ghga-transpiler 2.1.5__py3-none-any.whl → 2.2.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (8) hide show
  1. ghga_transpiler/__init__.py +1 -1
  2. ghga_transpiler/configs/2.0.yaml +170 -0
  3. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/METADATA +1 -1
  4. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/RECORD +8 -7
  5. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/WHEEL +1 -1
  6. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/LICENSE +0 -0
  7. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/entry_points.txt +0 -0
  8. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/top_level.txt +0 -0
ghga_transpiler/__init__.py CHANGED
@@ -18,7 +18,7 @@
18
18
 
19
19
  from openpyxl.xml import DEFUSEDXML
20
20
 
21
- __version__ = "2.1.5"
21
+ __version__ = "2.2.1"
22
22
 
23
23
  if not DEFUSEDXML:
24
24
  raise RuntimeError(
ghga_transpiler/configs/2.0.yaml ADDED
@@ -0,0 +1,170 @@
1
+ ghga_metadata_version: 2.0.0
2
+ default_settings:
3
+ header_row: 1
4
+ start_row: 7
5
+ start_column: 1
6
+ transformations:
7
+ attributes:
8
+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
9
+ format:
10
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
11
+ worksheets:
12
+ - settings:
13
+ end_column: 7
14
+ name: analyses
15
+ transformations:
16
+ research_data_files:
17
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
18
+ sheet_name: Analysis
19
+ - settings:
20
+ end_column: 11
21
+ name: analysis_methods
22
+ transformations:
23
+ parameters:
24
+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
25
+ software_versions:
26
+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
27
+ sheet_name: AnalysisMethod
28
+ - settings:
29
+ end_column: 7
30
+ name: analysis_method_supporting_files
31
+ sheet_name: AnalysisMethodSupportingFile
32
+ - settings:
33
+ end_column: 7
34
+ name: studies
35
+ transformations:
36
+ affiliations:
37
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
38
+ attributes:
39
+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
40
+ types:
41
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
42
+ attributes:
43
+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
44
+ sheet_name: Study
45
+ - settings:
46
+ end_column: 10
47
+ name: individuals
48
+ transformations:
49
+ phenotypic_features_terms:
50
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
51
+ phenotypic_features_ids:
52
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
53
+ diagnosis_ids:
54
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
55
+ diagnosis_terms:
56
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
57
+ sex:
58
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
59
+ ancestry_terms:
60
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
61
+ ancestry_ids:
62
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
63
+ sheet_name: Individual
64
+ - settings:
65
+ end_column: 7
66
+ name: individual_supporting_files
67
+ sheet_name: IndividualSupportingFile
68
+ - settings:
69
+ end_column: 21
70
+ name: samples
71
+ transformations:
72
+ type:
73
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
74
+ storage:
75
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
76
+ disease_or_healthy:
77
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
78
+ case_control_status:
79
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
80
+ xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
81
+ biospecimen_age_at_sampling:
82
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
83
+ biospecimen_vital_status_at_sampling:
84
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
85
+ biospecimen_isolation:
86
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
87
+ biospecimen_storage:
88
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
89
+ attributes:
90
+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
91
+ sheet_name: Sample
92
+ - settings:
93
+ end_column: 23
94
+ name: experiment_methods
95
+ transformations:
96
+ library_type:
97
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
98
+ library_selection_methods:
99
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
100
+ library_preparation_kit_retail_name:
101
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
102
+ primer:
103
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
104
+ end_bias:
105
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
106
+ target_regions:
107
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
108
+ rnaseq_strandedness:
109
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
110
+ instrument_model:
111
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
112
+ sequencing_layout:
113
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
114
+ flow_cell_type:
115
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
116
+ sample_barcode_read:
117
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
118
+ sequencing_layout:
119
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
120
+ attributes:
121
+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
122
+ sheet_name: ExperimentMethod
123
+ - settings:
124
+ end_column: 7
125
+ name: experiment_method_supporting_files
126
+ sheet_name: ExperimentMethodSupportingFile
127
+ - settings:
128
+ end_column: 8
129
+ name: experiments
130
+ sheet_name: Experiment
131
+ - settings:
132
+ end_column: 9
133
+ name: research_data_files
134
+ transformations:
135
+ experiments:
136
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
137
+ format:
138
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
139
+ sheet_name: ResearchDataFile
140
+ - settings:
141
+ end_column: 7
142
+ name: process_data_files
143
+ sheet_name: ProcessDataFile
144
+ - settings:
145
+ end_column: 7
146
+ name: datasets
147
+ transformations:
148
+ types: !!python/object/apply:ghga_transpiler.transformations.to_list []
149
+ sheet_name: Dataset
150
+ - settings:
151
+ end_column: 11
152
+ name: data_access_policies
153
+ transformations:
154
+ data_use_modifier_terms:
155
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
156
+ data_use_permission_term:
157
+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
158
+ data_use_modifier_ids:
159
+ !!python/object/apply:ghga_transpiler.transformations.to_list []
160
+ sheet_name: DataAccessPolicy
161
+ - settings:
162
+ end_column: 4
163
+ name: data_access_committees
164
+ sheet_name: DataAccessCommittee
165
+ - settings:
166
+ end_column: 9
167
+ name: publications
168
+ transformations:
169
+ xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
170
+ sheet_name: Publication
{ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: ghga_transpiler
3
- Version: 2.1.5
3
+ Version: 2.2.1
4
4
  Summary: GHGA-Transpiler - excel to JSON converter
5
5
  Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
6
6
  License: Apache 2.0
{ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
1
- ghga_transpiler/__init__.py,sha256=8cxE0fm7rs3CJ91SKgBGROUseHyG3A5655lFtWJX5DU,908
1
+ ghga_transpiler/__init__.py,sha256=58eVmIOrztgGdUW8SxujAGlzfj0Rg4iMwp4RiXldbcU,908
2
2
  ghga_transpiler/__main__.py,sha256=EVGi0SsK--oaDF_c6PhVvNyPDnItrJzVapNAsKhgBmM,847
3
3
  ghga_transpiler/cli.py,sha256=76TEXMPUCVnFqoQQWDvLBNw2iNjv3LgXAkJK-qjJNrE,2522
4
4
  ghga_transpiler/core.py,sha256=i3JIaqWNsHryEphEHWOlLUI0BRUkTHGdphCs4KvMawY,5235
@@ -10,10 +10,11 @@ ghga_transpiler/config/exceptions.py,sha256=H2xLk9YV3yHuwBDxQDgumbymX_-xSXctlh-r
10
10
  ghga_transpiler/configs/0.10.yaml,sha256=hsS8xwzJ00SRSb-VIfM-oM8UM0hOdR3xeuflf1fra4Y,5683
11
11
  ghga_transpiler/configs/1.0.yaml,sha256=MgSEkDpZjn7I76uLFAfpCfmOqOaCBjEojn6VDX6TnUc,5683
12
12
  ghga_transpiler/configs/1.1.yaml,sha256=rgxTV7bEVMwk1UeJ8hAeCZcqTwX10KXQKoaYnpV0bxI,5683
13
+ ghga_transpiler/configs/2.0.yaml,sha256=3lwXFjtbEW-mWGj99d3PaWJflLnuy7WAS5AvNubDJlI,6637
13
14
  ghga_transpiler/configs/__init__.py,sha256=109RyIL2rxVrEiOS9D0q-PGVqw1_VZblvvFxOh4ZUjU,686
14
- ghga_transpiler-2.1.5.dist-info/LICENSE,sha256=fBYaxYJmvm_AQEYU4gRvUAWbqhO0bgqPj9Yl6f8RXuU,11452
15
- ghga_transpiler-2.1.5.dist-info/METADATA,sha256=CpoyraNrzl0jbIW1KuepKDD1Zhajh1UUBni7nc3Kjfw,4595
16
- ghga_transpiler-2.1.5.dist-info/WHEEL,sha256=mguMlWGMX-VHnMpKOjjQidIo1ssRlCFu4a4mBpz1s2M,91
17
- ghga_transpiler-2.1.5.dist-info/entry_points.txt,sha256=Fr_VQJynZZl95NXjrQW2gE0bCocgjKVNEZQpaLls8po,65
18
- ghga_transpiler-2.1.5.dist-info/top_level.txt,sha256=TksRpDO3Y4mvK-B09UhQU3ceZpG19fljNlVDGTfjg8o,16
19
- ghga_transpiler-2.1.5.dist-info/RECORD,,
15
+ ghga_transpiler-2.2.1.dist-info/LICENSE,sha256=fBYaxYJmvm_AQEYU4gRvUAWbqhO0bgqPj9Yl6f8RXuU,11452
16
+ ghga_transpiler-2.2.1.dist-info/METADATA,sha256=j6xZq_k-yZVenxGCcXgF0xZDuQUs7ckcAGb6LlRT8Yc,4595
17
+ ghga_transpiler-2.2.1.dist-info/WHEEL,sha256=Rp8gFpivVLXx-k3U95ozHnQw8yDcPxmhOpn_Gx8d5nc,91
18
+ ghga_transpiler-2.2.1.dist-info/entry_points.txt,sha256=Fr_VQJynZZl95NXjrQW2gE0bCocgjKVNEZQpaLls8po,65
19
+ ghga_transpiler-2.2.1.dist-info/top_level.txt,sha256=TksRpDO3Y4mvK-B09UhQU3ceZpG19fljNlVDGTfjg8o,16
20
+ ghga_transpiler-2.2.1.dist-info/RECORD,,
{ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.1.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (70.1.1)
2
+ Generator: setuptools (72.0.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
5
5