impc-api 1.0.5__tar.gz → 1.0.7__tar.gz

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 (23) hide show
  1. {impc_api-1.0.5 → impc_api-1.0.7}/PKG-INFO +34 -13
  2. impc_api-1.0.5/impc_api.egg-info/PKG-INFO → impc_api-1.0.7/README.md +28 -26
  3. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api/solr_request.py +24 -3
  4. impc_api-1.0.7/impc_api/utils/core_fields.json +463 -0
  5. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api/utils/validators.py +1 -1
  6. impc_api-1.0.5/README.md → impc_api-1.0.7/impc_api.egg-info/PKG-INFO +47 -9
  7. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api.egg-info/SOURCES.txt +0 -1
  8. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api.egg-info/requires.txt +2 -0
  9. {impc_api-1.0.5 → impc_api-1.0.7}/pyproject.toml +4 -2
  10. {impc_api-1.0.5 → impc_api-1.0.7}/tests/test_solr_request.py +91 -0
  11. impc_api-1.0.5/impc_api/utils/core_fields.json +0 -15
  12. impc_api-1.0.5/setup.py +0 -39
  13. {impc_api-1.0.5 → impc_api-1.0.7}/LICENSE +0 -0
  14. {impc_api-1.0.5 → impc_api-1.0.7}/MANIFEST.in +0 -0
  15. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api/__init__.py +0 -0
  16. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api/batch_solr_request.py +0 -0
  17. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api/utils/__init__.py +0 -0
  18. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api/utils/warnings.py +0 -0
  19. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api.egg-info/dependency_links.txt +0 -0
  20. {impc_api-1.0.5 → impc_api-1.0.7}/impc_api.egg-info/top_level.txt +0 -0
  21. {impc_api-1.0.5 → impc_api-1.0.7}/setup.cfg +0 -0
  22. {impc_api-1.0.5 → impc_api-1.0.7}/tests/test_batch_solr_request.py +0 -0
  23. {impc_api-1.0.5 → impc_api-1.0.7}/tests/test_helpers.py +0 -0
{impc_api-1.0.5 → impc_api-1.0.7}/PKG-INFO RENAMED
@@ -1,42 +1,43 @@
1
- Metadata-Version: 2.1
1
+ Metadata-Version: 2.4
2
2
  Name: impc_api
3
- Version: 1.0.5
3
+ Version: 1.0.7
4
4
  Summary: A package to facilitate making API requests to the IMPC Solr API
5
- Home-page: https://github.com/mpi2/impc-data-api-workshop
6
5
  Author: MPI2, Marina Kan, Diego Pava
7
- Project-URL: Homepage, https://github.com/mpi2/impc-data-api-workshop
6
+ Project-URL: Homepage, https://github.com/mpi2/impc-api
8
7
  Requires-Python: >=3.10
9
8
  Description-Content-Type: text/markdown
10
9
  License-File: LICENSE
10
+ Requires-Dist: ipykernel>=6.29.5
11
+ Requires-Dist: notebook>=7.2.2
11
12
  Requires-Dist: pandas>=2.2.0
12
13
  Requires-Dist: requests>=2.31.0
13
14
  Requires-Dist: tqdm>=4.66.4
14
15
  Requires-Dist: pydantic>=2.9
15
16
  Provides-Extra: dev
16
17
  Requires-Dist: pytest>=8.2.2; extra == "dev"
18
+ Dynamic: license-file
17
19
 
18
20
  # IMPC_API
19
21
 
20
- `impc_api` is a Python package.
21
-
22
- The functions in this package are intended for use in a Jupyter Notebook.
22
+ `impc_api` is a Python package which provides several helper functions that wrap around the IMPC SOLR API. The functions in this package are intended for use in a Jupyter Notebook.
23
23
 
24
24
  ## Installation Instructions
25
25
 
26
+ 0. Ensure that Python is installed on your system. The minimum required version is 3.10.
27
+
26
28
  1. **Create a virtual environment (optional but recommended)**:
27
- On Mac:
29
+ On Mac or Linux:
28
30
  ```bash
29
31
  python3 -m venv .venv
30
32
  source .venv/bin/activate
31
33
  ```
32
34
 
33
35
  2. **Install the package**: `pip install impc_api`
34
- 3. **Install Jupyter**: `pip install jupyter`
35
- 4. **Run the Jupyter Notebook**: `jupyter notebook`
36
+ 3. **Run the Jupyter Notebook**: `jupyter notebook`
36
37
 
37
38
  After executing the command, the Jupyter interface should open in your browser. If it does not, follow the instructions provided in the terminal.
38
39
 
39
- 5. **Try it out**:
40
+ 4. **Try it out**:
40
41
 
41
42
  Create a [Jupyter Notebook](https://jupyter-notebook.readthedocs.io/en/latest/) and try some of the examples below:
42
43
 
@@ -97,7 +98,7 @@ num_found, df = solr_request(
97
98
  validate=True
98
99
  )
99
100
 
100
- > InvalidCoreWarning: Invalid core: "genotype-phenotyp", select from the available cores:
101
+ > InvalidCoreWarning: Invalid core: "invalid_core", select from the available cores:
101
102
  > dict_keys(['experiment', 'genotype-phenotype', 'impc_images', 'phenodigm', 'statistical-result'])
102
103
  ```
103
104
 
@@ -117,13 +118,33 @@ num_found, df = solr_request(
117
118
  > To see expected fields check the documentation at: https://www.ebi.ac.uk/mi/impc/solrdoc/
118
119
  ```
119
120
 
121
+ ## c. URL only
122
+
123
+ Users might want help producing the URL to fetch the data without the need of a DataFrame. Use the flag `url_only=True` to print or return the URL for your query.
124
+
125
+ ```python
126
+ url, _ = solr_request(
127
+ core='genotype-phenotype',
128
+ params={
129
+ 'q': '*:*',
130
+ 'rows': 10,
131
+ 'fl': 'marker_symbol,allele_symbol'
132
+ },
133
+ url_only=True
134
+ )
135
+ > "https://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select?q=%2A%3A%2A&rows=10&fl=marker_symbol%2Callele_symbol"
136
+
137
+ print(url)
138
+ > "https://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select?q=%2A%3A%2A&rows=10&fl=marker_symbol%2Callele_symbol"
139
+ ```
140
+
120
141
  # 2. Batch Solr Request
121
142
 
122
143
  `batch_solr_request` is available for large queries. This solves issues where a request is too large to fit into memory or where it puts a lot of strain on the API.
123
144
 
124
145
  Use `batch_solr_request` for:
125
146
 
126
- - Large queries (>1,000,000)
147
+ - Large queries (>100,000 rows)
127
148
  - Querying multiple items in a list
128
149
  - Downloading data in `json` or `csv` format.
129
150
 
impc_api-1.0.5/impc_api.egg-info/PKG-INFO → impc_api-1.0.7/README.md RENAMED
@@ -1,42 +1,24 @@
1
- Metadata-Version: 2.1
2
- Name: impc_api
3
- Version: 1.0.5
4
- Summary: A package to facilitate making API requests to the IMPC Solr API
5
- Home-page: https://github.com/mpi2/impc-data-api-workshop
6
- Author: MPI2, Marina Kan, Diego Pava
7
- Project-URL: Homepage, https://github.com/mpi2/impc-data-api-workshop
8
- Requires-Python: >=3.10
9
- Description-Content-Type: text/markdown
10
- License-File: LICENSE
11
- Requires-Dist: pandas>=2.2.0
12
- Requires-Dist: requests>=2.31.0
13
- Requires-Dist: tqdm>=4.66.4
14
- Requires-Dist: pydantic>=2.9
15
- Provides-Extra: dev
16
- Requires-Dist: pytest>=8.2.2; extra == "dev"
17
-
18
1
  # IMPC_API
19
2
 
20
- `impc_api` is a Python package.
21
-
22
- The functions in this package are intended for use in a Jupyter Notebook.
3
+ `impc_api` is a Python package which provides several helper functions that wrap around the IMPC SOLR API. The functions in this package are intended for use in a Jupyter Notebook.
23
4
 
24
5
  ## Installation Instructions
25
6
 
7
+ 0. Ensure that Python is installed on your system. The minimum required version is 3.10.
8
+
26
9
  1. **Create a virtual environment (optional but recommended)**:
27
- On Mac:
10
+ On Mac or Linux:
28
11
  ```bash
29
12
  python3 -m venv .venv
30
13
  source .venv/bin/activate
31
14
  ```
32
15
 
33
16
  2. **Install the package**: `pip install impc_api`
34
- 3. **Install Jupyter**: `pip install jupyter`
35
- 4. **Run the Jupyter Notebook**: `jupyter notebook`
17
+ 3. **Run the Jupyter Notebook**: `jupyter notebook`
36
18
 
37
19
  After executing the command, the Jupyter interface should open in your browser. If it does not, follow the instructions provided in the terminal.
38
20
 
39
- 5. **Try it out**:
21
+ 4. **Try it out**:
40
22
 
41
23
  Create a [Jupyter Notebook](https://jupyter-notebook.readthedocs.io/en/latest/) and try some of the examples below:
42
24
 
@@ -97,7 +79,7 @@ num_found, df = solr_request(
97
79
  validate=True
98
80
  )
99
81
 
100
- > InvalidCoreWarning: Invalid core: "genotype-phenotyp", select from the available cores:
82
+ > InvalidCoreWarning: Invalid core: "invalid_core", select from the available cores:
101
83
  > dict_keys(['experiment', 'genotype-phenotype', 'impc_images', 'phenodigm', 'statistical-result'])
102
84
  ```
103
85
 
@@ -117,13 +99,33 @@ num_found, df = solr_request(
117
99
  > To see expected fields check the documentation at: https://www.ebi.ac.uk/mi/impc/solrdoc/
118
100
  ```
119
101
 
102
+ ## c. URL only
103
+
104
+ Users might want help producing the URL to fetch the data without the need of a DataFrame. Use the flag `url_only=True` to print or return the URL for your query.
105
+
106
+ ```python
107
+ url, _ = solr_request(
108
+ core='genotype-phenotype',
109
+ params={
110
+ 'q': '*:*',
111
+ 'rows': 10,
112
+ 'fl': 'marker_symbol,allele_symbol'
113
+ },
114
+ url_only=True
115
+ )
116
+ > "https://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select?q=%2A%3A%2A&rows=10&fl=marker_symbol%2Callele_symbol"
117
+
118
+ print(url)
119
+ > "https://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select?q=%2A%3A%2A&rows=10&fl=marker_symbol%2Callele_symbol"
120
+ ```
121
+
120
122
  # 2. Batch Solr Request
121
123
 
122
124
  `batch_solr_request` is available for large queries. This solves issues where a request is too large to fit into memory or where it puts a lot of strain on the API.
123
125
 
124
126
  Use `batch_solr_request` for:
125
127
 
126
- - Large queries (>1,000,000)
128
+ - Large queries (>100,000 rows)
127
129
  - Querying multiple items in a list
128
130
  - Downloading data in `json` or `csv` format.
129
131
 
{impc_api-1.0.5 → impc_api-1.0.7}/impc_api/solr_request.py RENAMED
@@ -10,7 +10,7 @@ pd.set_option("display.max_rows", 15)
10
10
  pd.set_option("display.max_columns", None)
11
11
 
12
12
  # Create helper function
13
- def solr_request(core, params, silent=False, validate=False):
13
+ def solr_request(core, params, silent=False, validate=False, url_only=False):
14
14
  """Performs a single Solr request to the IMPC Solr API.
15
15
 
16
16
  Args:
@@ -22,11 +22,22 @@ def solr_request(core, params, silent=False, validate=False):
22
22
  validate (bool, optional): default False
23
23
  If True, validates the parameters against the core schema and raises warnings
24
24
  if any parameter seems invalid.
25
+ url_only (bool, optional): default False
26
+ If true, returns the request URL but no data.
25
27
 
26
28
 
27
29
  Returns:
28
- num_found: Number of docs found.
29
- pandas.DataFrame: Pandas.DataFrame object with the information requested.
30
+ Union[Tuple[int, pandas.DataFrame], Tuple[str, None]]:
31
+ - If url_only is False:
32
+ A tuple containing:
33
+ num_found (int): Number of documents found.
34
+ df (pandas.DataFrame): DataFrame object with the information requested.
35
+
36
+ - If url_only is True:
37
+ A tuple containing:
38
+ url (str): The URL of the request if status_code is 200, otherwise None.
39
+ None: Placeholder for consistency.
40
+
30
41
 
31
42
  Example query:
32
43
  num_found, df = solr_request(
@@ -70,6 +81,16 @@ def solr_request(core, params, silent=False, validate=False):
70
81
  solr_url = base_url + core + "/select"
71
82
 
72
83
  response = requests.get(solr_url, params=params)
84
+
85
+ if url_only:
86
+ if response.status_code == 200:
87
+ print(response.request.url)
88
+ return response.request.url, None
89
+ else:
90
+ print(f"Error: {response.status_code}\n{response.text}")
91
+ return None, None
92
+
93
+
73
94
  if not silent:
74
95
  print(f"\nYour request:\n{response.request.url}\n")
75
96
 
impc_api-1.0.7/impc_api/utils/core_fields.json ADDED
@@ -0,0 +1,463 @@
1
+ {
2
+ "experiment": [
3
+ "id",
4
+ "observation_id",
5
+ "specimen_id",
6
+ "phenotyping_center_id",
7
+ "phenotyping_center",
8
+ "production_center_id",
9
+ "production_center",
10
+ "specimen_project_id",
11
+ "specimen_project_name",
12
+ "gene_accession_id",
13
+ "gene_symbol",
14
+ "allele_accession_id",
15
+ "allele_symbol",
16
+ "zygosity",
17
+ "sex",
18
+ "biological_model_id",
19
+ "biological_sample_id",
20
+ "biological_sample_group",
21
+ "strain_accession_id",
22
+ "strain_name",
23
+ "genetic_background",
24
+ "allelic_composition",
25
+ "colony_id",
26
+ "litter_id",
27
+ "date_of_birth",
28
+ "external_sample_id",
29
+ "life_stage_name",
30
+ "life_stage_acc",
31
+ "datasource_id",
32
+ "datasource_name",
33
+ "project_id",
34
+ "project_name",
35
+ "pipeline_id",
36
+ "pipeline_name",
37
+ "pipeline_stable_id",
38
+ "procedure_id",
39
+ "procedure_name",
40
+ "procedure_stable_id",
41
+ "procedure_group",
42
+ "parameter_id",
43
+ "parameter_name",
44
+ "parameter_stable_id",
45
+ "procedure_sequence_id",
46
+ "experiment_id",
47
+ "observation_type",
48
+ "data_type",
49
+ "experiment_source_id",
50
+ "date_of_experiment",
51
+ "weight_parameter_stable_id",
52
+ "weight_date",
53
+ "weight_days_old",
54
+ "weight",
55
+ "data_point",
56
+ "order_index",
57
+ "dimension",
58
+ "time_point",
59
+ "discrete_point",
60
+ "category",
61
+ "raw_category",
62
+ "metadata",
63
+ "metadata_group",
64
+ "anatomy_id",
65
+ "anatomy_term",
66
+ "anatomy_id_term",
67
+ "anatomy_term_synonym",
68
+ "top_level_anatomy_id",
69
+ "top_level_anatomy_term",
70
+ "top_level_anatomy_term_synonym",
71
+ "selected_top_level_anatomy_id",
72
+ "selected_top_level_anatomy_term",
73
+ "selected_top_level_anatomy_term_synonym",
74
+ "intermediate_anatomy_id",
75
+ "intermediate_anatomy_term",
76
+ "intermediate_anatomy_term_synonym",
77
+ "parent_anatomy_id",
78
+ "parent_anatomy_term",
79
+ "parent_anatomy_term_synonym",
80
+ "child_anatomy_id",
81
+ "child_anatomy_term",
82
+ "child_anatomy_term_synonym",
83
+ "download_file_path",
84
+ "image_link",
85
+ "file_type",
86
+ "increment_value",
87
+ "parameter_association_stable_id",
88
+ "parameter_association_sequence_id",
89
+ "parameter_association_dim_id",
90
+ "parameter_association_name",
91
+ "parameter_association_value",
92
+ "developmental_stage_acc",
93
+ "developmental_stage_name",
94
+ "text_value",
95
+ "sub_term_id",
96
+ "sub_term_name",
97
+ "sub_term_description",
98
+ "age_in_days",
99
+ "age_in_weeks"
100
+ ],
101
+ "genotype-phenotype": [
102
+ "doc_id",
103
+ "ontology_db_id",
104
+ "assertion_type",
105
+ "assertion_type_id",
106
+ "mpath_term_id",
107
+ "mpath_term_name",
108
+ "anatomy_term_id",
109
+ "anatomy_term_name",
110
+ "intermediate_anatomy_term_id",
111
+ "intermediate_anatomy_term_name",
112
+ "top_level_anatomy_term_id",
113
+ "top_level_anatomy_term_name",
114
+ "mp_term_id",
115
+ "mp_term_name",
116
+ "alt_mp_term_id",
117
+ "top_level_mp_term_id",
118
+ "top_level_mp_term_name",
119
+ "intermediate_mp_term_id",
120
+ "intermediate_mp_term_name",
121
+ "marker_symbol",
122
+ "marker_accession_id",
123
+ "colony_id",
124
+ "allele_name",
125
+ "allele_symbol",
126
+ "allele_accession_id",
127
+ "strain_name",
128
+ "strain_accession_id",
129
+ "phenotyping_center",
130
+ "project_external_id",
131
+ "project_name",
132
+ "project_fullname",
133
+ "resource_name",
134
+ "resource_fullname",
135
+ "sex",
136
+ "zygosity",
137
+ "pipeline_name",
138
+ "pipeline_stable_id",
139
+ "pipeline_stable_key",
140
+ "procedure_name",
141
+ "procedure_stable_id",
142
+ "procedure_stable_key",
143
+ "parameter_name",
144
+ "parameter_stable_id",
145
+ "parameter_stable_key",
146
+ "statistical_method",
147
+ "percentage_change",
148
+ "p_value",
149
+ "effect_size",
150
+ "external_id",
151
+ "life_stage_acc",
152
+ "life_stage_name"
153
+ ],
154
+ "impc_images": [
155
+ "id",
156
+ "observation_id",
157
+ "specimen_id",
158
+ "phenotyping_center_id",
159
+ "phenotyping_center",
160
+ "production_center_id",
161
+ "production_center",
162
+ "specimen_project_id",
163
+ "specimen_project_name",
164
+ "gene_accession_id",
165
+ "gene_symbol",
166
+ "allele_accession_id",
167
+ "allele_symbol",
168
+ "zygosity",
169
+ "sex",
170
+ "biological_model_id",
171
+ "biological_sample_id",
172
+ "biological_sample_group",
173
+ "strain_accession_id",
174
+ "strain_name",
175
+ "genetic_background",
176
+ "allelic_composition",
177
+ "colony_id",
178
+ "litter_id",
179
+ "date_of_birth",
180
+ "external_sample_id",
181
+ "life_stage_name",
182
+ "life_stage_acc",
183
+ "datasource_id",
184
+ "datasource_name",
185
+ "project_id",
186
+ "project_name",
187
+ "pipeline_id",
188
+ "pipeline_name",
189
+ "pipeline_stable_id",
190
+ "procedure_id",
191
+ "procedure_name",
192
+ "procedure_stable_id",
193
+ "procedure_group",
194
+ "parameter_id",
195
+ "parameter_name",
196
+ "parameter_stable_id",
197
+ "procedure_sequence_id",
198
+ "experiment_id",
199
+ "observation_type",
200
+ "data_type",
201
+ "experiment_source_id",
202
+ "date_of_experiment",
203
+ "weight_parameter_stable_id",
204
+ "weight_date",
205
+ "weight_days_old",
206
+ "weight",
207
+ "data_point",
208
+ "order_index",
209
+ "dimension",
210
+ "time_point",
211
+ "discrete_point",
212
+ "category",
213
+ "raw_category",
214
+ "metadata",
215
+ "metadata_group",
216
+ "mp_id",
217
+ "mp_term",
218
+ "top_level_mp_id",
219
+ "top_level_mp_term",
220
+ "intermediate_mp_id",
221
+ "intermediate_mp_term",
222
+ "anatomy_id",
223
+ "anatomy_term",
224
+ "anatomy_id_term",
225
+ "anatomy_term_synonym",
226
+ "top_level_anatomy_id",
227
+ "top_level_anatomy_term",
228
+ "top_level_anatomy_term_synonym",
229
+ "selected_top_level_anatomy_id",
230
+ "selected_top_level_anatomy_term",
231
+ "selected_top_level_anatomy_term_synonym",
232
+ "intermediate_anatomy_id",
233
+ "intermediate_anatomy_term",
234
+ "intermediate_anatomy_term_synonym",
235
+ "parent_anatomy_id",
236
+ "parent_anatomy_term",
237
+ "parent_anatomy_term_synonym",
238
+ "child_anatomy_id",
239
+ "child_anatomy_term",
240
+ "child_anatomy_term_synonym",
241
+ "download_file_path",
242
+ "image_link",
243
+ "file_type",
244
+ "parameter_association_stable_id",
245
+ "parameter_association_sequence_id",
246
+ "parameter_association_dim_id",
247
+ "parameter_association_name",
248
+ "parameter_association_value",
249
+ "developmental_stage_acc",
250
+ "developmental_stage_name",
251
+ "text_value",
252
+ "sub_term_id",
253
+ "sub_term_name",
254
+ "sub_term_description",
255
+ "sequence_id",
256
+ "age_in_days",
257
+ "age_in_weeks",
258
+ "download_url",
259
+ "jpeg_url",
260
+ "thumbnail_url",
261
+ "omero_id"
262
+ ],
263
+ "phenodigm": [
264
+ "type",
265
+ "disease_id",
266
+ "disease_source",
267
+ "disease_term",
268
+ "disease_alts",
269
+ "disease_locus",
270
+ "disease_classes",
271
+ "disease_phenotypes",
272
+ "gene_id",
273
+ "gene_symbol",
274
+ "gene_symbols_withdrawn",
275
+ "gene_locus",
276
+ "hgnc_gene_id",
277
+ "hgnc_gene_symbol",
278
+ "hgnc_gene_symbols_withdrawn",
279
+ "hgnc_gene_locus",
280
+ "mouse_model",
281
+ "impc_model",
282
+ "model_id",
283
+ "model_source",
284
+ "model_description",
285
+ "model_genetic_background",
286
+ "marker_id",
287
+ "marker_symbol",
288
+ "marker_locus",
289
+ "marker_num_models",
290
+ "model_phenotypes",
291
+ "ontology",
292
+ "phenotype_id",
293
+ "phenotype_term",
294
+ "phenotype_synonym",
295
+ "hp_id",
296
+ "hp_term",
297
+ "mp_id",
298
+ "mp_term",
299
+ "association_curated",
300
+ "association_ortholog",
301
+ "marker_symbols_withdrawn",
302
+ "disease_matched_phenotypes",
303
+ "model_matched_phenotypes",
304
+ "disease_model_avg_raw",
305
+ "disease_model_avg_norm",
306
+ "disease_model_max_raw",
307
+ "disease_model_max_norm",
308
+ "search_qf",
309
+ "human_curated_gene",
310
+ "impc_model_with_curated_gene",
311
+ "mgi_model_with_curated_gene",
312
+ "impc_model_with_computed_association",
313
+ "mgi_model_with_computed_association"
314
+ ],
315
+ "statistical-result": [
316
+ "additional_information",
317
+ "allele_accession_id",
318
+ "allele_name",
319
+ "allele_symbol",
320
+ "anatomy_term_id",
321
+ "anatomy_term_name",
322
+ "batch_significant",
323
+ "blups_test",
324
+ "categorical_effect_size",
325
+ "categorical_p_value",
326
+ "categories",
327
+ "classification_tag",
328
+ "colony_id",
329
+ "control_biological_model_id",
330
+ "control_selection_method",
331
+ "data_frame",
332
+ "data_type",
333
+ "db_id",
334
+ "dependent_variable",
335
+ "doc_id",
336
+ "effect_size",
337
+ "external_db_id",
338
+ "female_control_count",
339
+ "female_control_mean",
340
+ "female_effect_size",
341
+ "female_effect_size_low_normal_vs_high",
342
+ "female_effect_size_low_vs_normal_high",
343
+ "female_intermediate_mp_term_id",
344
+ "female_intermediate_mp_term_name",
345
+ "female_ko_effect_p_value",
346
+ "female_ko_effect_stderr_estimate",
347
+ "female_ko_parameter_estimate",
348
+ "female_mp_term_id",
349
+ "female_mp_term_name",
350
+ "female_mutant_count",
351
+ "female_mutant_mean",
352
+ "female_percentage_change",
353
+ "female_pvalue_low_normal_vs_high",
354
+ "female_pvalue_low_vs_normal_high",
355
+ "female_top_level_mp_term_id",
356
+ "female_top_level_mp_term_name",
357
+ "genetic_background",
358
+ "genotype_effect_p_value",
359
+ "genotype_effect_parameter_estimate",
360
+ "genotype_effect_size_low_normal_vs_high",
361
+ "genotype_effect_size_low_vs_normal_high",
362
+ "genotype_effect_stderr_estimate",
363
+ "genotype_pvalue_low_normal_vs_high",
364
+ "genotype_pvalue_low_vs_normal_high",
365
+ "group_1_genotype",
366
+ "group_1_residuals_normality_test",
367
+ "group_2_genotype",
368
+ "group_2_residuals_normality_test",
369
+ "id",
370
+ "interaction_effect_p_value",
371
+ "interaction_significant",
372
+ "intercept_estimate",
373
+ "intercept_estimate_stderr_estimate",
374
+ "intermediate_anatomy_term_id",
375
+ "intermediate_anatomy_term_name",
376
+ "intermediate_mp_term_id",
377
+ "intermediate_mp_term_name",
378
+ "life_stage_acc",
379
+ "life_stage_name",
380
+ "male_control_count",
381
+ "male_control_mean",
382
+ "male_effect_size",
383
+ "male_effect_size_low_normal_vs_high",
384
+ "male_effect_size_low_vs_normal_high",
385
+ "male_intermediate_mp_term_id",
386
+ "male_intermediate_mp_term_name",
387
+ "male_ko_effect_p_value",
388
+ "male_ko_effect_stderr_estimate",
389
+ "male_ko_parameter_estimate",
390
+ "male_mp_term_id",
391
+ "male_mp_term_name",
392
+ "male_mutant_count",
393
+ "male_mutant_mean",
394
+ "male_percentage_change",
395
+ "male_pvalue_low_normal_vs_high",
396
+ "male_pvalue_low_vs_normal_high",
397
+ "male_top_level_mp_term_id",
398
+ "male_top_level_mp_term_name",
399
+ "marker_accession_id",
400
+ "marker_symbol",
401
+ "metadata",
402
+ "metadata_group",
403
+ "mp_term_id",
404
+ "mp_term_id_options",
405
+ "mp_term_name",
406
+ "mp_term_name_options",
407
+ "mutant_biological_model_id",
408
+ "null_test_p_value",
409
+ "organisation_id",
410
+ "p_value",
411
+ "parameter_id",
412
+ "parameter_name",
413
+ "parameter_stable_id",
414
+ "parameter_stable_key",
415
+ "phenotype_sex",
416
+ "phenotyping_center",
417
+ "phenotyping_center_id",
418
+ "pipeline_id",
419
+ "pipeline_name",
420
+ "pipeline_stable_id",
421
+ "pipeline_stable_key",
422
+ "procedure_id",
423
+ "procedure_name",
424
+ "procedure_stable_id",
425
+ "procedure_stable_key",
426
+ "production_center",
427
+ "project_id",
428
+ "project_name",
429
+ "raw_output",
430
+ "resource_fullname",
431
+ "resource_id",
432
+ "resource_name",
433
+ "rotated_residuals_test",
434
+ "sex",
435
+ "sex_effect_p_value",
436
+ "sex_effect_parameter_estimate",
437
+ "sex_effect_stderr_estimate",
438
+ "significant",
439
+ "soft_windowing_bandwidth",
440
+ "soft_windowing_doe_note",
441
+ "soft_windowing_min_obs_required",
442
+ "soft_windowing_number_of_doe",
443
+ "soft_windowing_peaks",
444
+ "soft_windowing_shape",
445
+ "soft_windowing_threshold",
446
+ "soft_windowing_total_obs_or_weight",
447
+ "statistical_method",
448
+ "status",
449
+ "strain_accession_id",
450
+ "strain_name",
451
+ "text",
452
+ "top_level_anatomy_term_id",
453
+ "top_level_anatomy_term_name",
454
+ "top_level_mp_term_id",
455
+ "top_level_mp_term_name",
456
+ "variance_significant",
457
+ "weight_effect_p_value",
458
+ "weight_effect_parameter_estimate",
459
+ "weight_effect_stderr_estimate",
460
+ "workflow",
461
+ "zygosity"
462
+ ]
463
+ }
{impc_api-1.0.5 → impc_api-1.0.7}/impc_api/utils/validators.py RENAMED
@@ -93,7 +93,7 @@ class CoreParamsValidator(BaseModel):
93
93
  # Validate each field in params
94
94
  if invalid_core is not True:
95
95
  for fl in field_list:
96
- if fl not in jv.valid_fields(core):
96
+ if fl.strip() not in jv.valid_fields(core):
97
97
  warnings.warn(
98
98
  message=f"""Unexpected field name: "{fl}". Check the spelling of fields.\nTo see expected fields check the documentation at: https://www.ebi.ac.uk/mi/impc/solrdoc/""",
99
99
  category=InvalidFieldWarning,
impc_api-1.0.5/README.md → impc_api-1.0.7/impc_api.egg-info/PKG-INFO RENAMED
@@ -1,25 +1,43 @@
1
+ Metadata-Version: 2.4
2
+ Name: impc_api
3
+ Version: 1.0.7
4
+ Summary: A package to facilitate making API requests to the IMPC Solr API
5
+ Author: MPI2, Marina Kan, Diego Pava
6
+ Project-URL: Homepage, https://github.com/mpi2/impc-api
7
+ Requires-Python: >=3.10
8
+ Description-Content-Type: text/markdown
9
+ License-File: LICENSE
10
+ Requires-Dist: ipykernel>=6.29.5
11
+ Requires-Dist: notebook>=7.2.2
12
+ Requires-Dist: pandas>=2.2.0
13
+ Requires-Dist: requests>=2.31.0
14
+ Requires-Dist: tqdm>=4.66.4
15
+ Requires-Dist: pydantic>=2.9
16
+ Provides-Extra: dev
17
+ Requires-Dist: pytest>=8.2.2; extra == "dev"
18
+ Dynamic: license-file
19
+
1
20
  # IMPC_API
2
21
 
3
- `impc_api` is a Python package.
4
-
5
- The functions in this package are intended for use in a Jupyter Notebook.
22
+ `impc_api` is a Python package which provides several helper functions that wrap around the IMPC SOLR API. The functions in this package are intended for use in a Jupyter Notebook.
6
23
 
7
24
  ## Installation Instructions
8
25
 
26
+ 0. Ensure that Python is installed on your system. The minimum required version is 3.10.
27
+
9
28
  1. **Create a virtual environment (optional but recommended)**:
10
- On Mac:
29
+ On Mac or Linux:
11
30
  ```bash
12
31
  python3 -m venv .venv
13
32
  source .venv/bin/activate
14
33
  ```
15
34
 
16
35
  2. **Install the package**: `pip install impc_api`
17
- 3. **Install Jupyter**: `pip install jupyter`
18
- 4. **Run the Jupyter Notebook**: `jupyter notebook`
36
+ 3. **Run the Jupyter Notebook**: `jupyter notebook`
19
37
 
20
38
  After executing the command, the Jupyter interface should open in your browser. If it does not, follow the instructions provided in the terminal.
21
39
 
22
- 5. **Try it out**:
40
+ 4. **Try it out**:
23
41
 
24
42
  Create a [Jupyter Notebook](https://jupyter-notebook.readthedocs.io/en/latest/) and try some of the examples below:
25
43
 
@@ -80,7 +98,7 @@ num_found, df = solr_request(
80
98
  validate=True
81
99
  )
82
100
 
83
- > InvalidCoreWarning: Invalid core: "genotype-phenotyp", select from the available cores:
101
+ > InvalidCoreWarning: Invalid core: "invalid_core", select from the available cores:
84
102
  > dict_keys(['experiment', 'genotype-phenotype', 'impc_images', 'phenodigm', 'statistical-result'])
85
103
  ```
86
104
 
@@ -100,13 +118,33 @@ num_found, df = solr_request(
100
118
  > To see expected fields check the documentation at: https://www.ebi.ac.uk/mi/impc/solrdoc/
101
119
  ```
102
120
 
121
+ ## c. URL only
122
+
123
+ Users might want help producing the URL to fetch the data without the need of a DataFrame. Use the flag `url_only=True` to print or return the URL for your query.
124
+
125
+ ```python
126
+ url, _ = solr_request(
127
+ core='genotype-phenotype',
128
+ params={
129
+ 'q': '*:*',
130
+ 'rows': 10,
131
+ 'fl': 'marker_symbol,allele_symbol'
132
+ },
133
+ url_only=True
134
+ )
135
+ > "https://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select?q=%2A%3A%2A&rows=10&fl=marker_symbol%2Callele_symbol"
136
+
137
+ print(url)
138
+ > "https://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select?q=%2A%3A%2A&rows=10&fl=marker_symbol%2Callele_symbol"
139
+ ```
140
+
103
141
  # 2. Batch Solr Request
104
142
 
105
143
  `batch_solr_request` is available for large queries. This solves issues where a request is too large to fit into memory or where it puts a lot of strain on the API.
106
144
 
107
145
  Use `batch_solr_request` for:
108
146
 
109
- - Large queries (>1,000,000)
147
+ - Large queries (>100,000 rows)
110
148
  - Querying multiple items in a list
111
149
  - Downloading data in `json` or `csv` format.
112
150
 
{impc_api-1.0.5 → impc_api-1.0.7}/impc_api.egg-info/SOURCES.txt RENAMED
@@ -2,7 +2,6 @@ LICENSE
2
2
  MANIFEST.in
3
3
  README.md
4
4
  pyproject.toml
5
- setup.py
6
5
  impc_api/__init__.py
7
6
  impc_api/batch_solr_request.py
8
7
  impc_api/solr_request.py
{impc_api-1.0.5 → impc_api-1.0.7}/impc_api.egg-info/requires.txt RENAMED
@@ -1,3 +1,5 @@
1
+ ipykernel>=6.29.5
2
+ notebook>=7.2.2
1
3
  pandas>=2.2.0
2
4
  requests>=2.31.0
3
5
  tqdm>=4.66.4
{impc_api-1.0.5 → impc_api-1.0.7}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
4
4
 
5
5
  [project]
6
6
  name = "impc_api"
7
- version = "1.0.5"
7
+ version = "1.0.7"
8
8
  description = "A package to facilitate making API requests to the IMPC Solr API"
9
9
  authors = [
10
10
  { name = "MPI2" },
@@ -12,6 +12,8 @@ authors = [
12
12
  { name = "Diego Pava" }
13
13
  ]
14
14
  dependencies = [
15
+ "ipykernel>=6.29.5",
16
+ "notebook>=7.2.2",
15
17
  "pandas>=2.2.0",
16
18
  "requests>=2.31.0",
17
19
  "tqdm>=4.66.4",
@@ -30,5 +32,5 @@ dev = [
30
32
  include = ["impc_api", "impc_api.*"]
31
33
 
32
34
  [project.urls]
33
- "Homepage" = "https://github.com/mpi2/impc-data-api-workshop"
35
+ "Homepage" = "https://github.com/mpi2/impc-api"
34
36
 
{impc_api-1.0.5 → impc_api-1.0.7}/tests/test_solr_request.py RENAMED
@@ -4,6 +4,7 @@ from impc_api.utils.warnings import InvalidCoreWarning, InvalidFieldWarning
4
4
  from solr_request import solr_request, _process_faceting
5
5
  from .test_helpers import check_url_status_code_and_params
6
6
 
7
+
7
8
  class TestSolrRequest:
8
9
  """Test class for the Solr Request function
9
10
 
@@ -316,3 +317,93 @@ class TestSolrRequest:
316
317
  params={"q": "*:*", "fl": "invalid_field,another_invalid_field"},
317
318
  validate=True,
318
319
  )
320
+
321
+ @pytest.mark.parametrize(
322
+ "mock_response", [_validation_response()], indirect=["mock_response"]
323
+ )
324
+ def test_solr_request_fields_validation_spacing(self, common_params, mock_response):
325
+ try:
326
+ _ = solr_request(
327
+ core="experiment",
328
+ params={
329
+ **common_params,
330
+ "fl": "experiment_id, parameter_stable_id , parameter_name",
331
+ },
332
+ validate=True,
333
+ )
334
+ except InvalidFieldWarning:
335
+ pytest.fail("InvalidFieldWarning raised when it shouldn't have been")
336
+
337
+
338
+ @pytest.fixture
339
+ def test_url(self):
340
+ return "http://test.url/url_only"
341
+
342
+ @pytest.fixture
343
+ def mock_response_url(self, request, test_url):
344
+ """
345
+ Fixture to mock the response from the Solr API
346
+
347
+ Args:
348
+ request (FixtureRequest): Request object provided by pytest containing the parameterized data
349
+
350
+ Yields:
351
+ MagicMock: A mock object "representing" the requests.get function used in solr_request.py.
352
+ Its returned value is configured according to the parameterized data.
353
+ """
354
+ with patch("solr_request.requests.get") as mock_get:
355
+ mock_response = mock_get.return_value
356
+ mock_response.status_code = request.param.get("status_code")
357
+ mock_response.request.url = test_url
358
+ yield mock_get
359
+
360
+ @pytest.mark.parametrize(
361
+ "mock_response_url",
362
+ [
363
+ (
364
+ {
365
+ "status_code": 200,
366
+ }
367
+ )
368
+ ],
369
+ indirect=True
370
+ )
371
+ def test_solr_request_url_only_success(self, core, common_params, capsys, mock_response_url, test_url):
372
+ # Assert when the params are status_code 200, the URL is printed and returned
373
+ url, _ = solr_request(
374
+ core=core,
375
+ params=common_params,
376
+ url_only=True
377
+ )
378
+ # Assert url is returned
379
+ assert url == test_url, f"Expected URL {test_url}, got {url}"
380
+ captured = capsys.readouterr()
381
+
382
+ # Assert test url is printed to console
383
+ assert test_url in captured.out, "Expected test URL to be printed on console output"
384
+
385
+ @pytest.mark.parametrize(
386
+ "mock_response_url",
387
+ [
388
+ (
389
+ {
390
+ "status_code": 404,
391
+ }
392
+ )
393
+ ],
394
+ indirect=True
395
+ )
396
+ def test_solr_request_url_only_fail(self, core, common_params, capsys, mock_response_url, test_url):
397
+ # Assert that when status code is not 200, it returns None and the error message
398
+ url, _ = solr_request(
399
+ core=core,
400
+ params=common_params,
401
+ url_only=True
402
+ )
403
+ # Assert url is returned
404
+ assert url is None, "Expected no URL to be returned"
405
+ captured = capsys.readouterr()
406
+
407
+ # Assert test url is printed to console
408
+ assert "Error" in captured.out, "Expected error message to be printed in console output"
409
+
impc_api-1.0.5/impc_api/utils/core_fields.json DELETED
@@ -1,15 +0,0 @@
1
- {
2
- "experiment": [
3
- "id", "observation_id", "specimen_id", "phenotyping_center_id", "phenotyping_center", "production_center_id", "production_center", "specimen_project_id", "specimen_project_name", "gene_accession_id", "gene_symbol", "allele_accession_id", "allele_symbol", "zygosity", "sex", "biological_model_id", "biological_sample_id", "biological_sample_group", "strain_accession_id", "strain_name", "genetic_background", "allelic_composition", "colony_id", "litter_id", "date_of_birth", "external_sample_id", "life_stage_name", "life_stage_acc", "datasource_id", "datasource_name", "project_id", "project_name", "pipeline_id", "pipeline_name", "pipeline_stable_id", "procedure_id", "procedure_name", "procedure_stable_id", "procedure_group", "parameter_id", "parameter_name", "parameter_stable_id", "procedure_sequence_id", "experiment_id", "observation_type", "data_type", "experiment_source_id", "date_of_experiment", "weight_parameter_stable_id", "weight_date", "weight_days_old", "weight", "data_point", "order_index", "dimension", "time_point", "discrete_point", "category", "raw_category", "metadata", "metadata_group", "anatomy_id", "anatomy_term", "anatomy_id_term", "anatomy_term_synonym", "top_level_anatomy_id", "top_level_anatomy_term", "top_level_anatomy_term_synonym", "selected_top_level_anatomy_id", "selected_top_level_anatomy_term", "selected_top_level_anatomy_term_synonym", "intermediate_anatomy_id", "intermediate_anatomy_term", "intermediate_anatomy_term_synonym", "parent_anatomy_id", "parent_anatomy_term", "parent_anatomy_term_synonym", "child_anatomy_id", "child_anatomy_term", "child_anatomy_term_synonym", "download_file_path", "image_link", "file_type", "increment_value", "parameter_association_stable_id", "parameter_association_sequence_id", "parameter_association_dim_id", "parameter_association_name", "parameter_association_value", "developmental_stage_acc", "developmental_stage_name", "text_value", "sub_term_id", "sub_term_name", "sub_term_description", "age_in_days", "age_in_weeks"
4
- ],
5
- "genotype-phenotype": [
6
- "doc_id", "ontology_db_id", "assertion_type", "assertion_type_id", "mpath_term_id", "mpath_term_name", "anatomy_term_id", "anatomy_term_name", "intermediate_anatomy_term_id", "intermediate_anatomy_term_name", "top_level_anatomy_term_id", "top_level_anatomy_term_name", "mp_term_id", "mp_term_name", "alt_mp_term_id", "top_level_mp_term_id", "top_level_mp_term_name", "intermediate_mp_term_id", "intermediate_mp_term_name", "marker_symbol", "marker_accession_id", "colony_id", "allele_name", "allele_symbol", "allele_accession_id", "strain_name", "strain_accession_id", "phenotyping_center", "project_external_id", "project_name", "project_fullname", "resource_name", "resource_fullname", "sex", "zygosity", "pipeline_name", "pipeline_stable_id", "pipeline_stable_key", "procedure_name", "procedure_stable_id", "procedure_stable_key", "parameter_name", "parameter_stable_id", "parameter_stable_key", "statistical_method", "percentage_change", "p_value", "effect_size", "external_id", "life_stage_acc", "life_stage_name"
7
- ],
8
- "impc_images": [
9
- "id", "observation_id", "specimen_id", "phenotyping_center_id", "phenotyping_center", "production_center_id", "production_center", "specimen_project_id", "specimen_project_name", "gene_accession_id", "gene_symbol", "allele_accession_id", "allele_symbol", "zygosity", "sex", "biological_model_id", "biological_sample_id", "biological_sample_group", "strain_accession_id", "strain_name", "genetic_background", "allelic_composition", "colony_id", "litter_id", "date_of_birth", "external_sample_id", "life_stage_name", "life_stage_acc", "datasource_id", "datasource_name", "project_id", "project_name", "pipeline_id", "pipeline_name", "pipeline_stable_id", "procedure_id", "procedure_name", "procedure_stable_id", "procedure_group", "parameter_id", "parameter_name", "parameter_stable_id", "procedure_sequence_id", "experiment_id", "observation_type", "data_type", "experiment_source_id", "date_of_experiment", "weight_parameter_stable_id", "weight_date", "weight_days_old", "weight", "data_point", "order_index", "dimension", "time_point", "discrete_point", "category", "raw_category", "metadata", "metadata_group", "mp_id", "mp_term", "top_level_mp_id", "top_level_mp_term", "intermediate_mp_id", "intermediate_mp_term", "anatomy_id", "anatomy_term", "anatomy_id_term", "anatomy_term_synonym", "top_level_anatomy_id", "top_level_anatomy_term", "top_level_anatomy_term_synonym", "selected_top_level_anatomy_id", "selected_top_level_anatomy_term", "selected_top_level_anatomy_term_synonym", "intermediate_anatomy_id", "intermediate_anatomy_term", "intermediate_anatomy_term_synonym", "parent_anatomy_id", "parent_anatomy_term", "parent_anatomy_term_synonym", "child_anatomy_id", "child_anatomy_term", "child_anatomy_term_synonym", "download_file_path", "image_link", "file_type", "parameter_association_stable_id", "parameter_association_sequence_id", "parameter_association_dim_id", "parameter_association_name", "parameter_association_value", "developmental_stage_acc", "developmental_stage_name", "text_value", "sub_term_id", "sub_term_name", "sub_term_description", "sequence_id", "age_in_days", "age_in_weeks", "download_url", "jpeg_url", "thumbnail_url", "omero_id"
10
- ],
11
- "phenodigm": [
12
- "type", "disease_id", "disease_source", "disease_term", "disease_alts", "disease_locus", "disease_classes", "disease_phenotypes", "gene_id", "gene_symbol", "gene_symbols_withdrawn", "gene_locus", "hgnc_gene_id", "hgnc_gene_symbol", "hgnc_gene_symbols_withdrawn", "hgnc_gene_locus", "mouse_model", "impc_model", "model_id", "model_source", "model_description", "model_genetic_background", "marker_id", "marker_symbol", "marker_locus", "marker_num_models", "model_phenotypes", "ontology", "phenotype_id", "phenotype_term", "phenotype_synonym", "hp_id", "hp_term", "mp_id", "mp_term", "association_curated", "association_ortholog", "marker_symbols_withdrawn", "disease_matched_phenotypes", "model_matched_phenotypes", "disease_model_avg_raw", "disease_model_avg_norm", "disease_model_max_raw", "disease_model_max_norm", "search_qf", "human_curated_gene", "impc_model_with_curated_gene", "mgi_model_with_curated_gene", "impc_model_with_computed_association", "mgi_model_with_computed_association"
13
- ],
14
- "statistical-result": ["doc_id", "db_id", "data_type", "anatomy_term_id", "anatomy_term_name", "intermediate_anatomy_term_id", "intermediate_anatomy_term_name", "top_level_anatomy_term_id", "top_level_anatomy_term_name", "mp_term_id_options", "mp_term_name_options", "mp_term_id", "mp_term_name", "top_level_mp_term_id", "top_level_mp_term_name", "intermediate_mp_term_id", "intermediate_mp_term_name", "male_mp_term_id", "male_mp_term_name", "male_top_level_mp_term_id", "male_top_level_mp_term_name", "male_intermediate_mp_term_id", "male_intermediate_mp_term_name", "female_mp_term_id", "female_mp_term_name", "female_top_level_mp_term_id", "female_top_level_mp_term_name", "female_intermediate_mp_term_id", "female_intermediate_mp_term_name", "resource_name", "resource_fullname", "resource_id", "project_name", "phenotyping_center", "pipeline_stable_id", "pipeline_stable_key", "pipeline_name", "pipeline_id", "procedure_stable_id", "procedure_stable_key", "procedure_name", "procedure_id", "parameter_stable_id", "parameter_stable_key", "parameter_name", "parameter_id", "colony_id", "marker_symbol", "marker_accession_id", "allele_symbol", "allele_name", "allele_accession_id", "strain_name", "strain_accession_id", "sex", "zygosity", "control_selection_method", "dependent_variable", "metadata_group", "data_frame", "genetic_background", "production_center", "external_db_id", "id", "organisation_id", "phenotyping_center_id", "project_id", "male_control_mean", "male_mutant_mean", "female_control_mean", "female_mutant_mean", "genotype_p_value_low_vs_normal_high", "genotype_p_value_low_normal_vs_high", "genotype_effect_size_low_vs_normal_high", "genotype_effect_size_low_normal_vs_high", "female_p_value_low_vs_normal_high", "female_p_value_low_normal_vs_high", "female_effect_size_low_vs_normal_high", "female_effect_size_low_normal_vs_high", "male_p_value_low_vs_normal_high", "male_p_value_low_normal_vs_high", "male_effect_size_low_vs_normal_high", "male_effect_size_low_normal_vs_high", "categories", "categorical_p_value", "categorical_effect_size", "batch_significant", "variance_significant", "null_test_p_value", "genotype_effect_p_value", "genotype_effect_stderr_estimate", "genotype_effect_parameter_estimate", "male_percentage_change", "female_percentage_change", "sex_effect_p_value", "sex_effect_stderr_estimate", "sex_effect_parameter_estimate", "weight_effect_p_value", "weight_effect_stderr_estimate", "weight_effect_parameter_estimate", "group1_genotype", "group1_residuals_normality_test", "group2_genotype", "group2_residuals_normality_test", "blups_test", "rotated_residuals_test", "intercept_estimate", "intercept_estimate_stderr_estimate", "interaction_significant", "interaction_effect_p_value", "female_ko_effect_p_value", "female_ko_effect_stderr_estimate", "female_ko_parameter_estimate", "female_effect_size", "male_ko_effect_p_value", "male_ko_effect_stderr_estimate", "male_ko_parameter_estimate", "male_effect_size", "classification_tag", "phenotype_sex", "life_stage_acc", "life_stage_name", "significant", "soft_windowing_bandwidth", "soft_windowing_shape", "soft_windowing_peaks", "soft_windowing_min_obs_required", "soft_windowing_total_obs_or_weight", "soft_windowing_threshold", "soft_windowing_number_of_doe", "soft_windowing_doe_note", "metadata"]
15
- }
impc_api-1.0.5/setup.py DELETED
@@ -1,39 +0,0 @@
1
- from setuptools import setup, find_packages
2
-
3
-
4
- # Read the README file for the long description
5
- with open("README.md", "r", encoding="utf-8") as fh:
6
- long_description = fh.read()
7
-
8
- setup(
9
- name='impc_api',
10
- version='1.0.5',
11
- description='A package to facilitate making API request to the IMPC Solr API',
12
- author='MPI2, Marina Kan, Diego Pava',
13
- url='https://github.com/mpi2/impc-data-api-workshop',
14
- packages=find_packages(include=["impc_api", "impc_api.*"]),
15
- include_package_data=True,
16
- install_requires=[
17
- 'pandas>=2.2.0',
18
- 'requests>=2.31.0',
19
- 'tqdm>=4.66.4',
20
- 'pydantic>=2.9'
21
- ],
22
-
23
- extras_require={
24
- 'dev': [
25
- 'pytest>=8.2.2',
26
- ],
27
- },
28
- long_description=long_description,
29
- long_description_content_type='text/markdown',
30
- # classifiers=[
31
- # 'Development Status :: 3 - Alpha',
32
- # 'Intended Audience :: IMPC data users',
33
- # 'License :: OSI Approved :: MIT License',
34
- # 'Programming Language :: Python :: 3.10',
35
- # 'Operating System :: MacOS',
36
- # 'Operating System :: Microsoft :: Windows'
37
- # ],
38
- python_requires='>=3.10'
39
- )
{impc_api-1.0.5 → impc_api-1.0.7}/LICENSE RENAMED
File without changes
{impc_api-1.0.5 → impc_api-1.0.7}/MANIFEST.in RENAMED
File without changes
{impc_api-1.0.5 → impc_api-1.0.7}/impc_api/__init__.py RENAMED
File without changes
{impc_api-1.0.5 → impc_api-1.0.7}/setup.cfg RENAMED
File without changes
{impc_api-1.0.5 → impc_api-1.0.7}/tests/test_helpers.py RENAMED
File without changes