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  1. {
  2. "cells": [
  3. {
  4. "cell_type": "code",
  5. "execution_count": 1,
  6. "metadata": {},
  7. "outputs": [
  8. {
  9. "name": "stderr",
  10. "output_type": "stream",
  11. "text": [
  12. "/home/epassaro/miniconda3/envs/carsus/lib/python3.6/site-packages/tqdm/autonotebook/__init__.py:14: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
  13. " \" (e.g. in jupyter console)\", TqdmExperimentalWarning)\n"
  14. ]
  15. }
  16. ],
  17. "source": [
  18. "from sqlalchemy import create_engine, inspect\n",
  19. "from sqlalchemy.orm import Session\n",
  20. "from carsus.model import Level, DataSource # I don't know so much about the Carsus data model"
  21. ]
  22. },
  23. {
  24. "cell_type": "code",
  25. "execution_count": 2,
  26. "metadata": {},
  27. "outputs": [],
  28. "source": [
  29. "engine = create_engine('sqlite:////home/epassaro/carsus-db/test_databases/test.db')\n",
  30. "connection = engine.connect()\n",
  31. "\n",
  32. "trans = connection.begin()\n",
  33. "session = Session(bind=connection)"
  34. ]
  35. },
  36. {
  37. "cell_type": "code",
  38. "execution_count": 3,
  39. "metadata": {},
  40. "outputs": [
  41. {
  42. "name": "stdout",
  43. "output_type": "stream",
  44. "text": [
  45. "\n",
  46. "Table: atom\n",
  47. "Column: atomic_number\n",
  48. "Column: symbol\n",
  49. "Column: name\n",
  50. "Column: group\n",
  51. "Column: period\n",
  52. "\n",
  53. "Table: atom_quantity\n",
  54. "Column: _value\n",
  55. "Column: uncert\n",
  56. "Column: method\n",
  57. "Column: reference\n",
  58. "Column: atom_qty_id\n",
  59. "Column: atomic_number\n",
  60. "Column: type\n",
  61. "Column: data_source_id\n",
  62. "\n",
  63. "Table: data_source\n",
  64. "Column: data_source_id\n",
  65. "Column: short_name\n",
  66. "Column: name\n",
  67. "Column: description\n",
  68. "Column: data_source_quality\n",
  69. "\n",
  70. "Table: e_collision\n",
  71. "Column: e_col_id\n",
  72. "Column: bt92_ttype\n",
  73. "Column: bt92_cups\n",
  74. "\n",
  75. "Table: e_collision_qty\n",
  76. "Column: _value\n",
  77. "Column: uncert\n",
  78. "Column: method\n",
  79. "Column: reference\n",
  80. "Column: e_col_qty_id\n",
  81. "Column: e_col_id\n",
  82. "Column: type\n",
  83. "Column: data_source_id\n",
  84. "\n",
  85. "Table: e_collision_temp_strength\n",
  86. "Column: e_col_temp_strength_id\n",
  87. "Column: temp\n",
  88. "Column: strength\n",
  89. "Column: e_col_id\n",
  90. "\n",
  91. "Table: ion\n",
  92. "Column: atomic_number\n",
  93. "Column: ion_charge\n",
  94. "\n",
  95. "Table: ion_quantity\n",
  96. "Column: _value\n",
  97. "Column: uncert\n",
  98. "Column: method\n",
  99. "Column: reference\n",
  100. "Column: ion_qty_id\n",
  101. "Column: atomic_number\n",
  102. "Column: ion_charge\n",
  103. "Column: type\n",
  104. "Column: data_source_id\n",
  105. "\n",
  106. "Table: level\n",
  107. "Column: level_id\n",
  108. "Column: atomic_number\n",
  109. "Column: ion_charge\n",
  110. "Column: data_source_id\n",
  111. "Column: level_index\n",
  112. "Column: configuration\n",
  113. "Column: L\n",
  114. "Column: J\n",
  115. "Column: spin_multiplicity\n",
  116. "Column: parity\n",
  117. "Column: term\n",
  118. "\n",
  119. "Table: level_quantity\n",
  120. "Column: _value\n",
  121. "Column: uncert\n",
  122. "Column: method\n",
  123. "Column: reference\n",
  124. "Column: level_qty_id\n",
  125. "Column: level_id\n",
  126. "Column: type\n",
  127. "Column: data_source_id\n",
  128. "\n",
  129. "Table: line\n",
  130. "Column: line_id\n",
  131. "\n",
  132. "Table: line_quantity\n",
  133. "Column: _value\n",
  134. "Column: uncert\n",
  135. "Column: method\n",
  136. "Column: reference\n",
  137. "Column: line_qty_id\n",
  138. "Column: line_id\n",
  139. "Column: type\n",
  140. "Column: data_source_id\n",
  141. "Column: medium\n",
  142. "\n",
  143. "Table: temperature\n",
  144. "Column: id\n",
  145. "Column: value\n",
  146. "\n",
  147. "Table: transition\n",
  148. "Column: transition_id\n",
  149. "Column: type\n",
  150. "Column: lower_level_id\n",
  151. "Column: upper_level_id\n",
  152. "Column: data_source_id\n",
  153. "\n",
  154. "Table: zeta\n",
  155. "Column: id\n",
  156. "Column: atomic_number\n",
  157. "Column: ion_charge\n",
  158. "Column: zeta\n",
  159. "Column: temp_id\n",
  160. "Column: data_source_id\n"
  161. ]
  162. }
  163. ],
  164. "source": [
  165. "# Inspect the database\n",
  166. "inspector = inspect(engine)\n",
  167. "for table_name in inspector.get_table_names():\n",
  168. " print('\\nTable: %s' % table_name)\n",
  169. " for column in inspector.get_columns(table_name):\n",
  170. " print(\"Column: %s\" % column['name'])"
  171. ]
  172. },
  173. {
  174. "cell_type": "code",
  175. "execution_count": 4,
  176. "metadata": {},
  177. "outputs": [],
  178. "source": [
  179. "# Trying with nist-asd data source\n",
  180. "nist_ds = session.query(DataSource).filter(DataSource.short_name == 'nist-asd').one()"
  181. ]
  182. },
  183. {
  184. "cell_type": "code",
  185. "execution_count": 5,
  186. "metadata": {},
  187. "outputs": [],
  188. "source": [
  189. "subq = (\n",
  190. " session.\n",
  191. " query(Level.level_id).\n",
  192. " filter(Level.atomic_number.in_([4])).\n",
  193. " filter(Level.data_source_id == nist_ds.data_source_id)\n",
  194. " ).subquery()"
  195. ]
  196. },
  197. {
  198. "cell_type": "code",
  199. "execution_count": 6,
  200. "metadata": {},
  201. "outputs": [],
  202. "source": [
  203. "levels_data_q = (\n",
  204. " session.\n",
  205. " query(\n",
  206. " Level.level_id.label('level_id'),\n",
  207. " Level.atomic_number.label('atomic_number'),\n",
  208. " Level.ion_charge.label('ion_number'),\n",
  209. " Level.g.label('g'))\n",
  210. " ).join(subq,\n",
  211. " Level.level_id == subq.c.level_id\n",
  212. " )"
  213. ]
  214. },
  215. {
  216. "cell_type": "code",
  217. "execution_count": 7,
  218. "metadata": {},
  219. "outputs": [
  220. {
  221. "data": {
  222. "text/plain": [
  223. "[(7, 4, 0, 1), (8, 4, 1, 2), (9, 4, 2, 1), (10, 4, 3, 2)]"
  224. ]
  225. },
  226. "execution_count": 7,
  227. "metadata": {},
  228. "output_type": "execute_result"
  229. }
  230. ],
  231. "source": [
  232. "levels_data_q.all() # Seems ok"
  233. ]
  234. },
  235. {
  236. "cell_type": "code",
  237. "execution_count": 8,
  238. "metadata": {},
  239. "outputs": [],
  240. "source": [
  241. "# Trying with chianti_v8.0.2 data source (the one used in the fixtures)\n",
  242. "ch_ds = session.query(DataSource).filter(DataSource.short_name == 'chianti_v8.0.2').one()"
  243. ]
  244. },
  245. {
  246. "cell_type": "code",
  247. "execution_count": 9,
  248. "metadata": {},
  249. "outputs": [],
  250. "source": [
  251. "subq = (\n",
  252. " session.\n",
  253. " query(Level.level_id).\n",
  254. " filter(Level.atomic_number.in_([4])).\n",
  255. " filter(Level.data_source_id == ch_ds.data_source_id)\n",
  256. " ).subquery()"
  257. ]
  258. },
  259. {
  260. "cell_type": "code",
  261. "execution_count": 10,
  262. "metadata": {},
  263. "outputs": [],
  264. "source": [
  265. "levels_data_q = (\n",
  266. " session.\n",
  267. " query(\n",
  268. " Level.level_id.label('level_id'),\n",
  269. " Level.atomic_number.label('atomic_number'),\n",
  270. " Level.ion_charge.label('ion_number'),\n",
  271. " Level.g.label('g'))\n",
  272. " ).join(subq,\n",
  273. " Level.level_id == subq.c.level_id\n",
  274. " )"
  275. ]
  276. },
  277. {
  278. "cell_type": "code",
  279. "execution_count": 11,
  280. "metadata": {},
  281. "outputs": [
  282. {
  283. "data": {
  284. "text/plain": [
  285. "[]"
  286. ]
  287. },
  288. "execution_count": 11,
  289. "metadata": {},
  290. "output_type": "execute_result"
  291. }
  292. ],
  293. "source": [
  294. "levels_data_q.all()"
  295. ]
  296. },
  297. {
  298. "cell_type": "code",
  299. "execution_count": 12,
  300. "metadata": {},
  301. "outputs": [],
  302. "source": [
  303. "# subq for data source chianti_v8.0.2 gives an empty list -> this is the problem!"
  304. ]
  305. }
  306. ],
  307. "metadata": {
  308. "kernelspec": {
  309. "display_name": "Python 3",
  310. "language": "python",
  311. "name": "python3"
  312. },
  313. "language_info": {
  314. "codemirror_mode": {
  315. "name": "ipython",
  316. "version": 3
  317. },
  318. "file_extension": ".py",
  319. "mimetype": "text/x-python",
  320. "name": "python",
  321. "nbconvert_exporter": "python",
  322. "pygments_lexer": "ipython3",
  323. "version": "3.6.7"
  324. },
  325. "widgets": {
  326. "application/vnd.jupyter.widget-state+json": {
  327. "state": {},
  328. "version_major": 2,
  329. "version_minor": 0
  330. }
  331. }
  332. },
  333. "nbformat": 4,
  334. "nbformat_minor": 2
  335. }
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