Révision 4fcefb60
| b/README | ||
|---|---|---|
| 222 | 222 |
password for basic and administrative access. To use this script, |
| 223 | 223 |
simply type the following command line: |
| 224 | 224 |
|
| 225 |
php mylabstocks/src/install_db.phpsh |
|
| 225 |
sudo php mylabstocks/src/install_db.phpsh
|
|
| 226 | 226 |
|
| 227 | 227 |
Congratulations! Your MyLabStocks instance is now available here: |
| 228 | 228 |
http://your_server/labstocks. |
| ... | ... | |
| 249 | 249 |
|
| 250 | 250 |
In the strain section, the form *Search in genotype* filters strains |
| 251 | 251 |
where the fields *locus1*, *locus2*, *locus3*, *locus4*, *locus5*, |
| 252 |
*ADE2*, *HIS3*, *LEU2*, *LYS2*, *MET15*, *TRP1*, *URA3*, *HO_*, |
|
| 252 |
*ADE2*, *HIS3*, *LE U2*, *LYS2*, *MET15*, *TRP1*, *URA3*, *HO_*,
|
|
| 253 | 253 |
*Cytoplasmic_Character* or *extrachromosomal_plasmid* contain the |
| 254 | 254 |
given expression. This filter is case insensitive. |
| 255 | 255 |
|
| ... | ... | |
| 278 | 278 |
integrate it in a robust file backup system using for example a cron |
| 279 | 279 |
that regularly pull the archives (*wget |
| 280 | 280 |
http://.../labstocks/backup.php?FULL_BACK=1*). |
| 281 |
|
|
| 282 |
|
|
| 283 |
Reporting Bugs |
|
| 284 |
-------------- |
|
| 285 |
|
|
| 286 |
If you think you have found a bug and would like to report the |
|
| 287 |
problem, then please ensure you have applied all applicable updates. |
|
| 288 |
Else, send a description of your problem and some screenshot to |
|
| 289 |
florent.chuffart on its ens-lyon.fr email. Thank you for your |
|
| 290 |
contribution. |
|
| b/doc/conf.py | ||
|---|---|---|
| 50 | 50 |
# built documents. |
| 51 | 51 |
# |
| 52 | 52 |
# The short X.Y version. |
| 53 |
version = '0.1.1'
|
|
| 53 |
version = '0.1.2'
|
|
| 54 | 54 |
# The full version, including alpha/beta/rc tags. |
| 55 |
release = '0.1.1'
|
|
| 55 |
release = '0.1.2'
|
|
| 56 | 56 |
|
| 57 | 57 |
# The language for content autogenerated by Sphinx. Refer to documentation |
| 58 | 58 |
# for a list of supported languages. |
| b/doc/index.rst | ||
|---|---|---|
| 187 | 187 |
|
| 188 | 188 |
.. code:: bash |
| 189 | 189 |
|
| 190 |
php mylabstocks/src/install_db.phpsh |
|
| 190 |
sudo php mylabstocks/src/install_db.phpsh
|
|
| 191 | 191 |
.. |
| 192 | 192 |
|
| 193 | 193 |
Congratulations! Your MyLabStocks instance is now available here: http://your_server/labstocks. |
| ... | ... | |
| 212 | 212 |
--------------- |
| 213 | 213 |
|
| 214 | 214 |
In the strain section, the form `Search in genotype` filters strains where the |
| 215 |
fields `locus1`, `locus2`, `locus3`, `locus4`, `locus5`, `ADE2`, `HIS3`, `LEU2`, |
|
| 215 |
fields `locus1`, `locus2`, `locus3`, `locus4`, `locus5`, `ADE2`, `HIS3`, `LE U2`,
|
|
| 216 | 216 |
`LYS2`, `MET15`, `TRP1`, `URA3`, `HO_`, `Cytoplasmic_Character` or |
| 217 | 217 |
`extrachromosomal_plasmid` contain the given expression. This filter is case |
| 218 | 218 |
insensitive. |
| ... | ... | |
| 235 | 235 |
|
| 236 | 236 |
|
| 237 | 237 |
|
| 238 |
Reporting Bugs |
|
| 239 |
-------------- |
|
| 238 | 240 |
|
| 239 |
|
|
| 241 |
If you think you have found a bug and would like to report the problem, then please ensure you have applied all applicable updates. Else, |
|
| 242 |
send a description of your problem and some screenshot to florent.chuffart on its ens-lyon.fr email. Thank you for your contribution. |
|
| 240 | 243 |
|
| 241 | 244 |
|
| 242 | 245 |
|
| b/src/antibodies.php | ||
|---|---|---|
| 223 | 223 |
'maxlen' => 200, |
| 224 | 224 |
'sort' => true |
| 225 | 225 |
); |
| 226 |
$opts['fdd']['storage_minus20freezers'] = array( |
|
| 227 |
'name' => '-20 Freezer', |
|
| 228 |
'select' => 'D', |
|
| 229 |
'maxlen' => 25, |
|
| 230 |
'sort' => true, |
|
| 231 |
'values' => array( |
|
| 232 |
'table' => 'storage_minus20freezers', |
|
| 233 |
'column' => 'name'), |
|
| 234 |
'default' => 'Amp' |
|
| 235 |
); |
|
| 236 |
$opts['fdd']['storage_minus80freezers'] = array( |
|
| 237 |
'name' => '-80 Freezer', |
|
| 238 |
'select' => 'D', |
|
| 239 |
'maxlen' => 25, |
|
| 240 |
'sort' => true, |
|
| 241 |
'values' => array( |
|
| 242 |
'table' => 'storage_minus80freezers', |
|
| 243 |
'column' => 'name'), |
|
| 244 |
'default' => 'Amp' |
|
| 245 |
); |
|
| 246 |
$opts['fdd']['storage_fridges'] = array( |
|
| 247 |
'name' => 'Fridge', |
|
| 248 |
'select' => 'D', |
|
| 249 |
'maxlen' => 25, |
|
| 250 |
'sort' => true, |
|
| 251 |
'values' => array( |
|
| 252 |
'table' => 'storage_fridges', |
|
| 253 |
'column' => 'name'), |
|
| 254 |
'default' => 'Amp' |
|
| 255 |
); |
|
| 256 |
$opts['fdd']['storage_rooms'] = array( |
|
| 257 |
'name' => 'Room', |
|
| 258 |
'select' => 'D', |
|
| 259 |
'maxlen' => 25, |
|
| 260 |
'sort' => true, |
|
| 261 |
'values' => array( |
|
| 262 |
'table' => 'storage_rooms', |
|
| 263 |
'column' => 'name'), |
|
| 264 |
'default' => 'Amp' |
|
| 265 |
); |
|
| 226 | 266 |
|
| 227 | 267 |
// TRIGGER |
| 228 | 268 |
// Before displaying the view page |
| b/src/headers.php | ||
|---|---|---|
| 22 | 22 |
<li id="pl_features"><span><a href="pl_features.php"> Plasmids Features </a></span></li> |
| 23 | 23 |
<li id="strains"><span><a href="strains.php"> Strains </a></span></li> |
| 24 | 24 |
<li id="oligos"><span><a href="oligos.php"> Oligos </a></span></li> |
| 25 |
<li id="wwwblast"><span><a href="wwwblast.php"> wwwBlast </a></span></li>
|
|
| 25 |
<li id="wwwblast"><span><a href="wwwblast.php"> wwwBLAST </a></span></li>
|
|
| 26 | 26 |
<li id="antibodies"><span><a href="antibodies.php"> Antibodies </a></span></li> |
| 27 | 27 |
<li id="collections"><span><a href="collections.php"> Collections </a></span></li> |
| 28 | 28 |
<li id="pip_stock"><span><a href="pip_stock.php"> Pipets </a></span></li> |
| b/src/oligos.php | ||
|---|---|---|
| 175 | 175 |
'table' => 'olig_purif', |
| 176 | 176 |
'column' => 'type') |
| 177 | 177 |
); |
| 178 |
$opts['fdd']['storage_minus20freezers'] = array( |
|
| 179 |
'name' => '-20 Freezer', |
|
| 180 |
'select' => 'D', |
|
| 181 |
'maxlen' => 25, |
|
| 182 |
'sort' => true, |
|
| 183 |
'values' => array( |
|
| 184 |
'table' => 'storage_minus20freezers', |
|
| 185 |
'column' => 'name'), |
|
| 186 |
'default' => 'Amp' |
|
| 187 |
); |
|
| 188 |
$opts['fdd']['storage_minus80freezers'] = array( |
|
| 189 |
'name' => '-80 Freezer', |
|
| 190 |
'select' => 'D', |
|
| 191 |
'maxlen' => 25, |
|
| 192 |
'sort' => true, |
|
| 193 |
'values' => array( |
|
| 194 |
'table' => 'storage_minus80freezers', |
|
| 195 |
'column' => 'name'), |
|
| 196 |
'default' => 'Amp' |
|
| 197 |
); |
|
| 198 |
$opts['fdd']['storage_fridges'] = array( |
|
| 199 |
'name' => 'Fridge', |
|
| 200 |
'select' => 'D', |
|
| 201 |
'maxlen' => 25, |
|
| 202 |
'sort' => true, |
|
| 203 |
'values' => array( |
|
| 204 |
'table' => 'storage_fridges', |
|
| 205 |
'column' => 'name'), |
|
| 206 |
'default' => 'Amp' |
|
| 207 |
); |
|
| 208 |
$opts['fdd']['storage_rooms'] = array( |
|
| 209 |
'name' => 'Room', |
|
| 210 |
'select' => 'D', |
|
| 211 |
'maxlen' => 25, |
|
| 212 |
'sort' => true, |
|
| 213 |
'values' => array( |
|
| 214 |
'table' => 'storage_rooms', |
|
| 215 |
'column' => 'name'), |
|
| 216 |
'default' => 'Amp' |
|
| 217 |
); |
|
| 178 | 218 |
|
| 179 | 219 |
require("footers.php");
|
| 180 | 220 |
?> |
| b/src/plasmids.php | ||
|---|---|---|
| 279 | 279 |
'column' => 'type'), |
| 280 | 280 |
'default' => 'Amp' |
| 281 | 281 |
); |
| 282 |
$opts['fdd']['storage_minus20freezers'] = array( |
|
| 283 |
'name' => '-20 Freezer', |
|
| 284 |
'select' => 'D', |
|
| 285 |
'maxlen' => 25, |
|
| 286 |
'sort' => true, |
|
| 287 |
'values' => array( |
|
| 288 |
'table' => 'storage_minus20freezers', |
|
| 289 |
'column' => 'name'), |
|
| 290 |
'default' => 'Amp' |
|
| 291 |
); |
|
| 292 |
$opts['fdd']['storage_minus80freezers'] = array( |
|
| 293 |
'name' => '-80 Freezer', |
|
| 294 |
'select' => 'D', |
|
| 295 |
'maxlen' => 25, |
|
| 296 |
'sort' => true, |
|
| 297 |
'values' => array( |
|
| 298 |
'table' => 'storage_minus80freezers', |
|
| 299 |
'column' => 'name'), |
|
| 300 |
'default' => 'Amp' |
|
| 301 |
); |
|
| 302 |
$opts['fdd']['storage_fridges'] = array( |
|
| 303 |
'name' => 'Fridge', |
|
| 304 |
'select' => 'D', |
|
| 305 |
'maxlen' => 25, |
|
| 306 |
'sort' => true, |
|
| 307 |
'values' => array( |
|
| 308 |
'table' => 'storage_fridges', |
|
| 309 |
'column' => 'name'), |
|
| 310 |
'default' => 'Amp' |
|
| 311 |
); |
|
| 312 |
$opts['fdd']['storage_rooms'] = array( |
|
| 313 |
'name' => 'Room', |
|
| 314 |
'select' => 'D', |
|
| 315 |
'maxlen' => 25, |
|
| 316 |
'sort' => true, |
|
| 317 |
'values' => array( |
|
| 318 |
'table' => 'storage_rooms', |
|
| 319 |
'column' => 'name'), |
|
| 320 |
'default' => 'Amp' |
|
| 321 |
); |
|
| 282 | 322 |
|
| 283 | 323 |
|
| 284 | 324 |
|
| b/src/sql/labstocks_db.sql | ||
|---|---|---|
| 1 |
|
|
| 2 |
CREATE TABLE IF NOT EXISTS `storage_minus20freezers` ( |
|
| 3 |
`name` varchar(100) COLLATE utf8_general_ci NOT NULL, |
|
| 4 |
PRIMARY KEY (`name`) |
|
| 5 |
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_general_ci; |
|
| 6 |
|
|
| 7 |
INSERT INTO `storage_minus20freezers` (`name`) VALUES ('GY -20 freezer');
|
|
| 8 |
|
|
| 9 |
|
|
| 10 |
CREATE TABLE IF NOT EXISTS `storage_minus80freezers` ( |
|
| 11 |
`name` varchar(100) COLLATE utf8_general_ci NOT NULL, |
|
| 12 |
PRIMARY KEY (`name`) |
|
| 13 |
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_general_ci; |
|
| 14 |
|
|
| 15 |
INSERT INTO `storage_minus80freezers` (`name`) VALUES ('GY -80 freezer');
|
|
| 16 |
|
|
| 17 |
|
|
| 18 |
CREATE TABLE IF NOT EXISTS `storage_fridges` ( |
|
| 19 |
`name` varchar(100) COLLATE utf8_general_ci NOT NULL, |
|
| 20 |
PRIMARY KEY (`name`) |
|
| 21 |
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_general_ci; |
|
| 22 |
|
|
| 23 |
INSERT INTO `storage_fridges` (`name`) VALUES ('GY fridge');
|
|
| 24 |
|
|
| 25 |
|
|
| 26 |
CREATE TABLE IF NOT EXISTS `storage_rooms` ( |
|
| 27 |
`name` varchar(100) COLLATE utf8_general_ci NOT NULL, |
|
| 28 |
PRIMARY KEY (`name`) |
|
| 29 |
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_general_ci; |
|
| 30 |
|
|
| 31 |
INSERT INTO `storage_rooms` (`name`) VALUES ('GY room');
|
|
| 32 |
|
|
| 33 |
|
|
| 34 |
|
|
| 35 |
|
|
| 1 | 36 |
-- phpMyAdmin SQL Dump |
| 2 | 37 |
-- version 3.4.11.1deb2 |
| 3 | 38 |
-- http://www.phpmyadmin.net |
| ... | ... | |
| 143 | 178 |
`Dilution-WB` text NOT NULL, |
| 144 | 179 |
`Volume-ChIP` text NOT NULL, |
| 145 | 180 |
`ProductID` varchar(20) NOT NULL, |
| 181 |
`storage_minus20freezers` varchar(100) DEFAULT NULL, |
|
| 182 |
`storage_minus80freezers` varchar(100) DEFAULT NULL, |
|
| 183 |
`storage_fridges` varchar(100) DEFAULT NULL, |
|
| 184 |
`storage_rooms` varchar(100) DEFAULT NULL, |
|
| 146 | 185 |
PRIMARY KEY (`id`), |
| 147 | 186 |
KEY `Author` (`Ordered_by`) |
| 148 | 187 |
) ENGINE=InnoDB DEFAULT CHARSET=utf8 ROW_FORMAT=DYNAMIC; |
| ... | ... | |
| 216 | 255 |
`PCR_conditions_predicted` longtext, |
| 217 | 256 |
`Author` varchar(50) DEFAULT NULL, |
| 218 | 257 |
`Purif` varchar(40) NOT NULL, |
| 258 |
`storage_minus20freezers` varchar(100) DEFAULT NULL, |
|
| 259 |
`storage_minus80freezers` varchar(100) DEFAULT NULL, |
|
| 260 |
`storage_fridges` varchar(100) DEFAULT NULL, |
|
| 261 |
`storage_rooms` varchar(100) DEFAULT NULL, |
|
| 219 | 262 |
PRIMARY KEY (`id`), |
| 220 | 263 |
KEY `Author` (`Author`) |
| 221 | 264 |
) ENGINE=InnoDB DEFAULT CHARSET=utf8 ROW_FORMAT=DYNAMIC; |
| ... | ... | |
| 493 | 536 |
`sequence` text, |
| 494 | 537 |
`image_file` varchar(100) DEFAULT NULL, |
| 495 | 538 |
`Author` varchar(50) DEFAULT NULL, |
| 539 |
`storage_minus20freezers` varchar(100) DEFAULT NULL, |
|
| 540 |
`storage_minus80freezers` varchar(100) DEFAULT NULL, |
|
| 541 |
`storage_fridges` varchar(100) DEFAULT NULL, |
|
| 542 |
`storage_rooms` varchar(100) DEFAULT NULL, |
|
| 496 | 543 |
PRIMARY KEY (`id`), |
| 497 | 544 |
UNIQUE KEY `Link_to_file` (`Link_to_file`), |
| 498 | 545 |
UNIQUE KEY `Link_to_file_2` (`Link_to_file`), |
| ... | ... | |
| 741 | 788 |
`Last_modified` date DEFAULT NULL, |
| 742 | 789 |
`MET15` varchar(25) CHARACTER SET utf8 COLLATE utf8_general_ci DEFAULT NULL, |
| 743 | 790 |
`Author` varchar(50) DEFAULT NULL, |
| 791 |
`storage_minus20freezers` varchar(100) DEFAULT NULL, |
|
| 792 |
`storage_minus80freezers` varchar(100) DEFAULT NULL, |
|
| 793 |
`storage_fridges` varchar(100) DEFAULT NULL, |
|
| 794 |
`storage_rooms` varchar(100) DEFAULT NULL, |
|
| 744 | 795 |
PRIMARY KEY (`id`), |
| 745 | 796 |
KEY `Author` (`Author`) |
| 746 | 797 |
) ENGINE=InnoDB DEFAULT CHARSET=utf8 ROW_FORMAT=DYNAMIC; |
| b/src/strains.php | ||
|---|---|---|
| 363 | 363 |
'sort' => true, |
| 364 | 364 |
'default' => date("Y-m-d", strtotime("now"))
|
| 365 | 365 |
); |
| 366 |
$opts['fdd']['storage_minus20freezers'] = array( |
|
| 367 |
'name' => '-20 Freezer', |
|
| 368 |
'select' => 'D', |
|
| 369 |
'maxlen' => 25, |
|
| 370 |
'sort' => true, |
|
| 371 |
'values' => array( |
|
| 372 |
'table' => 'storage_minus20freezers', |
|
| 373 |
'column' => 'name'), |
|
| 374 |
'default' => 'Amp' |
|
| 375 |
); |
|
| 376 |
$opts['fdd']['storage_minus80freezers'] = array( |
|
| 377 |
'name' => '-80 Freezer', |
|
| 378 |
'select' => 'D', |
|
| 379 |
'maxlen' => 25, |
|
| 380 |
'sort' => true, |
|
| 381 |
'values' => array( |
|
| 382 |
'table' => 'storage_minus80freezers', |
|
| 383 |
'column' => 'name'), |
|
| 384 |
'default' => 'Amp' |
|
| 385 |
); |
|
| 386 |
$opts['fdd']['storage_fridges'] = array( |
|
| 387 |
'name' => 'Fridge', |
|
| 388 |
'select' => 'D', |
|
| 389 |
'maxlen' => 25, |
|
| 390 |
'sort' => true, |
|
| 391 |
'values' => array( |
|
| 392 |
'table' => 'storage_fridges', |
|
| 393 |
'column' => 'name'), |
|
| 394 |
'default' => 'Amp' |
|
| 395 |
); |
|
| 396 |
$opts['fdd']['storage_rooms'] = array( |
|
| 397 |
'name' => 'Room', |
|
| 398 |
'select' => 'D', |
|
| 399 |
'maxlen' => 25, |
|
| 400 |
'sort' => true, |
|
| 401 |
'values' => array( |
|
| 402 |
'table' => 'storage_rooms', |
|
| 403 |
'column' => 'name'), |
|
| 404 |
'default' => 'Amp' |
|
| 405 |
); |
|
| 366 | 406 |
|
| 367 | 407 |
// TRIGGER |
| 368 | 408 |
// Before displaying the view page |
| b/src/wwwblast.php | ||
|---|---|---|
| 28 | 28 |
echo "Error while formatting the FASTA database into BLAST format"; |
| 29 | 29 |
exit; |
| 30 | 30 |
} |
| 31 |
echo "Blast has been updated with the latest oligostock.";
|
|
| 31 |
echo "BLAST has been updated with the latest oligostock.";
|
|
| 32 | 32 |
|
| 33 | 33 |
// Create an updated fasta |
| 34 | 34 |
// file of all plasmids |
| ... | ... | |
| 57 | 57 |
echo "Error while formatting the FASTA database into BLAST format"; |
| 58 | 58 |
exit; |
| 59 | 59 |
} |
| 60 |
echo "Blast has been updated with the latest plasmidstock.";
|
|
| 60 |
echo "BLAST has been updated with the latest plasmidstock.";
|
|
| 61 | 61 |
|
| 62 | 62 |
// Create an updated fasta |
| 63 | 63 |
// file of all pl_features |
| ... | ... | |
| 94 | 94 |
echo "Error while formatting the FASTA database into BLAST format"; |
| 95 | 95 |
exit; |
| 96 | 96 |
} |
| 97 |
echo "Blast has been updated with the latest plfeatstock.";
|
|
| 97 |
echo "BLAST has been updated with the latest plfeatstock.";
|
|
| 98 | 98 |
|
| 99 | 99 |
|
| 100 | 100 |
|
| ... | ... | |
| 164 | 164 |
$fp = fopen($html_feat_filename, 'w'); |
| 165 | 165 |
fwrite($fp, $html_feat_cnt); |
| 166 | 166 |
fclose($fp); |
| 167 |
echo "Blast has updated PlasMapper with the latest plasmid's features.";
|
|
| 167 |
echo "BLAST has updated PlasMapper with the latest plasmid's features.";
|
|
| 168 | 168 |
?> |
| 169 | 169 |
|
| 170 | 170 |
<center> |
| 171 | 171 |
<iframe src="/blast/blast.html" width="100%" height="90%" border="0"/> |
| 172 |
</center> |
|
| 172 |
</center> |
|
Formats disponibles : Unified diff