diff --git a/pybis/src/python/.gitignore b/pybis/src/python/.gitignore
index f0c705a2289d77b10c653b6f26c401a4bc5d46fc..f786b8afd5ad428b61e131aff783e967d813e6ee 100644
--- a/pybis/src/python/.gitignore
+++ b/pybis/src/python/.gitignore
@@ -1,3 +1,4 @@
*~
.*.sw?
.ipynb_checkpoints/
+*.ipynb
diff --git a/pybis/src/python/notebooks/pybis demo.ipynb b/pybis/src/python/notebooks/pybis demo.ipynb
index d19b3d371e344f634651d729baa3ec749b04c3b8..3ca052bc6bd5ac6e5c8aa21fd0ba7102a55f666a 100644
--- a/pybis/src/python/notebooks/pybis demo.ipynb
+++ b/pybis/src/python/notebooks/pybis demo.ipynb
@@ -18,21 +18,8 @@
{
"cell_type": "code",
"execution_count": 1,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "'vermeul-170213105629815x0CF2F2467FF08E65E79A1E25E0334BC3'"
- ]
- },
- "execution_count": 1,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "metadata": {},
+ "outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
@@ -49,9 +36,7 @@
{
"cell_type": "code",
"execution_count": 2,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -77,10 +62,8 @@
},
{
"cell_type": "code",
- "execution_count": 85,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 1,
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -92,10 +75,10 @@
{
"data": {
"text/plain": [
- "'vermeul-170213105629815x0CF2F2467FF08E65E79A1E25E0334BC3'"
+ "'vermeul-180926010607740x90FB53D7BFEB6F8D6E3F634753E5E5E5'"
]
},
- "execution_count": 85,
+ "execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
@@ -120,9 +103,7 @@
{
"cell_type": "code",
"execution_count": 82,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -161,9 +142,7 @@
{
"cell_type": "code",
"execution_count": 29,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"o2.logout()"
@@ -186,9 +165,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -238,9 +215,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -312,9 +287,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -360,9 +333,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -419,9 +390,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -485,9 +454,7 @@
{
"cell_type": "code",
"execution_count": 87,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"pr = o.get_project('/MY_NEW_SPACE/VERMEUL_PROJECT')"
@@ -497,7 +464,6 @@
"cell_type": "code",
"execution_count": 88,
"metadata": {
- "collapsed": false,
"scrolled": true
},
"outputs": [
@@ -583,9 +549,7 @@
{
"cell_type": "code",
"execution_count": 90,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -668,9 +632,7 @@
{
"cell_type": "code",
"execution_count": 24,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -729,9 +691,7 @@
{
"cell_type": "code",
"execution_count": 12,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -797,9 +757,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -962,9 +920,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1006,9 +962,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1122,9 +1076,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1172,9 +1124,7 @@
{
"cell_type": "code",
"execution_count": 17,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1215,9 +1165,7 @@
{
"cell_type": "code",
"execution_count": 17,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1266,7 +1214,6 @@
"cell_type": "code",
"execution_count": 2,
"metadata": {
- "collapsed": false,
"scrolled": false
},
"outputs": [
@@ -1474,9 +1421,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1522,9 +1467,7 @@
{
"cell_type": "code",
"execution_count": 20,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1617,9 +1560,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1648,9 +1589,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"sp = o.get_space('VERMEUL')"
@@ -1659,9 +1598,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1721,9 +1658,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1759,9 +1694,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1781,9 +1714,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1828,9 +1759,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1850,9 +1779,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -1870,9 +1797,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"p.add_attachment(fileName='testfile', description= 'another file', title= 'one more attachment')"
@@ -1881,9 +1806,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -1918,9 +1841,7 @@
{
"cell_type": "code",
"execution_count": 12,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -1944,9 +1865,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"from pybis import Openbis\n",
@@ -1964,7 +1883,6 @@
"cell_type": "code",
"execution_count": 2,
"metadata": {
- "collapsed": false,
"scrolled": true
},
"outputs": [
@@ -2025,9 +1943,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2063,9 +1979,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"e0.project = p"
@@ -2074,9 +1988,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"e0.add_tags('uno')"
@@ -2085,9 +1997,7 @@
{
"cell_type": "code",
"execution_count": 12,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -2104,9 +2014,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2157,7 +2065,6 @@
"cell_type": "code",
"execution_count": 19,
"metadata": {
- "collapsed": false,
"scrolled": true
},
"outputs": [
@@ -2194,9 +2101,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2227,9 +2132,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"e_new.project ='VERMEUL_PROJECT'"
@@ -2238,9 +2141,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"e_new.tags = 'too_late'"
@@ -2249,9 +2150,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"e_new.code = 'exp_new'"
@@ -2260,9 +2159,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -2279,9 +2176,7 @@
{
"cell_type": "code",
"execution_count": 45,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2317,9 +2212,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2354,9 +2247,7 @@
{
"cell_type": "code",
"execution_count": 11,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2419,9 +2310,7 @@
{
"cell_type": "code",
"execution_count": 12,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2491,9 +2380,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2552,9 +2439,7 @@
{
"cell_type": "code",
"execution_count": 27,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2590,9 +2475,7 @@
{
"cell_type": "code",
"execution_count": 26,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"ex.set_properties({'FINISHED_FLAG': False})"
@@ -2600,9 +2483,7 @@
},
{
"cell_type": "raw",
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"source": [
"e = o.new_experiment('/MATERIALS/YEASTS', 'my_experiment0815', 'DEFAULT_EXPERIMENT', properties={\"Name\":\"blast\"})"
]
@@ -2628,9 +2509,7 @@
{
"cell_type": "code",
"execution_count": 23,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"from pybis import Openbis\n",
@@ -2640,9 +2519,7 @@
{
"cell_type": "code",
"execution_count": 26,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2678,9 +2555,7 @@
{
"cell_type": "code",
"execution_count": 27,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2715,9 +2590,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2770,9 +2643,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"sa.add_attachment('testfile')"
@@ -2781,9 +2652,7 @@
{
"cell_type": "code",
"execution_count": 17,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -2800,9 +2669,7 @@
{
"cell_type": "code",
"execution_count": 11,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -2820,9 +2687,7 @@
{
"cell_type": "code",
"execution_count": 2,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -2958,9 +2823,7 @@
{
"cell_type": "code",
"execution_count": 11,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3003,9 +2866,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3053,9 +2914,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3082,9 +2941,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3119,9 +2976,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3162,9 +3017,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3184,9 +3037,7 @@
{
"cell_type": "code",
"execution_count": 12,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3337,9 +3188,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3381,9 +3230,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3419,9 +3266,7 @@
},
{
"cell_type": "markdown",
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"source": [
"fetch just a single property: sample.p.芦property_name禄"
]
@@ -3429,9 +3274,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3458,9 +3301,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3504,9 +3345,7 @@
{
"cell_type": "code",
"execution_count": 24,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"ename": "ValueError",
@@ -3535,9 +3374,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3566,9 +3403,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"from pybis import Openbis\n",
@@ -3578,9 +3413,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3616,9 +3449,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3656,9 +3487,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3710,9 +3539,7 @@
{
"cell_type": "code",
"execution_count": 65,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"ename": "NameError",
@@ -3733,9 +3560,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -3752,9 +3577,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -3806,9 +3629,7 @@
{
"cell_type": "code",
"execution_count": 22,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -3843,9 +3664,7 @@
{
"cell_type": "code",
"execution_count": 23,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -3869,9 +3688,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"from pybis import Openbis\n",
@@ -3881,9 +3698,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -3931,10 +3746,17 @@
},
{
"cell_type": "code",
- "execution_count": 26,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "s_new = o.new_sample(type='YEAST', space='VERMEUL', parents=['/VERMEUL/BLAJLSD'])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
"outputs": [],
"source": [
"s_new = o.new_sample(type='YEAST', space='VERMEUL')"
@@ -3942,11 +3764,199 @@
},
{
"cell_type": "code",
- "execution_count": 25,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 11,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th>attribute</th>\n",
+ " <th>value</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr> <td>code</td> <td></td> </tr><tr> <td>permId</td> <td></td> </tr><tr> <td>identifier</td> <td></td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td></td> </tr><tr> <td>children</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr>\n",
+ " </tbody>\n",
+ " </table>\n",
+ " "
+ ],
+ "text/plain": [
+ "attribute value\n",
+ "----------- -------\n",
+ "code\n",
+ "permId\n",
+ "identifier\n",
+ "type YEAST\n",
+ "project\n",
+ "parents\n",
+ "children\n",
+ "components\n",
+ "space VERMEUL\n",
+ "experiment\n",
+ "tags []"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s_new"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "s_new.add_parents('/VERMEUL/BLAJLSD')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th>attribute</th>\n",
+ " <th>value</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr> <td>code</td> <td></td> </tr><tr> <td>permId</td> <td></td> </tr><tr> <td>identifier</td> <td></td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td>['/VERMEUL/BLAJLSD']</td> </tr><tr> <td>children</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr>\n",
+ " </tbody>\n",
+ " </table>\n",
+ " "
+ ],
+ "text/plain": [
+ "attribute value\n",
+ "----------- --------------------\n",
+ "code\n",
+ "permId\n",
+ "identifier\n",
+ "type YEAST\n",
+ "project\n",
+ "parents ['/VERMEUL/BLAJLSD']\n",
+ "children\n",
+ "components\n",
+ "space VERMEUL\n",
+ "experiment\n",
+ "tags []"
+ ]
+ },
+ "execution_count": 13,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s_new"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 45,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "s_new.get_parents()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 33,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Sample successfully created.\n"
+ ]
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th>attribute</th>\n",
+ " <th>value</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr> <td>code</td> <td>YEA86</td> </tr><tr> <td>permId</td> <td>20180926000051715-743</td> </tr><tr> <td>identifier</td> <td>/VERMEUL/YEA86</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>components</td> <td>[]</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
+ " </tbody>\n",
+ " </table>\n",
+ " "
+ ],
+ "text/plain": [
+ "attribute value\n",
+ "----------- ---------------------\n",
+ "code YEA86\n",
+ "permId 20180926000051715-743\n",
+ "identifier /VERMEUL/YEA86\n",
+ "type YEAST\n",
+ "project\n",
+ "parents []\n",
+ "children []\n",
+ "components []\n",
+ "space VERMEUL\n",
+ "experiment\n",
+ "tags []"
+ ]
+ },
+ "execution_count": 33,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s_new.save()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 36,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Sample 20180926000051715-743 successfully deleted.\n"
+ ]
+ }
+ ],
+ "source": [
+ "s_new.delete('dfd')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
"outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Sample successfully created.\n"
+ ]
+ },
{
"data": {
"text/html": [
@@ -3959,41 +3969,1505 @@
" </tr>\n",
" </thead>\n",
" <tbody>\n",
- " <tr> <td>code</td> <td></td> </tr><tr> <td>permId</td> <td></td> </tr><tr> <td>identifier</td> <td></td> </tr><tr> <td>type</td> <td></td> </tr><tr> <td>parents</td> <td></td> </tr><tr> <td>children</td> <td></td> </tr><tr> <td>space</td> <td></td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td></td> </tr>\n",
+ " <tr> <td>code</td> <td>YEA85</td> </tr><tr> <td>permId</td> <td>20180925234950217-726</td> </tr><tr> <td>identifier</td> <td>/VERMEUL/YEA85</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>components</td> <td>[]</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
- "<pybis.pybis.Sample at 0x7f8177455898>"
+ "attribute value\n",
+ "----------- ---------------------\n",
+ "code YEA85\n",
+ "permId 20180925234950217-726\n",
+ "identifier /VERMEUL/YEA85\n",
+ "type YEAST\n",
+ "project\n",
+ "parents []\n",
+ "children []\n",
+ "components []\n",
+ "space VERMEUL\n",
+ "experiment\n",
+ "tags []"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s_new.save()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "路路路路路路路路\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "'vermeul-180926010643993x968AC0C20F32D8AE95DF2E00E2291B8B'"
+ ]
+ },
+ "execution_count": 2,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from pybis import Openbis\n",
+ "o = Openbis('https://localhost:8443', verify_certificates=False)\n",
+ "\n",
+ "import getpass\n",
+ "password = getpass.getpass()\n",
+ "\n",
+ "o.login('vermeul',password, save_token=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.get_samples(chil)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "s_new = o.get_sample('20180925234950217-726')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[{'@type': 'as.dto.sample.Sample',\n",
+ " '@id': 2,\n",
+ " 'fetchOptions': {'@type': 'as.dto.sample.fetchoptions.SampleFetchOptions',\n",
+ " '@id': 3,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'type': {'@type': 'as.dto.sample.fetchoptions.SampleTypeFetchOptions',\n",
+ " '@id': 4,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'propertyAssignments': None,\n",
+ " 'semanticAnnotations': None,\n",
+ " 'validationPlugin': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'project': None,\n",
+ " 'space': None,\n",
+ " 'experiment': {'@type': 'as.dto.experiment.fetchoptions.ExperimentFetchOptions',\n",
+ " '@id': 5,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'type': {'@type': 'as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions',\n",
+ " '@id': 6,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'propertyAssignments': None,\n",
+ " 'validationPlugin': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'project': None,\n",
+ " 'dataSets': None,\n",
+ " 'samples': None,\n",
+ " 'history': None,\n",
+ " 'properties': None,\n",
+ " 'materialProperties': None,\n",
+ " 'tags': None,\n",
+ " 'registrator': None,\n",
+ " 'modifier': None,\n",
+ " 'attachments': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'properties': {'@type': 'as.dto.property.fetchoptions.PropertyFetchOptions',\n",
+ " '@id': 7,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'sortBy': None},\n",
+ " 'materialProperties': None,\n",
+ " 'parents': None,\n",
+ " 'children': None,\n",
+ " 'container': None,\n",
+ " 'components': None,\n",
+ " 'dataSets': None,\n",
+ " 'history': None,\n",
+ " 'tags': {'@type': 'as.dto.tag.fetchoptions.TagFetchOptions',\n",
+ " '@id': 8,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'experiments': None,\n",
+ " 'samples': None,\n",
+ " 'dataSets': None,\n",
+ " 'materials': None,\n",
+ " 'owner': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'registrator': {'@type': 'as.dto.person.fetchoptions.PersonFetchOptions',\n",
+ " '@id': 9,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None,\n",
+ " 'allWebAppSettings': False,\n",
+ " 'sort': None},\n",
+ " 'modifier': {'@type': 'as.dto.person.fetchoptions.PersonFetchOptions',\n",
+ " '@id': 10,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None,\n",
+ " 'allWebAppSettings': False,\n",
+ " 'sort': None},\n",
+ " 'attachments': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'permId': {'@type': 'as.dto.sample.id.SamplePermId',\n",
+ " '@id': 11,\n",
+ " 'permId': '20170327113258723-442'},\n",
+ " 'identifier': {'@type': 'as.dto.sample.id.SampleIdentifier',\n",
+ " '@id': 12,\n",
+ " 'identifier': '/VERMEUL/YEA67'},\n",
+ " 'code': 'YEA67',\n",
+ " 'registrationDate': 1490607178723,\n",
+ " 'modificationDate': 1490609025723,\n",
+ " 'type': {'@type': 'as.dto.sample.SampleType',\n",
+ " '@id': 13,\n",
+ " 'fetchOptions': 4,\n",
+ " 'permId': {'@type': 'as.dto.entitytype.id.EntityTypePermId',\n",
+ " '@id': 14,\n",
+ " 'permId': 'YEAST',\n",
+ " 'entityKind': 'SAMPLE'},\n",
+ " 'code': 'YEAST',\n",
+ " 'description': '',\n",
+ " 'listable': True,\n",
+ " 'subcodeUnique': False,\n",
+ " 'autoGeneratedCode': True,\n",
+ " 'showContainer': False,\n",
+ " 'showParents': True,\n",
+ " 'showParentMetadata': False,\n",
+ " 'generatedCodePrefix': 'YEA',\n",
+ " 'modificationDate': 1466758081653,\n",
+ " 'propertyAssignments': None,\n",
+ " 'semanticAnnotations': None,\n",
+ " 'validationPlugin': None},\n",
+ " 'project': None,\n",
+ " 'space': None,\n",
+ " 'experiment': None,\n",
+ " 'properties': {},\n",
+ " 'materialProperties': None,\n",
+ " 'parents': None,\n",
+ " 'children': None,\n",
+ " 'container': None,\n",
+ " 'components': None,\n",
+ " 'dataSets': None,\n",
+ " 'history': None,\n",
+ " 'tags': [],\n",
+ " 'registrator': {'@type': 'as.dto.person.Person',\n",
+ " '@id': 15,\n",
+ " 'fetchOptions': {'@type': 'as.dto.person.fetchoptions.PersonFetchOptions',\n",
+ " '@id': 16,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None,\n",
+ " 'allWebAppSettings': False,\n",
+ " 'sort': None},\n",
+ " 'permId': {'@type': 'as.dto.person.id.PersonPermId',\n",
+ " '@id': 17,\n",
+ " 'permId': 'vermeul'},\n",
+ " 'userId': 'vermeul',\n",
+ " 'firstName': '',\n",
+ " 'lastName': '',\n",
+ " 'email': '',\n",
+ " 'registrationDate': 1466761847802,\n",
+ " 'active': True,\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None},\n",
+ " 'modifier': {'@type': 'as.dto.person.Person',\n",
+ " '@id': 15,\n",
+ " 'fetchOptions': {'@type': 'as.dto.person.fetchoptions.PersonFetchOptions',\n",
+ " '@id': 16,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None,\n",
+ " 'allWebAppSettings': False,\n",
+ " 'sort': None},\n",
+ " 'permId': {'@type': 'as.dto.person.id.PersonPermId',\n",
+ " '@id': 17,\n",
+ " 'permId': 'vermeul'},\n",
+ " 'userId': 'vermeul',\n",
+ " 'firstName': '',\n",
+ " 'lastName': '',\n",
+ " 'email': '',\n",
+ " 'registrationDate': 1466761847802,\n",
+ " 'active': True,\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None},\n",
+ " 'attachments': None},\n",
+ " {'@type': 'as.dto.sample.Sample',\n",
+ " '@id': 18,\n",
+ " 'fetchOptions': {'@type': 'as.dto.sample.fetchoptions.SampleFetchOptions',\n",
+ " '@id': 19,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'type': {'@type': 'as.dto.sample.fetchoptions.SampleTypeFetchOptions',\n",
+ " '@id': 4,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'propertyAssignments': None,\n",
+ " 'semanticAnnotations': None,\n",
+ " 'validationPlugin': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'project': None,\n",
+ " 'space': None,\n",
+ " 'experiment': {'@type': 'as.dto.experiment.fetchoptions.ExperimentFetchOptions',\n",
+ " '@id': 5,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'type': {'@type': 'as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions',\n",
+ " '@id': 6,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'propertyAssignments': None,\n",
+ " 'validationPlugin': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'project': None,\n",
+ " 'dataSets': None,\n",
+ " 'samples': None,\n",
+ " 'history': None,\n",
+ " 'properties': None,\n",
+ " 'materialProperties': None,\n",
+ " 'tags': None,\n",
+ " 'registrator': None,\n",
+ " 'modifier': None,\n",
+ " 'attachments': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'properties': {'@type': 'as.dto.property.fetchoptions.PropertyFetchOptions',\n",
+ " '@id': 7,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'sortBy': None},\n",
+ " 'materialProperties': None,\n",
+ " 'parents': None,\n",
+ " 'children': None,\n",
+ " 'container': None,\n",
+ " 'components': None,\n",
+ " 'dataSets': None,\n",
+ " 'history': None,\n",
+ " 'tags': {'@type': 'as.dto.tag.fetchoptions.TagFetchOptions',\n",
+ " '@id': 8,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'experiments': None,\n",
+ " 'samples': None,\n",
+ " 'dataSets': None,\n",
+ " 'materials': None,\n",
+ " 'owner': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'registrator': {'@type': 'as.dto.person.fetchoptions.PersonFetchOptions',\n",
+ " '@id': 9,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None,\n",
+ " 'allWebAppSettings': False,\n",
+ " 'sort': None},\n",
+ " 'modifier': {'@type': 'as.dto.person.fetchoptions.PersonFetchOptions',\n",
+ " '@id': 10,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None,\n",
+ " 'allWebAppSettings': False,\n",
+ " 'sort': None},\n",
+ " 'attachments': None,\n",
+ " 'sort': None,\n",
+ " 'sortBy': None},\n",
+ " 'permId': {'@type': 'as.dto.sample.id.SamplePermId',\n",
+ " '@id': 20,\n",
+ " 'permId': '20170327122105199-443'},\n",
+ " 'identifier': {'@type': 'as.dto.sample.id.SampleIdentifier',\n",
+ " '@id': 21,\n",
+ " 'identifier': '/VERMEUL/YEA68'},\n",
+ " 'code': 'YEA68',\n",
+ " 'registrationDate': 1490610065199,\n",
+ " 'modificationDate': 1490610341369,\n",
+ " 'type': {'@type': 'as.dto.sample.SampleType',\n",
+ " '@id': 13,\n",
+ " 'fetchOptions': 4,\n",
+ " 'permId': {'@type': 'as.dto.entitytype.id.EntityTypePermId',\n",
+ " '@id': 14,\n",
+ " 'permId': 'YEAST',\n",
+ " 'entityKind': 'SAMPLE'},\n",
+ " 'code': 'YEAST',\n",
+ " 'description': '',\n",
+ " 'listable': True,\n",
+ " 'subcodeUnique': False,\n",
+ " 'autoGeneratedCode': True,\n",
+ " 'showContainer': False,\n",
+ " 'showParents': True,\n",
+ " 'showParentMetadata': False,\n",
+ " 'generatedCodePrefix': 'YEA',\n",
+ " 'modificationDate': 1466758081653,\n",
+ " 'propertyAssignments': None,\n",
+ " 'semanticAnnotations': None,\n",
+ " 'validationPlugin': None},\n",
+ " 'project': None,\n",
+ " 'space': None,\n",
+ " 'experiment': None,\n",
+ " 'properties': {},\n",
+ " 'materialProperties': None,\n",
+ " 'parents': None,\n",
+ " 'children': None,\n",
+ " 'container': None,\n",
+ " 'components': None,\n",
+ " 'dataSets': None,\n",
+ " 'history': None,\n",
+ " 'tags': [],\n",
+ " 'registrator': {'@type': 'as.dto.person.Person',\n",
+ " '@id': 15,\n",
+ " 'fetchOptions': {'@type': 'as.dto.person.fetchoptions.PersonFetchOptions',\n",
+ " '@id': 16,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None,\n",
+ " 'allWebAppSettings': False,\n",
+ " 'sort': None},\n",
+ " 'permId': {'@type': 'as.dto.person.id.PersonPermId',\n",
+ " '@id': 17,\n",
+ " 'permId': 'vermeul'},\n",
+ " 'userId': 'vermeul',\n",
+ " 'firstName': '',\n",
+ " 'lastName': '',\n",
+ " 'email': '',\n",
+ " 'registrationDate': 1466761847802,\n",
+ " 'active': True,\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None},\n",
+ " 'modifier': {'@type': 'as.dto.person.Person',\n",
+ " '@id': 15,\n",
+ " 'fetchOptions': {'@type': 'as.dto.person.fetchoptions.PersonFetchOptions',\n",
+ " '@id': 16,\n",
+ " 'count': None,\n",
+ " 'from': None,\n",
+ " 'cacheMode': 'NO_CACHE',\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None,\n",
+ " 'allWebAppSettings': False,\n",
+ " 'sort': None},\n",
+ " 'permId': {'@type': 'as.dto.person.id.PersonPermId',\n",
+ " '@id': 17,\n",
+ " 'permId': 'vermeul'},\n",
+ " 'userId': 'vermeul',\n",
+ " 'firstName': '',\n",
+ " 'lastName': '',\n",
+ " 'email': '',\n",
+ " 'registrationDate': 1466761847802,\n",
+ " 'active': True,\n",
+ " 'space': None,\n",
+ " 'registrator': None,\n",
+ " 'roleAssignments': None,\n",
+ " 'webAppSettings': None},\n",
+ " 'attachments': None}]"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s = o.get_sample('/VERMEUL/YEA65')\n",
+ "s.get_parents()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 32,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'vermeul-180926001234992x52BBEEB7B4501439020612E056FBE763'"
+ ]
+ },
+ "execution_count": 32,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "o.token"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>identifier</th>\n",
+ " <th>permId</th>\n",
+ " <th>experiment</th>\n",
+ " <th>sample_type</th>\n",
+ " <th>registrator</th>\n",
+ " <th>registrationDate</th>\n",
+ " <th>modifier</th>\n",
+ " <th>modificationDate</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>/VERMEUL/YEA67</td>\n",
+ " <td>20170327113258723-442</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 11:32:59</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 12:03:46</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>/VERMEUL/YEA68</td>\n",
+ " <td>20170327122105199-443</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 12:21:05</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 12:25:41</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " identifier permId experiment sample_type registrator registrationDate modifier modificationDate\n",
+ "-- -------------- --------------------- ------------ ------------- ------------- ------------------- ---------- -------------------\n",
+ " 0 /VERMEUL/YEA67 20170327113258723-442 None YEAST vermeul 2017-03-27 11:32:59 vermeul 2017-03-27 12:03:46\n",
+ " 1 /VERMEUL/YEA68 20170327122105199-443 None YEAST vermeul 2017-03-27 12:21:05 vermeul 2017-03-27 12:25:41"
+ ]
+ },
+ "execution_count": 29,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s.get_parents()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 31,
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "AttributeError",
+ "evalue": "'list' object has no attribute 'upper'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m<ipython-input-31-b836cfdee30a>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mo\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_samples\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'/VERMEUL/YEA67'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m'/VERMEUL/YEA68'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+ "\u001b[0;32m~/openbis/pybis/src/python/pybis/pybis.py\u001b[0m in \u001b[0;36mget_samples\u001b[0;34m(self, code, permId, space, project, experiment, type, withParents, withChildren, tags, props, **properties)\u001b[0m\n\u001b[1;32m 1287\u001b[0m \u001b[0msub_criteria\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_subcriteria_for_tags\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtags\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1288\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcode\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1289\u001b[0;31m \u001b[0msub_criteria\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_criteria_for_code\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1290\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpermId\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1291\u001b[0m \u001b[0msub_criteria\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_common_search\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"as.dto.common.search.PermIdSearchCriteria\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpermId\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/openbis/pybis/src/python/pybis/pybis.py\u001b[0m in \u001b[0;36m_criteria_for_code\u001b[0;34m(code)\u001b[0m\n\u001b[1;32m 235\u001b[0m return {\n\u001b[1;32m 236\u001b[0m \"fieldValue\": {\n\u001b[0;32m--> 237\u001b[0;31m \u001b[0;34m\"value\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mcode\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 238\u001b[0m \u001b[0;34m\"@type\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m\"as.dto.common.search.StringEqualToValue\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 239\u001b[0m },\n",
+ "\u001b[0;31mAttributeError\u001b[0m: 'list' object has no attribute 'upper'"
+ ]
+ }
+ ],
+ "source": [
+ "o.get_samples(['/VERMEUL/YEA67','/VERMEUL/YEA68'])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "s.add_parents(['/VERMEUL/YEA64'])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th>attribute</th>\n",
+ " <th>value</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr> <td>code</td> <td>YEA65</td> </tr><tr> <td>permId</td> <td>20170227154403209-436</td> </tr><tr> <td>identifier</td> <td>/VERMEUL/YEA65</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td>['/VERMEUL/YEA67', '/VERMEUL/YEA68', '/VERMEUL/YEA64']</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>components</td> <td>[]</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
+ " </tbody>\n",
+ " </table>\n",
+ " "
+ ],
+ "text/plain": [
+ "attribute value\n",
+ "----------- ------------------------------------------------------\n",
+ "code YEA65\n",
+ "permId 20170227154403209-436\n",
+ "identifier /VERMEUL/YEA65\n",
+ "type YEAST\n",
+ "project\n",
+ "parents ['/VERMEUL/YEA67', '/VERMEUL/YEA68', '/VERMEUL/YEA64']\n",
+ "children []\n",
+ "components []\n",
+ "space VERMEUL\n",
+ "experiment\n",
+ "tags []"
+ ]
+ },
+ "execution_count": 18,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>identifier</th>\n",
+ " <th>permId</th>\n",
+ " <th>experiment</th>\n",
+ " <th>sample_type</th>\n",
+ " <th>registrator</th>\n",
+ " <th>registrationDate</th>\n",
+ " <th>modifier</th>\n",
+ " <th>modificationDate</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>/VERMEUL/ANOTHER_SAMPLE1</td>\n",
+ " <td>20160706001644827-208</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-07-06 00:16:45</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-11-02 18:27:37</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>/ELN_SETTINGS/BENCH</td>\n",
+ " <td>20171208173222809-574</td>\n",
+ " <td>/ELN_SETTINGS/STORAGES/STORAGES_COLLECTION</td>\n",
+ " <td>STORAGE</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-08 17:32:23</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-08 17:32:23</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>/VERMEUL/BLAJLSD</td>\n",
+ " <td>20160630111949369-89</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-06-30 17:19:49</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-06-22 02:40:01</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>/MY_NEW_SPACE/CHILD_OF_SAMPLE1</td>\n",
+ " <td>20160705234504004-206</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-07-05 23:45:04</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-09-20 14:12:03</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_MON_171211_112532</td>\n",
+ " <td>20171211112551150-600</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 11:25:51</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 11:25:51</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>5</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_MON_171211_112859</td>\n",
+ " <td>20171211112918769-603</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 11:29:19</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 11:29:19</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>6</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_MON_171211_123501</td>\n",
+ " <td>20171211123518060-606</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 12:35:18</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 12:35:18</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>7</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_MON_171211_123653</td>\n",
+ " <td>20171211123710443-609</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 12:37:10</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 12:37:10</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>8</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_MON_171211_123736</td>\n",
+ " <td>20171211123753331-612</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 12:37:53</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 12:37:53</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>9</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_MON_171211_123757</td>\n",
+ " <td>20171211123813756-615</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 12:38:14</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 12:38:14</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>10</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_MON_171211_134640</td>\n",
+ " <td>20171211134641170-618</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 13:46:41</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 13:46:41</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>11</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_MON_171218_164249</td>\n",
+ " <td>20171218164250384-644</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-18 16:42:50</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-18 16:42:50</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>12</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_TUE_171219_110150</td>\n",
+ " <td>20171219110155327-649</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-19 11:01:55</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-19 11:01:55</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>13</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_TUE_180227_223411</td>\n",
+ " <td>20180227223408486-680</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:34:08</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:34:08</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>14</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_TUE_180227_223429</td>\n",
+ " <td>20180227223426765-684</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:34:27</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:34:27</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>15</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_TUE_180227_223705</td>\n",
+ " <td>20180227223703438-688</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:37:03</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:37:03</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>16</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_WED_180228_102753</td>\n",
+ " <td>20180228102751116-695</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-28 10:27:51</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-28 10:27:51</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>17</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_WED_180228_102803</td>\n",
+ " <td>20180228102800818-697</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-28 10:28:01</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-28 10:28:01</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>18</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_WED_180228_103709</td>\n",
+ " <td>20180228103707200-701</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-28 10:37:07</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-28 10:37:07</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>19</th>\n",
+ " <td>/DEFAULT/CHILD_SAMPLE_WED_180228_171049</td>\n",
+ " <td>20180228171050238-715</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-28 17:10:50</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-28 17:10:50</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>20</th>\n",
+ " <td>/ELN_SETTINGS/DEFAULT_STORAGE</td>\n",
+ " <td>20171208173222809-575</td>\n",
+ " <td>/ELN_SETTINGS/STORAGES/STORAGES_COLLECTION</td>\n",
+ " <td>STORAGE</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-08 17:32:23</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-08 17:32:23</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>21</th>\n",
+ " <td>/VERMEUL/EXP1</td>\n",
+ " <td>20170124170850531-422</td>\n",
+ " <td>/VERMEUL/PROJECT_ONE/PROJECT_ONE_EXP_1</td>\n",
+ " <td>EXPERIMENTAL_STEP</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-24 17:08:51</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-25 17:26:25</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>22</th>\n",
+ " <td>/MATERIALS/FLY43</td>\n",
+ " <td>20170104000802333-404</td>\n",
+ " <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
+ " <td>FLY</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-04 00:08:02</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-02-27 10:04:19</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>23</th>\n",
+ " <td>/MATERIALS/FLY45</td>\n",
+ " <td>20170104000847172-405</td>\n",
+ " <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
+ " <td>FLY</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-04 00:08:47</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-04 00:36:09</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>24</th>\n",
+ " <td>/MY_NEW_SPACE/FLY51</td>\n",
+ " <td>20170120010813349-416</td>\n",
+ " <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
+ " <td>FLY</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-20 01:08:13</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-15 14:41:20</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>25</th>\n",
+ " <td>/VERMEUL/FLY84</td>\n",
+ " <td>20180831174909928-725</td>\n",
+ " <td>None</td>\n",
+ " <td>FLY</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-08-31 17:49:10</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-08-31 17:49:10</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>26</th>\n",
+ " <td>/ELN_SETTINGS/GENERAL_ELN_SETTINGS</td>\n",
+ " <td>20171208173222969-576</td>\n",
+ " <td>None</td>\n",
+ " <td>GENERAL_ELN_SETTINGS</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-08 17:32:23</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-08 17:32:23</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>27</th>\n",
+ " <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
+ " <td>20160630105304285-81</td>\n",
+ " <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-06-30 16:53:04</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:22:52</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>28</th>\n",
+ " <td>/VERMEUL/HOW_WONDERFUL2</td>\n",
+ " <td>20160630105337180-82</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-06-30 16:53:37</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-07-22 11:20:03</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>29</th>\n",
+ " <td>/VERMEUL/HOW_WONDERFUL3</td>\n",
+ " <td>20160630105402002-83</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-06-30 16:54:02</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-06-30 16:54:02</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>...</th>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>63</th>\n",
+ " <td>/DEFAULT/TEST_GET_BY_PERMID_WED_171004_000946</td>\n",
+ " <td>20171004000946100-531</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-10-04 00:09:46</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-10-04 00:09:46</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>64</th>\n",
+ " <td>/DEFAULT/TEST_GET_BY_PERMID_WED_171004_001010</td>\n",
+ " <td>20171004001010530-534</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-10-04 00:10:11</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-10-04 00:10:11</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>65</th>\n",
+ " <td>/DEFAULT/TEST_GET_BY_PERMID_WED_171004_001021</td>\n",
+ " <td>20171004001020929-537</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-10-04 00:10:21</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-10-04 00:10:21</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>66</th>\n",
+ " <td>/DEFAULT/TEST_SAMPLE_FRI_171208_174600</td>\n",
+ " <td>20171208174559963-591</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-08 17:46:00</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-08 17:46:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>67</th>\n",
+ " <td>/DEFAULT/TEST_SAMPLE_MON_171211_105927</td>\n",
+ " <td>20171211105946839-592</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 10:59:47</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 10:59:47</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>68</th>\n",
+ " <td>/DEFAULT/TEST_SAMPLE_MON_171211_110318</td>\n",
+ " <td>20171211110357956-594</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 11:03:58</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-11 11:03:58</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>69</th>\n",
+ " <td>/DEFAULT/TEST_SAMPLE_TUE_180227_223409</td>\n",
+ " <td>20180227223406110-677</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:34:06</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:34:06</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>70</th>\n",
+ " <td>/DEFAULT/TEST_SAMPLE_TUE_180227_223428</td>\n",
+ " <td>20180227223424887-681</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:34:25</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2018-02-27 22:34:25</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>71</th>\n",
+ " <td>/MY_NEW_SPACE/YEA21</td>\n",
+ " <td>20161025010638912-382</td>\n",
+ " <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPER...</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-10-25 01:06:39</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-19 00:02:53</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>72</th>\n",
+ " <td>/MY_NEW_SPACE/YEA34</td>\n",
+ " <td>20161108230958839-384</td>\n",
+ " <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPER...</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:09:59</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-25 23:48:14</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>73</th>\n",
+ " <td>/VERMEUL/YEA35</td>\n",
+ " <td>20161108231507755-385</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:15:08</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:15:08</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>74</th>\n",
+ " <td>/VERMEUL/YEA36</td>\n",
+ " <td>20161108231536195-386</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:15:36</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:15:36</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>75</th>\n",
+ " <td>/VERMEUL/YEA37</td>\n",
+ " <td>20161108231604599-387</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:16:05</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:16:05</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>76</th>\n",
+ " <td>/MY_NEW_SPACE/YEA38</td>\n",
+ " <td>20161108232203635-388</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:22:04</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-01-18 17:16:50</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>77</th>\n",
+ " <td>/VERMEUL/YEA39</td>\n",
+ " <td>20161108232240159-389</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:22:40</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:22:40</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>78</th>\n",
+ " <td>/VERMEUL/YEA40</td>\n",
+ " <td>20161108233530315-390</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:35:30</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-08 23:35:30</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>79</th>\n",
+ " <td>/VERMEUL/YEA41</td>\n",
+ " <td>20161109142859057-391</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-09 14:28:59</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-11-09 14:28:59</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>80</th>\n",
+ " <td>/VERMEUL/YEA63</td>\n",
+ " <td>20170227104527381-434</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-02-27 10:45:27</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-02-27 10:45:27</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>81</th>\n",
+ " <td>/VERMEUL/YEA64</td>\n",
+ " <td>20170227104651646-435</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-02-27 10:46:52</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-02-27 15:51:34</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>82</th>\n",
+ " <td>/VERMEUL/YEA65</td>\n",
+ " <td>20170227154403209-436</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-02-27 15:44:03</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 12:21:05</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>83</th>\n",
+ " <td>/VERMEUL/YEA66</td>\n",
+ " <td>20170323101102451-441</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-23 10:11:02</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 12:21:05</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>84</th>\n",
+ " <td>/VERMEUL/YEA67</td>\n",
+ " <td>20170327113258723-442</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 11:32:59</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 12:03:46</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>85</th>\n",
+ " <td>/VERMEUL/YEA68</td>\n",
+ " <td>20170327122105199-443</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 12:21:05</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-03-27 12:25:41</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>86</th>\n",
+ " <td>/VERMEUL/YEA71</td>\n",
+ " <td>20170518112158124-516</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:21:58</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:21:58</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>87</th>\n",
+ " <td>/VERMEUL/YEA72</td>\n",
+ " <td>20170518112248330-517</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:22:48</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:22:48</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>88</th>\n",
+ " <td>/VERMEUL/YEA73</td>\n",
+ " <td>20170518112726306-519</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:27:26</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:27:26</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>89</th>\n",
+ " <td>/VERMEUL/YEA74</td>\n",
+ " <td>20170518112739712-520</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:27:40</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:27:40</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>90</th>\n",
+ " <td>/VERMEUL/YEA75</td>\n",
+ " <td>20170518112808649-521</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:28:09</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-05-18 11:28:12</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>91</th>\n",
+ " <td>/VERMEUL/YEA76</td>\n",
+ " <td>20171215141946133-620</td>\n",
+ " <td>None</td>\n",
+ " <td>YEAST</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-15 14:19:46</td>\n",
+ " <td>admin</td>\n",
+ " <td>2017-12-15 14:19:46</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>92</th>\n",
+ " <td>/VERMEUL/YET_ANOTHER_SAMPLE1</td>\n",
+ " <td>20160706002555747-209</td>\n",
+ " <td>None</td>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2016-07-06 00:25:56</td>\n",
+ " <td>vermeul</td>\n",
+ " <td>2017-06-22 10:56:33</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "<p>93 rows 脳 8 columns</p>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " identifier permId experiment sample_type registrator registrationDate modifier modificationDate\n",
+ "-- --------------------------------------------- --------------------- --------------------------------------------------- -------------------- ------------- ------------------- ---------- -------------------\n",
+ " 0 /VERMEUL/ANOTHER_SAMPLE1 20160706001644827-208 None UNKNOWN vermeul 2016-07-06 00:16:45 vermeul 2017-11-02 18:27:37\n",
+ " 1 /ELN_SETTINGS/BENCH 20171208173222809-574 /ELN_SETTINGS/STORAGES/STORAGES_COLLECTION STORAGE admin 2017-12-08 17:32:23 admin 2017-12-08 17:32:23\n",
+ " 2 /VERMEUL/BLAJLSD 20160630111949369-89 None UNKNOWN vermeul 2016-06-30 17:19:49 vermeul 2017-06-22 02:40:01\n",
+ " 3 /MY_NEW_SPACE/CHILD_OF_SAMPLE1 20160705234504004-206 None UNKNOWN vermeul 2016-07-05 23:45:04 vermeul 2017-09-20 14:12:03\n",
+ " 4 /DEFAULT/CHILD_SAMPLE_MON_171211_112532 20171211112551150-600 None UNKNOWN admin 2017-12-11 11:25:51 admin 2017-12-11 11:25:51\n",
+ " 5 /DEFAULT/CHILD_SAMPLE_MON_171211_112859 20171211112918769-603 None UNKNOWN admin 2017-12-11 11:29:19 admin 2017-12-11 11:29:19\n",
+ " 6 /DEFAULT/CHILD_SAMPLE_MON_171211_123501 20171211123518060-606 None UNKNOWN admin 2017-12-11 12:35:18 admin 2017-12-11 12:35:18\n",
+ " 7 /DEFAULT/CHILD_SAMPLE_MON_171211_123653 20171211123710443-609 None UNKNOWN admin 2017-12-11 12:37:10 admin 2017-12-11 12:37:10\n",
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]
},
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"metadata": {},
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}
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- "outputs": [],
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+ "o.get_samples()"
]
},
{
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"execution_count": 8,
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"outputs": [
{
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{
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{
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{
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{
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{
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"execution_count": 10,
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+ "metadata": {},
"outputs": [],
"source": [
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]
},
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"outputs": [],
"source": [
"ds.status # always fetches the current status from the server, no caching"
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{
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"outputs": [
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{
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{
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"outputs": [],
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{
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{
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{
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- "metadata": {
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"outputs": [],
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"metadata": {
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{
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{
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- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -5681,9 +7068,7 @@
{
"cell_type": "code",
"execution_count": 28,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -5711,9 +7096,7 @@
{
"cell_type": "code",
"execution_count": 32,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -5749,9 +7132,7 @@
{
"cell_type": "code",
"execution_count": 29,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -5800,9 +7181,7 @@
{
"cell_type": "code",
"execution_count": 30,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [
{
"data": {
@@ -5852,9 +7231,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.5.2"
+ "version": "3.6.0"
}
},
"nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
}