +1,8 @@
 {"abstract": {"textEnglish": "We present the results of a search in LIGO O2 public data for continuous gravitational waves from the neutron star in the low-mass X-ray binary Scorpius X-1. We search for signals with ≈ constant frequency in the range 40–180 Hz. Thanks to the efficiency of our search pipeline we can use a long coherence time and achieve unprecedented sensitivity, significantly improving on existing results. This is the first search that has been able to probe gravitational wave amplitudes that could balance the accretion torque at the neutron star radius. Our search excludes emission at this level between 67.5 and 131.5 Hz, for an inclination angle 44° ± 6° derived from radio observations, and assuming that the spin axis is perpendicular to the orbital plane. If the torque arm is ≈26 km—a conservative estimate of the Alfvén radius—our results are more constraining than the indirect limit across the band. This allows us to exclude certain mass–radius combinations and to place upper limits on the strength of the star’s magnetic field with a different probe than ever used before. We also correct a mistake that appears in the literature in the equation that gives the gravitational wave amplitude at the torque balance and we re-interpret the associated latest LIGO/Virgo results in light of this."},
- "authors": [{"name": {"given-name": "Yuanhao", "surname": "Zhang"}}, {"attrib": {"orcid": "0000-0002-1007-5298"},
-   "name": {"given-name": "Maria Alessandra", "surname": "Papa"}}, {"attrib": {"orcid": "0000-0003-3015-234X"},
-   "name": {"given-name": "Badri", "surname": "Krishnan"}}, {"attrib": {"orcid": "0000-0002-1009-2354"},
-   "name": {"given-name": "Anna L.", "surname": "Watts"}}],
+ "authors": [{"name": {"given_name": "Yuanhao", "surname": "Zhang"}}, {"attrib": {"orcid": "0000-0002-1007-5298"},
+   "name": {"given_name": "Maria Alessandra", "surname": "Papa"}}, {"attrib": {"orcid": "0000-0003-3015-234X"},
+   "name": {"given_name": "Badri", "surname": "Krishnan"}}, {"attrib": {"orcid": "0000-0002-1009-2354"},
+   "name": {"given_name": "Anna L.", "surname": "Watts"}}],
  "copyright": {"statement": "© 2021. The Author(s). Published by the American Astronomical Society.", "status": true},
  "editorialHistory": {"acceptedDate": "2020-12-09", "receivedDates": ["2020-11-09"]},
  "pagination": {"firstPage": "L14"},

tests/stubdata/output/crossref_book_10.1007-978-1-4614-3520-4.json

@@ -1,5 +1,5 @@
-{"otherContributor": [{"contrib": {"name": {"given-name": "Eric D.", "surname": "Feigelson"}}, "role": "editor"},
-                      {"contrib": {"name": {"given-name": "G. Jogesh", "surname": "Babu"}}, "role": "editor"}],
+{"otherContributor": [{"contrib": {"name": {"given_name": "Eric D.", "surname": "Feigelson"}}, "role": "editor"},
+                      {"contrib": {"name": {"given_name": "G. Jogesh", "surname": "Babu"}}, "role": "editor"}],
  "persistentIDs": [{"DOI": "10.1007/978-1-4614-3520-4", "ISBN": [{"isbnString": "978-1-4614-3519-8", "pubtype": "print"}, {"isbnString": "978-1-4614-3520-4", "pubtype": "electronic"}]}],
  "pubDate": {"printDate": "2012-00-00"},
  "publication": {"pubYear": "2012", "publisher": "Springer New York", "volumeNum": "902", "bookSeries": {"seriesDescription": "issn", "seriesID": "0930-0325", "seriesName": "Lecture Notes in Statistics"}},

tests/stubdata/output/crossref_book_10.1017-CBO9780511709265.json

@@ -1,4 +1,4 @@
-{"authors": [{"name": {"given-name": "Agnes Mary", "surname": "Clerke"}}],
+{"authors": [{"name": {"given_name": "Agnes Mary", "surname": "Clerke"}}],
  "persistentIDs": [{"DOI": "10.1017/CBO9780511709265", "ISBN": [{"isbnString": "9780511709265", "pubtype": "print"}]}],
  "pubDate": {"electrDate": "2009-00-00", "printDate": "2010-00-00"},
  "publication": {"pubYear": "2010", "publisher": "Cambridge University Press"},

tests/stubdata/output/crossref_conf_10.1109-MWSYM.2013.6697399.json

@@ -1,9 +1,9 @@
-{"authors": [{"name": {"given-name": "Ulrich J.", "surname": "Lewark"}},
-             {"name": {"given-name": "Axel", "surname": "Tessmann"}},
-             {"name": {"given-name": "Hermann", "surname": "Massler"}},
-             {"name": {"given-name": "Arnulf", "surname": "Leuther"}},
-             {"name": {"given-name": "Thomas", "surname": "Zwick"}},
-             {"name": {"given-name": "Ingmar", "surname": "Kallfass"}}],
+{"authors": [{"name": {"given_name": "Ulrich J.", "surname": "Lewark"}},
+             {"name": {"given_name": "Axel", "surname": "Tessmann"}},
+             {"name": {"given_name": "Hermann", "surname": "Massler"}},
+             {"name": {"given_name": "Arnulf", "surname": "Leuther"}},
+             {"name": {"given_name": "Thomas", "surname": "Zwick"}},
+             {"name": {"given_name": "Ingmar", "surname": "Kallfass"}}],
  "pagination": {"firstPage": "1", "lastPage": "3"},
  "persistentIDs": [{"DOI": "10.1109/MWSYM.2013.6697399", "ISBN": [{"isbnString": "978-1-4673-6176-7", "pubtype": "electronic"}]}],
  "pubDate": {"printDate": "2013-06-00"},

tests/stubdata/output/datacite_schema3.1_example-full.json

@@ -1,12 +1,12 @@
 {"abstract": {"textEnglish": "XML example of all DataCite Metadata Schema v3.1 properties."},
  "authors": [{"affiliation": [{"affPubRaw": "DataCite"}],
               "attrib": {"orcid": "0000-0001-5000-0007"},
-              "name": {"given-name": "Elizabeth", "pubraw": "Miller, Elizabeth", "surname": "Miller"}}],
+              "name": {"given_name": "Elizabeth", "pubraw": "Miller, Elizabeth", "surname": "Miller"}}],
  "doctype": "software",
  "keywords": [{"keyString": "000 computer science", "keySystem": "datacite"}],
  "otherContributor": [{"contrib": {"affiliation": [{"affPubRaw": "California Digital Library"}],
                                    "attrib": {"orcid": "0000-0002-7285-027X"},
-                                   "name": {"given-name": "Joan", "pubraw": "Starr, Joan", "surname": "Starr"}},
+                                   "name": {"given_name": "Joan", "pubraw": "Starr, Joan", "surname": "Starr"}},
                        "role": "ProjectLeader"}],
  "persistentIDs": [{"DOI": "10.5072/example-full"}],
  "pubDate": {"electrDate": "2014", "otherDate": [{"otherDateType": "Updated", "otherDateValue": "2014-10-17"}]},

tests/stubdata/output/datacite_schema4.1_example-full.json

@@ -1,12 +1,12 @@
 {"abstract": {"textEnglish": "XML example of all DataCite Metadata Schema v4.1 properties."},
  "authors": [{"affiliation": [{"affPubRaw": "DataCite"}],
               "attrib": {"orcid": "0000-0001-5000-0007"},
-              "name": {"given-name": "Elizabeth", "surname": "Miller"}}],
+              "name": {"given_name": "Elizabeth", "surname": "Miller"}}],
  "doctype": "software",
  "keywords": [{"keyString": "000 computer science", "keySystem": "datacite"}],
  "otherContributor": [{"contrib": {"affiliation": [{"affPubRaw": "California Digital Library"}],
                                    "attrib": {"orcid": "0000-0002-7285-027X"},
-                                   "name": {"given-name": "Joan", "surname": "Starr"}},
+                                   "name": {"given_name": "Joan", "surname": "Starr"}},
                        "role": "ProjectLeader"}],
  "persistentIDs": [{"DOI": "10.5072/example-full"}],
  "pubDate": {"electrDate": "2014", "otherDate": [{"otherDateType": "Updated", "otherDateValue": "2017-09-13"}]},