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@dvklopfenstein
dvklopfenstein committed May 16, 2021
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46 changes: 27 additions & 19 deletions doc/md/README_download_hints.md
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Expand Up @@ -41,7 +41,7 @@ Does the graph.db directory exist?
No? Go to step 4.

```
$ cd ~/neo4j/neo4j-community-3.4.7/data/databases/
$ cd ~/neo4j/neo4j-community-4.1.9/data/databases/
$ ls graph.db
ls: cannot access 'graph.db': No such file or directory
```
Expand All @@ -60,10 +60,10 @@ $ ls graph.db

### 4. Moved the Reactome database to the graph.db directory
```
$ mv reactome.graphdb.v67 ~/neo4j/neo4j-community-3.4.7/data/databases/graph.db
$ mv reactome.graphdb.v67 ~/neo4j/neo4j-community-4.1.9/data/databases/graph.db
# Confirm it is moved
$ cd ~/neo4j/neo4j-community-3.4.7/data/databases/graph.db
$ cd ~/neo4j/neo4j-community-4.1.9/data/databases/graph.db
$ ls graph.db
debug.log neostore.nodestore.db.labels neostore.relationshipgroupstore.db.id
index neostore.nodestore.db.labels.id neostore.relationshipstore.db
Expand All @@ -75,38 +75,46 @@ $ ls graph.db
[Where to look if it does not work](#where-to-look-if-it-does-not-work)

```
$ neo4j/neo4j-community-3.4.7/bin/neo4j start
$ neo4j/neo4j-community-4.1.9/bin/neo4j start
Active database: graph.db
Directories in use:
home: /home/neo4j/neo4j/neo4j-community-3.4.7
config: /home/neo4j/neo4j/neo4j-community-3.4.7/conf/
logs: /home/neo4j/neo4j/neo4j-community-3.4.7/logs
plugins: /home/neo4j/neo4j/neo4j-community-3.4.7/plugins
import: /home/neo4j/neo4j/neo4j-community-3.4.7/import
data: /home/neo4j/neo4j/neo4j-community-3.4.7/data
certificates: /home/neo4j/neo4j/neo4j-community-3.4.7/certificates
run: /home/neo4j/neo4j/neo4j-community-3.4.7/run
home: /home/neo4j/neo4j/neo4j-community-4.1.9
config: /home/neo4j/neo4j/neo4j-community-4.1.9/conf/
logs: /home/neo4j/neo4j/neo4j-community-4.1.9/logs
plugins: /home/neo4j/neo4j/neo4j-community-4.1.9/plugins
import: /home/neo4j/neo4j/neo4j-community-4.1.9/import
data: /home/neo4j/neo4j/neo4j-community-4.1.9/data
certificates: /home/neo4j/neo4j/neo4j-community-4.1.9/certificates
run: /home/neo4j/neo4j/neo4j-community-4.1.9/run
Starting Neo4j.
WARNING: Max 1024 open files allowed, minimum of 40000 recommended. See the Neo4j manual.
Started neo4j (pid 545). It is available at http://localhost:7474/
There may be a short delay until the server is ready.
See /home/neo4j/neo4j/neo4j-community-3.4.7/logs/neo4j.log for current status.
See /home/neo4j/neo4j/neo4j-community-4.1.9/logs/neo4j.log for current status.
```

#### Where to look if it does not work
Look at the bottom of both the **debug.log** and the **neo4j.log**
Look at the bottom of both the **debug.log** and the **neo4j.log**
```
$ find neo4j-community-3.4.7/logs -type f
neo4j-community-3.4.7/logs/debug.log
neo4j-community-3.4.7/logs/neo4j.log
$ find neo4j-community-4.1.9/logs -type f
neo4j-community-4.1.9/logs/debug.log
neo4j-community-4.1.9/logs/neo4j.log
```

Your neo4j config file is at `/home/neo4j/neo4j/neo4j-community-4.1.9/conf/neo4j.conf` if you see this in the `debug.log` file:
```
Neo4j cannot be started because the database files require
upgrading and upgrades are disabled in the configuration.
Please set 'dbms.allow_upgrade' to 'true' in your
configuration file and try again.
```

### 6. Connect to the server for the first time
#### You will need to create a password
Setting both *Username* and *Password* to *neo4j* worked for us. Your results may vary.
Setting both *Username* and *Password* to *neo4j* worked for us when loading a new Reactome database version for the first time.
![Authentification1](/doc/md/images/neo4j_reactome_connect1.png)

#### Create your password
#### You will be asked to create a new password
![new password](/doc/md/images/neo4j_reactome_connect2.png)

### 7. View the Reactome database in the neo4j browser
Expand Down
15 changes: 10 additions & 5 deletions notebooks/tutorial/fig4a_2018_molecules_in_interleukin_signaling.ipynb
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Expand Up @@ -14,7 +14,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -37,7 +37,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -56,7 +56,7 @@
"# Query and get the sub-pathways under R-HSA-983169\n",
"def _get_data():\n",
" with gdbdr.session() as session:\n",
" return [rec.data() for rec in session.run(query).records()]\n",
" return session.run(query).data()\n",
"\n",
"data = _get_data()"
]
Expand All @@ -70,14 +70,14 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"223 molecules participate in \"Interleukin-4 and 13 signaling\":\n",
"228 molecules participate in \"Interleukin-4 and 13 signaling\":\n",
"\n",
"Database| ID | Name\n",
"--------|-----------------|--------------------------\n",
Expand Down Expand Up @@ -181,6 +181,11 @@
"ENSEMBL | ENSG00000112715 | VEGFA gene [nucleoplasm]\n",
"ENSEMBL | ENSG00000026025 | VIM gene [nucleoplasm]\n",
"ENSEMBL | ENSG00000148516 | ZEB1 gene [nucleoplasm]\n",
"Guide to Pharmacology| 8912 | acalabrutinib [cytosol]\n",
"Guide to Pharmacology| 7792 | baricitinib [cytosol]\n",
"Guide to Pharmacology| 6912 | ibrutinib [cytosol]\n",
"Guide to Pharmacology| 5688 | ruxolitinib [cytosol]\n",
"Guide to Pharmacology| 5677 | tofacitinib [cytosol]\n",
"UniProt | P16671 | 4xPalmC-CD36 [plasma membrane]\n",
"UniProt | P31749 | AKT1 [cytosol]\n",
"UniProt | P16050 | ALOX15 [cytosol]\n",
Expand Down
10 changes: 5 additions & 5 deletions notebooks/tutorial/fig4b_2018_ccr5_pathways.ipynb
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Expand Up @@ -14,7 +14,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -37,7 +37,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -53,7 +53,7 @@
"# Query and get the sub-pathways under R-HSA-983169\n",
"def _get_data():\n",
" with gdbdr.session() as session:\n",
" return [rec.data() for rec in session.run(query).records()]\n",
" return session.run(query).data()\n",
"\n",
"data = _get_data()"
]
Expand All @@ -67,14 +67,14 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"18 sub-pathways found\n",
"18 sub-pathways found:\n",
"\n",
" ID | Pathway Name\n",
"--------------|----------------------\n",
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6 changes: 3 additions & 3 deletions notebooks/tutorial/s1a_get_pathway.ipynb
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Expand Up @@ -45,15 +45,15 @@
"output_type": "stream",
"text": [
" schemaClass Pathway\n",
" speciesName Homo sapiens\n",
" oldStId REACT_111119\n",
" isInDisease False\n",
" releaseDate 2011-09-20\n",
" displayName Antigen processing-Cross presentation\n",
" stId R-HSA-1236975\n",
" speciesName Homo sapiens\n",
" stIdVersion R-HSA-1236975.1\n",
" dbId 1236975\n",
" name ['Antigen processing-Cross presentation']\n",
" stId R-HSA-1236975\n",
" hasDiagram False\n",
" isInferred False\n"
]
Expand All @@ -63,7 +63,7 @@
"query = 'MATCH (pathway:Pathway{stId:\"R-HSA-1236975\"}) RETURN pathway'\n",
"\n",
"with gdbdr.session() as session:\n",
" for rec in session.run(query).records():\n",
" for rec in session.run(query).data():\n",
" for key, val in rec['pathway'].items():\n",
" print(\" {KEY:11} {VAL}\".format(KEY=key, VAL=val))"
]
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2 changes: 1 addition & 1 deletion notebooks/tutorial/s1b_get_protein.ipynb
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Expand Up @@ -64,7 +64,7 @@
"query = 'MATCH (ewas:EntityWithAccessionedSequence{stId:\"R-HSA-199420\"}) RETURN ewas'\n",
"\n",
"with gdbdr.session() as session:\n",
" for rec in session.run(query).records():\n",
" for rec in session.run(query).data():\n",
" for key, val in rec['ewas'].items():\n",
" print(\" {KEY:11} {VAL}\".format(KEY=key, VAL=val))"
]
Expand Down
8 changes: 4 additions & 4 deletions notebooks/tutorial/s2a_get_protein_fields.ipynb
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Expand Up @@ -14,7 +14,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -38,7 +38,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 2,
"metadata": {},
"outputs": [
{
Expand All @@ -55,15 +55,15 @@
" 'RETURN ewas.displayName AS Name, re.identifier AS ID')\n",
"\n",
"with gdbdr.session() as session:\n",
" for rec in session.run(query).records():\n",
" for rec in session.run(query).data():\n",
" print(\" {ID:11} {Name}\".format(**rec))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Copyright (C) 2018-2021, DV Klopfenstein. All rights reserved."
"Copyright (C) 2018-present, DV Klopfenstein. All rights reserved."
]
}
],
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2 changes: 1 addition & 1 deletion notebooks/tutorial/s2b_get_protein_fields_from_nodes.ipynb
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Expand Up @@ -58,7 +58,7 @@
" 'rd.displayName AS Database')\n",
"\n",
"with gdbdr.session() as session:\n",
" for rec in session.run(query).records():\n",
" for rec in session.run(query).data():\n",
" print(\" {ID} {Database} {Name}\".format(**rec))"
]
},
Expand Down
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